From ffb6bdc07ac97e0445fdd1c26d05c0e161888415 Mon Sep 17 00:00:00 2001
From: Sascha Herzinger <sascha.herzinger@uni.lu>
Date: Thu, 25 Jul 2019 14:36:10 +0200
Subject: [PATCH] formatted *.java with eclipse style guide
---
.../cdplugin/copypaste/CopyAction.java | 13 +-
.../copypaste/CopyPasteAbstractAction.java | 18 +-
.../cdplugin/copypaste/CopyPastePlugin.java | 22 +-
.../cdplugin/copypaste/CopyPluginAction.java | 13 +-
.../cdplugin/copypaste/PasteAction.java | 9 +-
.../cdplugin/copypaste/PastePluginAction.java | 11 +-
.../mapviewer/cdplugin/info/InfoFrame.java | 87 +-
.../mapviewer/cdplugin/info/InfoPlugin.java | 33 +-
.../mapviewer/cdplugin/CdPluginFunctions.java | 5 +-
.../cdplugin/copypaste/CopyActionTest.java | 3 +-
.../copypaste/CopyPastePluginTest.java | 4 +-
.../cdplugin/copypaste/PasteActionTest.java | 5 +-
.../cdplugin/info/InfoFrameTest.java | 7 +-
.../cdplugin/info/InfoPluginTest.java | 3 +-
.../annotation/SpringAnnotationConfig.java | 2 +-
.../cache/ApplicationLevelCache.java | 57 +-
.../annotation/cache/BigFileCache.java | 714 ++++---
.../annotation/cache/CachableInterface.java | 63 +-
.../annotation/cache/CacheException.java | 26 +-
.../annotation/cache/FtpClientFactory.java | 16 +-
.../annotation/cache/GeneralCache.java | 23 +-
.../cache/GeneralCacheWithExclusion.java | 5 +-
.../cache/PermanentDatabaseLevelCache.java | 504 +++--
.../PermanentDatabaseLevelCacheInterface.java | 5 +-
.../annotation/cache/QueryCacheInterface.java | 6 +-
.../annotation/cache/SourceNotAvailable.java | 66 +-
.../annotation/cache/WebPageDownloader.java | 319 ++-
.../annotation/cache/XmlSerializer.java | 168 +-
.../annotation/cache/package-info.java | 15 +-
.../mapviewer/annotation/data/Article.java | 352 ++--
.../data/ArticleCitationComparator.java | 8 +-
.../lcsb/mapviewer/annotation/data/Chebi.java | 451 +++--
.../annotation/data/ChebiRelation.java | 180 +-
.../mapviewer/annotation/data/Chemical.java | 551 +++---
.../data/ChemicalDirectEvidence.java | 43 +-
.../lcsb/mapviewer/annotation/data/Drug.java | 629 +++---
.../mapviewer/annotation/data/EntrezData.java | 261 +--
.../lcsb/mapviewer/annotation/data/Go.java | 128 +-
.../lcsb/mapviewer/annotation/data/MeSH.java | 325 ++--
.../lcsb/mapviewer/annotation/data/MiRNA.java | 37 +-
.../mapviewer/annotation/data/Target.java | 7 +-
.../mapviewer/annotation/data/TargetType.java | 84 +-
.../annotation/data/TargettingStructure.java | 22 +-
.../annotation/data/package-info.java | 1 -
.../annotation/services/ChEMBLParser.java | 231 +--
.../annotation/services/ChemicalParser.java | 136 +-
.../services/ChemicalSearchException.java | 66 +-
.../annotation/services/DrugAnnotation.java | 14 +-
.../services/DrugSearchException.java | 66 +-
.../services/DrugbankHTMLParser.java | 177 +-
.../services/ExternalServiceStatus.java | 138 +-
.../services/ExternalServiceStatusType.java | 100 +-
.../annotation/services/IExternalService.java | 36 +-
.../services/ImproperAnnotations.java | 100 +-
.../annotation/services/MeSHParser.java | 57 +-
.../annotation/services/MiRNAParser.java | 93 +-
.../services/MiRNASearchException.java | 66 +-
.../annotation/services/MiriamConnector.java | 38 +-
.../services/MissingAnnotation.java | 42 +-
.../services/MissingRequiredAnnotations.java | 90 +-
.../annotation/services/ModelAnnotator.java | 28 +-
.../services/ProblematicAnnotation.java | 12 +-
.../annotation/services/PubmedParser.java | 82 +-
.../services/PubmedSearchException.java | 48 +-
.../annotation/services/TaxonomyBackend.java | 57 +-
.../services/TaxonomySearchException.java | 32 +-
.../WrongResponseCodeIOException.java | 54 +-
.../services/annotators/BrendaAnnotator.java | 40 +-
.../services/annotators/CazyAnnotator.java | 80 +-
.../services/annotators/ChebiAnnotator.java | 141 +-
.../services/annotators/ElementAnnotator.java | 776 ++++----
.../services/annotators/EnsemblAnnotator.java | 70 +-
.../services/annotators/EntrezAnnotator.java | 121 +-
.../services/annotators/GoAnnotator.java | 101 +-
.../services/annotators/HgncAnnotator.java | 113 +-
.../services/annotators/KeggAnnotator.java | 123 +-
.../services/annotators/PdbAnnotator.java | 120 +-
.../services/annotators/ReconAnnotator.java | 120 +-
.../services/annotators/StitchAnnotator.java | 27 +-
.../services/annotators/StringAnnotator.java | 72 +-
.../services/annotators/TairAnnotator.java | 132 +-
.../services/annotators/UniprotAnnotator.java | 138 +-
.../services/annotators/package-info.java | 1 -
.../AbstractReferenceGenomeConnector.java | 737 ++++---
.../genome/FileNotAvailableException.java | 66 +-
.../genome/ReferenceGenomeConnector.java | 256 +--
.../ReferenceGenomeConnectorException.java | 66 +-
.../genome/UcscReferenceGenomeConnector.java | 339 ++--
.../annotation/services/package-info.java | 1 -
.../annotation/AllAnnotationTests.java | 12 +-
.../annotation/AnnotationTestFunctions.java | 44 +-
.../SpringAnnotationTestConfig.java | 4 +-
.../annotation/cache/AllCacheTests.java | 14 +-
.../annotation/cache/BigFileCacheTest.java | 5 +-
.../cache/CachableInterfaceMock.java | 16 +-
.../cache/CachableInterfaceTest.java | 4 +-
.../annotation/cache/MockCacheInterface.java | 36 +-
.../PermanentDatabaseLevelCacheTest.java | 2 +-
.../cache/SourceNotAvailableTest.java | 33 +-
.../cache/WebPageDownloaderTest.java | 2 +-
.../annotation/data/AllDataTests.java | 24 +-
.../data/ArticleCitationComparatorTest.java | 67 +-
.../mapviewer/annotation/data/ChebiTest.java | 2 +-
.../data/ChemicalDirectEvidenceTest.java | 35 +-
.../annotation/data/ChemicalTest.java | 89 +-
.../annotation/data/EntrezDataTest.java | 69 +-
.../mapviewer/annotation/data/MeSHTest.java | 3 +-
.../mapviewer/annotation/data/MiRNATest.java | 61 +-
.../mapviewer/annotation/data/TargetTest.java | 2 +-
.../annotation/data/TargetTypeTest.java | 43 +-
.../annotation/services/AllServicesTests.java | 42 +-
.../annotation/services/ChEMBLParserTest.java | 2 +-
.../services/ChemicalParserTest.java | 6 +-
.../services/ChemicalSearchExceptionTest.java | 35 +-
.../services/DrugAnnotationTest.java | 2 +-
.../services/DrugbankHTMLParserTest.java | 5 +-
.../services/ExternalServiceStatusTest.java | 41 +-
.../ExternalServiceStatusTypeTest.java | 45 +-
.../services/ImproperAnnotationsTest.java | 2 +-
.../annotation/services/MeSHParserTest.java | 7 +-
.../annotation/services/MiRNAParserTest.java | 4 +-
.../services/MiRNASearchExceptionTest.java | 51 +-
.../services/MiriamConnectorTest.java | 5 +-
.../services/MissingAnnotationTest.java | 33 +-
.../MissingRequiredAnnotationsTest.java | 69 +-
.../annotation/services/PubmedParserTest.java | 17 +-
.../services/TaxonomyBackendTest.java | 5 +-
.../annotators/AnnotatorExceptionTest.java | 5 +-
.../annotators/BrendaAnnotatorTest.java | 8 +-
.../annotators/CazyAnnotatorTest.java | 5 +-
.../annotators/ChebiAnnotatorTest.java | 2 +-
.../ElementAnnotatorImplementationsTest.java | 21 +-
.../annotators/ElementAnnotatorTest.java | 11 +-
.../annotators/EnsemblAnnotatorTest.java | 5 +-
.../annotators/EntrezAnnotatorTest.java | 2 +-
.../services/annotators/GoAnnotatorTest.java | 5 +-
.../annotators/HgncAnnotatorTest.java | 5 +-
.../annotators/KeggAnnotatorTest.java | 8 +-
.../annotators/MultipleAnnotatorsTest.java | 2 +-
.../services/annotators/PdbAnnotatorTest.java | 5 +-
.../annotators/ReconAnnotatorTest.java | 3 +-
.../annotators/StitchAnnotatorTest.java | 3 +-
.../annotators/StringAnnotatorTest.java | 3 +-
.../annotators/TairAnnotatorTest.java | 5 +-
.../annotators/UniprotAnnotatorTest.java | 5 +-
.../UcscReferenceGenomeConnectorTest.java | 2 +-
.../lcsb/mapviewer/common/Comparator.java | 2 +-
.../lcsb/mapviewer/common/Configuration.java | 73 +-
.../mapviewer/common/FrameworkVersion.java | 134 +-
.../mapviewer/common/IProgressUpdater.java | 30 +-
.../common/MinervaLoggerAppender.java | 23 +-
.../lcsb/mapviewer/common/ObjectUtils.java | 70 +-
.../main/java/lcsb/mapviewer/common/Pair.java | 114 +-
.../mapviewer/common/SystemClipboard.java | 90 +-
.../lcsb/mapviewer/common/TextFileUtils.java | 5 +-
.../java/lcsb/mapviewer/common/XmlParser.java | 43 +-
.../common/comparator/BooleanComparator.java | 26 +-
.../common/comparator/ColorComparator.java | 28 +-
.../common/comparator/DoubleComparator.java | 80 +-
.../common/comparator/EnumComparator.java | 28 +-
.../common/comparator/LineComparator.java | 2 +-
.../common/comparator/ListComparator.java | 3 +-
.../common/comparator/PointComparator.java | 82 +-
.../common/comparator/SetComparator.java | 3 +-
.../common/comparator/StringComparator.java | 83 +-
.../comparator/StringListComparator.java | 2 +-
.../comparator/StringSetComparator.java | 3 +-
.../common/comparator/package-info.java | 1 -
.../exception/InvalidArgumentException.java | 90 +-
.../exception/InvalidClassException.java | 49 +-
.../exception/InvalidStateException.java | 78 +-
.../exception/InvalidXmlSchemaException.java | 92 +-
.../exception/NotImplementedException.java | 38 +-
.../common/exception/package-info.java | 1 -
.../common/geometry/ColorParser.java | 4 +-
.../common/geometry/CompositeStroke.java | 53 +-
.../geometry/EllipseTransformation.java | 3 +-
.../common/geometry/LineTransformation.java | 6 +-
.../common/geometry/PointTransformation.java | 4 +-
.../common/geometry/TextAlignment.java | 24 +-
.../common/geometry/package-info.java | 1 -
.../lcsb/mapviewer/common/package-info.java | 1 -
.../lcsb/mapviewer/common/AllCommonTests.java | 20 +-
.../mapviewer/common/ConfigurationTest.java | 227 ++-
.../common/GlobalLoggerAppenderTest.java | 3 +-
.../lcsb/mapviewer/common/MimeTypeTest.java | 42 +-
.../mapviewer/common/ObjectUtilsTest.java | 3 +-
.../java/lcsb/mapviewer/common/PairTest.java | 106 +-
.../mapviewer/common/SystemClipboardTest.java | 13 +-
.../lcsb/mapviewer/common/XmlParserTest.java | 5 +-
.../comparator/BooleanComparatorTest.java | 55 +-
.../comparator/ColorComparatorTest.java | 57 +-
.../comparator/DoubleComparatorTest.java | 71 +-
.../comparator/IntegerComparatorTest.java | 49 +-
.../common/comparator/LineComparatorTest.java | 7 +-
.../common/comparator/ListComparatorTest.java | 5 +-
.../comparator/PointComparatorTest.java | 68 +-
.../common/comparator/SetComparatorTest.java | 9 +-
.../comparator/StringComparatorTest.java | 71 +-
.../comparator/StringListComparatorTest.java | 88 +-
.../comparator/StringSetComparatorTest.java | 93 +-
.../common/exception/AllExceptionTests.java | 5 +-
.../InvalidArgumentExceptionTest.java | 60 +-
.../exception/InvalidClassExceptionTest.java | 32 +-
.../exception/InvalidStateExceptionTest.java | 60 +-
.../InvalidXmlSchemaExceptionTest.java | 60 +-
.../NotImplementedExceptionTest.java | 34 +-
.../common/geometry/AllGeometryTests.java | 10 +-
.../common/geometry/ColorParserTest.java | 4 +-
.../common/geometry/CompositeStrokeTest.java | 28 +-
.../geometry/EllipseTransformationTest.java | 139 +-
.../geometry/LineTransformationTest.java | 34 +-
.../geometry/PointTransformationTest.java | 16 +-
.../common/geometry/TextAlignmentTest.java | 32 +-
.../CellDesignerElementCollection.java | 51 +-
.../celldesigner/CellDesignerXmlParser.java | 84 +-
.../model/celldesigner/CommonXmlParser.java | 161 +-
.../celldesigner/InvalidGroupException.java | 94 +-
.../model/celldesigner/LayerXmlParser.java | 17 +-
.../alias/AbstractAliasXmlParser.java | 9 +-
.../alias/AliasCollectionXmlParser.java | 428 ++--
.../alias/CompartmentAliasXmlParser.java | 13 +-
.../alias/ComplexAliasXmlParser.java | 97 +-
.../alias/SpeciesAliasXmlParser.java | 63 +-
.../celldesigner/alias/package-info.java | 1 -
.../celldesigner/annotation/NoteField.java | 4 +-
.../annotation/RestAnnotationParser.java | 22 +-
.../celldesigner/annotation/package-info.java | 1 -
.../CompartmentCollectionXmlParser.java | 11 +-
.../CompartmentParserException.java | 13 +-
.../compartment/CompartmentXmlParser.java | 87 +-
.../compartment/package-info.java | 1 -
.../function/FunctionXmlParser.java | 6 +-
.../AbstractCellDesignerAliasConverter.java | 281 ++-
...ntisenseRnaCellDesignerAliasConverter.java | 75 +-
.../geometry/CellDesignerAliasConverter.java | 71 +-
.../ComplexCellDesignerAliasConverter.java | 96 +-
.../DegradedCellDesignerAliasConverter.java | 154 +-
.../DrugCellDesignerAliasConverter.java | 128 +-
.../GeneCellDesignerAliasConverter.java | 80 +-
.../IonCellDesignerAliasConverter.java | 73 +-
.../PhenotypeCellDesignerAliasConverter.java | 135 +-
.../ProteinCellDesignerAliasConverter.java | 418 ++--
.../ReactionCellDesignerConverter.java | 19 +-
.../RnaCellDesignerAliasConverter.java | 81 +-
...pleMoleculeCellDesignerAliasConverter.java | 3 +-
.../UnknownCellDesignerAliasConverter.java | 13 +-
.../CellDesignerEllipseTransformation.java | 64 +-
.../CellDesignerPointTransformation.java | 133 +-
.../CellDesignerPolygonTransformation.java | 182 +-
.../CellDesignerRectangleTransformation.java | 83 +-
.../geometry/helper/package-info.java | 1 -
.../celldesigner/geometry/package-info.java | 1 -
.../model/celldesigner/package-info.java | 1 -
.../ParameterCollectionXmlParser.java | 3 +-
.../parameter/ParameterXmlParser.java | 5 +-
.../reaction/KineticsXmlParser.java | 11 +-
.../reaction/ReactionCollectionXmlParser.java | 4 +-
.../reaction/ReactionFromXml.java | 68 +-
.../reaction/ReactionLineData.java | 179 +-
.../celldesigner/reaction/ReactionToXml.java | 49 +-
.../reaction/ReactionXmlParser.java | 98 +-
.../UnknownModifierClassException.java | 74 +-
.../celldesigner/reaction/package-info.java | 1 -
.../species/AbstractElementXmlParser.java | 49 +-
.../species/AntisenseRnaXmlParser.java | 5 +-
.../celldesigner/species/GeneXmlParser.java | 65 +-
.../species/InternalModelSpeciesData.java | 382 ++--
.../species/ModificationResidueXmlParser.java | 17 +-
.../celldesigner/species/ProteinMapping.java | 271 ++-
.../species/ProteinXmlParser.java | 9 +-
.../celldesigner/species/RnaXmlParser.java | 61 +-
.../species/SpeciesCollection.java | 296 ++-
.../species/SpeciesCollectionXmlParser.java | 31 +-
.../celldesigner/species/SpeciesMapping.java | 108 +-
.../species/SpeciesSbmlParser.java | 31 +-
.../celldesigner/species/package-info.java | 1 -
.../structure/CellDesignerAntisenseRna.java | 80 +-
.../structure/CellDesignerChemical.java | 216 +--
.../structure/CellDesignerCompartment.java | 47 +-
.../structure/CellDesignerComplexSpecies.java | 302 +--
.../structure/CellDesignerDegraded.java | 72 +-
.../structure/CellDesignerDrug.java | 72 +-
.../structure/CellDesignerElement.java | 83 +-
.../structure/CellDesignerGene.java | 93 +-
.../structure/CellDesignerGenericProtein.java | 12 +-
.../CellDesignerIonChannelProtein.java | 74 +-
.../structure/CellDesignerPhenotype.java | 73 +-
.../structure/CellDesignerProtein.java | 71 +-
.../CellDesignerReceptorProtein.java | 74 +-
.../structure/CellDesignerRna.java | 60 +-
.../structure/CellDesignerSimpleMolecule.java | 87 +-
.../structure/CellDesignerSpecies.java | 261 +--
.../CellDesignerTruncatedProtein.java | 76 +-
.../structure/CellDesignerUnknown.java | 64 +-
.../CellDesignerModificationResidue.java | 105 +-
.../structure/fields/ConnectScheme.java | 195 +-
.../structure/fields/LineProperties.java | 2 +-
.../structure/fields/ModificationType.java | 8 +-
.../structure/fields/SingleLine.java | 38 +-
.../structure/fields/SpeciesState.java | 60 +-
.../celldesigner/structure/fields/View.java | 147 +-
.../celldesigner/types/ModifierType.java | 370 ++--
.../celldesigner/types/ModifierTypeUtils.java | 521 +++--
.../celldesigner/types/OperatorType.java | 140 +-
.../celldesigner/types/OperatorTypeUtils.java | 143 +-
.../celldesigner/types/package-info.java | 1 -
.../unit/UnitCollectionXmlParser.java | 2 +-
.../celldesigner/unit/UnitXmlParser.java | 7 +-
.../CellDesignerTestFunctions.java | 38 +-
.../CellDesignerXmlParserTest.java | 5 +-
.../celldesigner/ComplexParserTests.java | 33 +-
.../InvalidGroupExceptionTest.java | 30 +-
.../celldesigner/LayerXmlParserTest.java | 2 +-
.../NestedComplexParsingTests.java | 3 +-
.../celldesigner/SbmlValidationTests.java | 4 +-
.../celldesigner/alias/AllAliasTests.java | 6 +-
.../alias/ComplexAliasXmlParserTest.java | 5 +-
.../alias/SpeciesAliasXmlParserTest.java | 5 +-
.../annotation/NoteFieldTest.java | 43 +-
.../compartment/AllCompartmentTests.java | 4 +-
.../CompartmentCollectionXmlParserTest.java | 3 +-
.../compartment/CompartmentParserTests.java | 2 +-
.../FunctionCollectionXmlParserTest.java | 6 +-
.../function/FunctionXmlParserTest.java | 7 +-
...bstractCellDesignerAliasConverterTest.java | 22 +-
.../geometry/AllGeometryTests.java | 30 +-
...enseRnaCellDesignerAliasConverterTest.java | 79 +-
.../geometry/ComplexConverterTest.java | 2 +-
...egradedCellDesignerAliasConverterTest.java | 79 +-
.../GeneCellDesignerAliasConverterTest.java | 3 +-
.../IonCellDesignerAliasConverterTest.java | 5 +-
...ProteinCellDesignerAliasConverterTest.java | 2 +-
.../geometry/ProteinConverterTest.java | 2 +-
.../ReactionCellDesignerConverterTest.java | 35 +-
.../RnaCellDesignerAliasConverterTest.java | 79 +-
...oleculeCellDesignerAliasConverterTest.java | 3 +-
...UnknownCellDesignerAliasConverterTest.java | 5 +-
.../geometry/helper/AllHelperTests.java | 12 +-
.../helper/CellDesignerAnchorTest.java | 35 +-
...CellDesignerEllipseTransformationTest.java | 270 ++-
.../CellDesignerPointTransformationTest.java | 3 +-
...llDesignerRectangleTransformationTest.java | 35 +-
.../reaction/KineticsXmlParserTest.java | 33 +-
.../reaction/ModificationReactionTest.java | 2 +-
.../ReactionCollectionXmlParserTest.java | 335 ++--
.../reaction/ReactionLineDataTest.java | 3 +-
.../reaction/ReactionParserExceptionTest.java | 59 +-
.../reaction/ReactionParserTests.java | 5 +-
.../UnknownModifierClassExceptionTest.java | 45 +-
.../species/AntisenseRnaXmlParserTest.java | 3 +-
.../species/ComplexParserTest.java | 2 +-
.../species/InternalModelSpeciesDataTest.java | 2 +-
.../ModificationResidueXmlParserTest.java | 2 +-
.../species/ProteinMappingTest.java | 2 +-
.../species/ProteinXmlParserTest.java | 3 +-
.../species/SpeciesMappingTest.java | 2 +-
.../species/SpeciesSbmlParserTest.java | 8 +-
.../structure/AllStructureTests.java | 48 +-
.../structure/CellDesignerChemicalTest.java | 59 +-
.../structure/ComplexSpeciesTest.java | 3 +-
.../structure/ConnectSchemeTest.java | 59 +-
.../celldesigner/structure/DegradedTest.java | 2 +-
.../celldesigner/structure/DrugTest.java | 2 +-
.../celldesigner/structure/GeneTest.java | 3 +-
.../structure/GenericProteinTest.java | 2 +-
.../structure/IonChannelProteinTest.java | 2 +-
.../model/celldesigner/structure/IonTest.java | 2 +-
.../structure/LinePropertiesTest.java | 45 +-
.../celldesigner/structure/PhenotypeTest.java | 2 +-
.../celldesigner/structure/ProteinTest.java | 3 +-
.../structure/ReceptorProteinTest.java | 2 +-
.../structure/SimpleMoleculeTest.java | 2 +-
.../structure/SpeciesStateTest.java | 2 +-
.../structure/TruncatedProteinTest.java | 2 +-
.../celldesigner/structure/UnknownTest.java | 2 +-
.../celldesigner/structure/ViewTest.java | 45 +-
.../CellDesignerModificationResidueTest.java | 33 +-
.../celldesigner/types/AllTypesTests.java | 6 +-
.../celldesigner/types/ModifierTypeTest.java | 35 +-
.../types/ModifierTypeUtilsTest.java | 3 +-
.../celldesigner/types/OperatorTypeTest.java | 37 +-
.../types/OperatorTypeUtilsTest.java | 2 +-
.../model/sbgnml/SbgnmlXmlConverter.java | 9 +-
.../model/sbgnml/SbgnmlXmlExporter.java | 123 +-
.../model/sbgnml/SbgnmlXmlParser.java | 96 +-
.../converter/model/sbgnml/package-info.java | 3 +-
.../model/sbgnml/structures/Process.java | 440 ++---
.../model/sbgnml/structures/package-info.java | 3 +-
.../model/sbgnml/AllSbgnmlTests.java | 10 +-
.../model/sbgnml/CellDesignerToSbgnTest.java | 3 +-
.../model/sbgnml/DbSerializationTest.java | 8 +-
.../model/sbgnml/SbgnmlTestFunctions.java | 2 +-
.../model/sbgnml/SbgnmlXmlParserTest.java | 3 +-
.../graphics/AbstractImageGenerator.java | 1719 ++++++++---------
.../converter/graphics/ConverterParams.java | 188 +-
.../converter/graphics/DrawingException.java | 48 +-
.../converter/graphics/ImageGenerators.java | 290 +--
.../converter/graphics/JpgImageGenerator.java | 112 +-
.../converter/graphics/MapGenerator.java | 361 ++--
.../graphics/NormalImageGenerator.java | 91 +-
.../converter/graphics/PdfFontMapper.java | 5 +-
.../converter/graphics/PdfImageGenerator.java | 50 +-
.../converter/graphics/PngImageGenerator.java | 143 +-
.../converter/graphics/SvgImageGenerator.java | 159 +-
.../bioEntity/BioEntityConverter.java | 28 +-
.../bioEntity/BioEntityConverterImpl.java | 307 ++-
.../bioEntity/element/ElementConverter.java | 3 +-
.../BottomSquareCompartmentConverter.java | 134 +-
.../compartment/CompartmentConverter.java | 304 ++-
.../LeftSquareCompartmentConverter.java | 139 +-
.../compartment/OvalCompartmentConverter.java | 149 +-
.../PathwayCompartmentConverter.java | 5 +-
.../RightSquareCompartmentConverter.java | 148 +-
.../SquareCompartmentConverter.java | 166 +-
.../TopSquareCompartmentConverter.java | 131 +-
.../element/compartment/package-info.java | 4 +-
.../species/AntisenseRnaConverter.java | 12 +-
.../element/species/ComplexConverter.java | 25 +-
.../element/species/DegradedConverter.java | 223 ++-
.../element/species/DrugConverter.java | 197 +-
.../element/species/GeneConverter.java | 9 +-
.../element/species/IonConverter.java | 8 +-
.../element/species/PhenotypeConverter.java | 120 +-
.../element/species/ProteinConverter.java | 23 +-
.../element/species/RnaConverter.java | 12 +-
.../SBGNNucleicAcidFeatureConverter.java | 221 ++-
.../species/SimpleMoleculeConverter.java | 11 +-
.../element/species/SpeciesConverter.java | 122 +-
.../element/species/UnknownConverter.java | 8 +-
.../bioEntity/reaction/ReactionConverter.java | 93 +-
.../bioEntity/reaction/package-info.java | 1 -
.../geometry/ArrowTransformation.java | 23 +-
.../graphics/geometry/FontFinder.java | 462 ++---
.../geometry/RectangleTooSmallException.java | 26 +-
.../graphics/geometry/package-info.java | 1 -
.../graphics/layer/LayerConverter.java | 10 +-
.../graphics/layer/LayerLineConverter.java | 6 +-
.../graphics/layer/LayerOvalConverter.java | 6 +-
.../graphics/layer/LayerRectConverter.java | 6 +-
.../graphics/layer/LayerTextConverter.java | 16 +-
.../graphics/layer/package-info.java | 1 -
.../converter/graphics/package-info.java | 5 +-
.../graphics/placefinder/PlaceFinder.java | 915 +++++----
.../graphics/placefinder/package-info.java | 1 -
.../graphics/AbstractImageGeneratorTest.java | 10 +-
.../converter/graphics/AllGraphicsTests.java | 20 +-
.../graphics/GraphicsTestFunctions.java | 4 +-
.../graphics/ImageGeneratorsTest.java | 2 +-
.../converter/graphics/MapGeneratorTest.java | 3 +-
.../graphics/NormalImageGeneratorTest.java | 2 +-
.../converter/graphics/PdfFontMapperTest.java | 2 +-
.../graphics/PdfImageGeneratorTest.java | 11 +-
.../graphics/SvgImageGeneratorTest.java | 14 +-
.../bioEntity/BioEntityConverterImplTest.java | 18 +-
.../PathwayCompartmentConverterTest.java | 5 +-
.../element/species/ComplexConverterTest.java | 6 +-
.../element/species/SpeciesConverterTest.java | 6 +-
.../reaction/ReactionConverterTest.java | 24 +-
.../geometry/ArrowTransformationTest.java | 5 +-
.../graphics/geometry/FontFinderTest.java | 3 +-
.../placefinder/AllPlaceFinderTest.java | 254 +--
.../model/sbml/SbmlBioEntityExporter.java | 46 +-
.../model/sbml/SbmlBioEntityParser.java | 28 +-
.../model/sbml/SbmlElementExporter.java | 28 +-
.../model/sbml/SbmlElementParser.java | 17 +-
.../converter/model/sbml/SbmlExporter.java | 16 +-
.../model/sbml/SbmlFunctionExporter.java | 3 +-
.../model/sbml/SbmlFunctionParser.java | 15 +-
.../model/sbml/SbmlParameterExporter.java | 3 +-
.../model/sbml/SbmlParameterParser.java | 13 +-
.../converter/model/sbml/SbmlParser.java | 52 +-
.../compartment/SbmlCompartmentExporter.java | 82 +-
.../compartment/SbmlCompartmentParser.java | 39 +-
.../extension/multi/BioEntityFeature.java | 7 +-
.../multi/MultiPackageNamingUtils.java | 16 +-
.../sbml/reaction/SBOTermModifierType.java | 13 +-
.../sbml/reaction/SBOTermReactionType.java | 32 +-
.../sbml/reaction/SbmlReactionExporter.java | 169 +-
.../sbml/reaction/SbmlReactionParser.java | 53 +-
.../model/sbml/species/ElementColorEnum.java | 21 +-
.../sbml/species/SBOTermSpeciesType.java | 21 +-
.../sbml/species/SbmlSpeciesExporter.java | 177 +-
.../model/sbml/species/SbmlSpeciesParser.java | 180 +-
.../model/sbml/units/SbmlUnitExporter.java | 3 +-
.../model/sbml/units/SbmlUnitsParser.java | 13 +-
.../model/sbml/units/UnitMapping.java | 1 +
.../sbml/CellDesignerToMultiExportTest.java | 3 +-
.../model/sbml/CopasiImportTest.java | 2 +-
.../model/sbml/ElementPropertiesExport.java | 2 +-
.../ElementPropertiesExportToLayoutTest.java | 2 +-
.../ElementPropertiesExportToMultiTest.java | 2 +-
.../model/sbml/GenericSbmlParserTest.java | 3 +-
.../sbml/GenericSbmlToXmlParserTest.java | 3 +-
.../converter/model/sbml/MultiParserTest.java | 3 +-
.../ReactionPropertiesExportToMultiTest.java | 5 +-
.../model/sbml/SbmlBioEntityExporterTest.java | 6 +-
.../SbmlExporterFromCellDesignerTest.java | 2 +-
.../model/sbml/SbmlExporterTest.java | 3 +-
.../model/sbml/SbmlTestFunctions.java | 48 +-
.../SbmlCompartmentParserTest.java | 3 +-
.../reaction/SbmlReactionExportArrowType.java | 31 +-
.../reaction/SbmlReactionExporterTest.java | 4 +-
.../SbmlReactionParserExtractCurveTest.java | 23 +-
.../sbml/species/SbmlSpeciesExporterTest.java | 12 +-
.../sbml/species/SbmlSpeciesParserTest.java | 22 +-
.../converter/ComplexZipConverter.java | 34 +-
.../converter/ComplexZipConverterParams.java | 12 +-
.../lcsb/mapviewer/converter/Converter.java | 150 +-
.../converter/ConverterException.java | 82 +-
.../mapviewer/converter/ConverterParams.java | 4 +-
.../lcsb/mapviewer/converter/GlyphParser.java | 3 +-
.../converter/InvalidCoordinatesFile.java | 72 +-
.../converter/InvalidOverviewFile.java | 72 +-
.../mapviewer/converter/OverviewParser.java | 24 +-
.../mapviewer/converter/ProjectFactory.java | 22 +-
.../mapviewer/converter/ZIndexPopulator.java | 11 +-
.../annotation/XmlAnnotationParser.java | 20 +-
.../mapviewer/converter/package-info.java | 1 -
.../converter/zip/InputFileType.java | 56 +-
.../converter/zip/ModelZipEntryFile.java | 366 ++--
.../mapviewer/converter/zip/ZipEntryFile.java | 126 +-
.../converter/zip/ZipEntryFileFactory.java | 44 +-
.../mapviewer/converter/zip/package-info.java | 1 -
.../converter/ConverterTestFunctions.java | 35 +-
.../mapviewer/converter/MockConverter.java | 19 +-
.../converter/ZIndexPopulatorTest.java | 10 +-
.../commands/ClearColorModelCommand.java | 63 +-
.../mapviewer/commands/ColorExtractor.java | 166 +-
.../mapviewer/commands/ColorModelCommand.java | 39 +-
.../commands/CommandExecutionException.java | 78 +-
.../lcsb/mapviewer/commands/CopyCommand.java | 45 +-
.../commands/CreateHierarchyCommand.java | 38 +-
.../commands/InvalidModelException.java | 26 +-
.../lcsb/mapviewer/commands/ModelCommand.java | 401 ++--
.../commands/ModelCommandStatus.java | 24 +-
.../lcsb/mapviewer/commands/MoveCommand.java | 99 +-
.../commands/MoveElementsCommand.java | 16 +-
.../mapviewer/commands/NewModelCommand.java | 70 +-
.../commands/SemanticZoomLevelMatcher.java | 80 +-
.../SetFixedHierarchyLevelCommand.java | 13 +-
.../mapviewer/commands/SubModelCommand.java | 12 +-
.../layout/ApplyLayoutModelCommand.java | 3 +-
.../layout/ApplySimpleLayoutModelCommand.java | 58 +-
.../lcsb/mapviewer/commands/package-info.java | 1 -
.../AddElementFormerSymbolsCommand.java | 110 +-
.../AddElementMiriamDataCommand.java | 89 +-
.../AddElementPropertyListEntryCommand.java | 126 +-
.../properties/AddElementSynonymsCommand.java | 89 +-
.../ChangeElementAbbreviationCommand.java | 71 +-
.../properties/ChangeElementColorCommand.java | 67 +-
.../ChangeElementFontSizeCommand.java | 73 +-
.../ChangeElementFormerSymbolCommand.java | 85 +-
.../ChangeElementFormulaCommand.java | 71 +-
.../ChangeElementFullNameCommand.java | 73 +-
.../ChangeElementMiriamDataCommand.java | 91 +-
.../properties/ChangeElementNameCommand.java | 65 +-
.../properties/ChangeElementNotesCommand.java | 73 +-
.../ChangeElementPropertyCommand.java | 180 +-
...ChangeElementPropertyListEntryCommand.java | 195 +-
.../ChangeElementSymbolCommand.java | 73 +-
.../ChangeElementSynonymCommand.java | 85 +-
.../RemoveElementFormerSymbolsCommand.java | 90 +-
.../RemoveElementMiriamDataCommand.java | 90 +-
...RemoveElementPropertyListEntryCommand.java | 127 +-
.../RemoveElementSynonymsCommand.java | 90 +-
.../commands/properties/package-info.java | 1 -
.../mapviewer/commands/AllCommandsTests.java | 6 +-
.../commands/ColorModelCommandTest.java | 3 +-
.../commands/CommandTestFunctions.java | 19 +-
.../commands/SubModelCommandTest.java | 3 +-
.../properties/AllPropertyCommandTests.java | 22 +-
.../ChangeElementColorCommandTest.java | 2 +-
.../ChangeElementFormerSymbolCommandTest.java | 2 +-
.../java/lcsb/mapviewer/model/Project.java | 24 +-
.../mapviewer/model/cache/BigFileEntry.java | 4 +-
.../mapviewer/model/cache/CacheQuery.java | 26 +-
.../lcsb/mapviewer/model/cache/CacheType.java | 5 +-
.../lcsb/mapviewer/model/cache/FileEntry.java | 10 +-
.../model/cache/UploadedFileEntry.java | 5 +-
.../mapviewer/model/cache/package-info.java | 1 -
.../mapviewer/model/graphics/ArrowType.java | 16 +-
.../graphics/ArrowTypeDataComparator.java | 3 +-
.../mapviewer/model/graphics/LineType.java | 21 +-
.../model/graphics/MapCanvasType.java | 3 +-
.../model/graphics/PolylineData.java | 67 +-
.../graphics/PolylineDataComparator.java | 3 +-
.../model/graphics/package-info.java | 1 -
.../lcsb/mapviewer/model/map/BioEntity.java | 44 +-
.../lcsb/mapviewer/model/map/Comment.java | 33 +-
.../lcsb/mapviewer/model/map/MiriamData.java | 66 +-
.../model/map/MiriamRelationType.java | 18 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 112 +-
.../mapviewer/model/map/OverviewImage.java | 9 +-
.../model/map/OverviewImageComparator.java | 3 +-
.../model/map/OverviewImageLink.java | 5 +-
.../map/OverviewImageLinkComparator.java | 13 +-
.../mapviewer/model/map/OverviewLink.java | 12 +-
.../model/map/OverviewLinkComparator.java | 3 +-
.../model/map/OverviewModelLink.java | 35 +-
.../map/OverviewModelLinkComparator.java | 3 +-
.../lcsb/mapviewer/model/map/SearchIndex.java | 9 +-
.../model/map/compartment/Compartment.java | 32 +-
.../compartment/CompartmentComparator.java | 15 +-
.../map/compartment/PathwayCompartment.java | 2 +-
.../compartment/RightSquareCompartment.java | 39 +-
.../model/map/kinetics/SbmlFunction.java | 25 +-
.../map/kinetics/SbmlFunctionComparator.java | 3 +-
.../model/map/kinetics/SbmlKinetics.java | 31 +-
.../map/kinetics/SbmlKineticsComparator.java | 3 +-
.../model/map/kinetics/SbmlParameter.java | 19 +-
.../model/map/kinetics/SbmlUnit.java | 21 +-
.../map/kinetics/SbmlUnitComparator.java | 5 +-
.../map/kinetics/SbmlUnitTypeFactor.java | 22 +-
.../SbmlUnitTypeFactorComparator.java | 4 +-
.../model/map/layout/BlockDiagram.java | 14 +-
.../model/map/layout/ColorSchema.java | 7 +-
.../map/layout/DataOverlayImageLayer.java | 20 +-
.../model/map/layout/GeneVariation.java | 39 +-
.../map/layout/GeneVariationColorSchema.java | 4 +-
.../mapviewer/model/map/layout/Layout.java | 35 +-
.../model/map/layout/LayoutStatus.java | 18 +-
.../model/map/layout/ReferenceGenome.java | 11 +-
.../layout/ReferenceGenomeGeneMapping.java | 7 +-
.../model/map/layout/graphics/Glyph.java | 17 +-
.../model/map/layout/graphics/Layer.java | 71 +-
.../map/layout/graphics/LayerComparator.java | 7 +-
.../model/map/layout/graphics/LayerOval.java | 132 +-
.../layout/graphics/LayerOvalComparator.java | 4 +-
.../model/map/layout/graphics/LayerRect.java | 136 +-
.../layout/graphics/LayerRectComparator.java | 5 +-
.../model/map/layout/graphics/LayerText.java | 164 +-
.../layout/graphics/LayerTextComparator.java | 5 +-
.../map/layout/graphics/package-info.java | 1 -
.../model/map/layout/package-info.java | 1 -
.../mapviewer/model/map/model/Author.java | 18 +-
.../model/map/model/AuthorComparator.java | 3 +-
.../map/model/ElementSubmodelConnection.java | 4 +-
.../ElementSubmodelConnectionComparator.java | 3 +-
.../lcsb/mapviewer/model/map/model/Model.java | 213 +-
.../model/map/model/ModelComparator.java | 23 +-
.../mapviewer/model/map/model/ModelData.java | 102 +-
.../model/map/model/ModelFullIndexed.java | 305 ++-
.../map/model/ModelSubmodelConnection.java | 15 +-
.../ModelSubmodelConnectionComparator.java | 3 +-
.../model/map/model/SubmodelConnection.java | 41 +-
.../model/SubmodelConnectionComparator.java | 3 +-
.../model/map/model/package-info.java | 1 -
.../model/map/modifier/package-info.java | 5 +-
.../mapviewer/model/map/package-info.java | 1 -
.../model/map/reaction/AbstractNode.java | 14 +-
.../map/reaction/AbstractNodeComparator.java | 3 +-
.../model/map/reaction/AndOperator.java | 83 +-
.../map/reaction/AssociationOperator.java | 75 +-
.../map/reaction/DissociationOperator.java | 85 +-
.../model/map/reaction/Modifier.java | 78 +-
.../model/map/reaction/NandOperator.java | 85 +-
.../model/map/reaction/NodeOperator.java | 13 +-
.../map/reaction/NodeOperatorComparator.java | 13 +-
.../model/map/reaction/OrOperator.java | 85 +-
.../mapviewer/model/map/reaction/Product.java | 84 +-
.../model/map/reaction/Reactant.java | 84 +-
.../model/map/reaction/Reaction.java | 335 ++--
.../map/reaction/ReactionComparator.java | 11 +-
.../model/map/reaction/ReactionNode.java | 6 +-
.../map/reaction/ReactionNodeComparator.java | 11 +-
.../model/map/reaction/SplitOperator.java | 85 +-
.../map/reaction/TruncationOperator.java | 85 +-
.../model/map/reaction/UnknownOperator.java | 85 +-
.../model/map/reaction/package-info.java | 5 +-
.../model/map/reaction/type/package-info.java | 1 -
.../model/map/species/AntisenseRna.java | 25 +-
.../map/species/AntisenseRnaComparator.java | 3 +-
.../mapviewer/model/map/species/Chemical.java | 4 +-
.../model/map/species/ChemicalComparator.java | 13 +-
.../mapviewer/model/map/species/Complex.java | 13 +-
.../model/map/species/ComplexComparator.java | 13 +-
.../model/map/species/DegradedComparator.java | 13 +-
.../model/map/species/DrugComparator.java | 3 +-
.../mapviewer/model/map/species/Element.java | 655 +++----
.../model/map/species/ElementComparator.java | 11 +-
.../mapviewer/model/map/species/Gene.java | 31 +-
.../model/map/species/GeneComparator.java | 3 +-
.../map/species/GenericProteinComparator.java | 3 +-
.../species/IonChannelProteinComparator.java | 3 +-
.../model/map/species/IonComparator.java | 3 +-
.../map/species/PhenotypeComparator.java | 4 +-
.../mapviewer/model/map/species/Protein.java | 15 +-
.../model/map/species/ProteinComparator.java | 3 +-
.../species/ReceptorProteinComparator.java | 3 +-
.../lcsb/mapviewer/model/map/species/Rna.java | 32 +-
.../model/map/species/RnaComparator.java | 3 +-
.../map/species/SimpleMoleculeComparator.java | 3 +-
.../mapviewer/model/map/species/Species.java | 52 +-
.../model/map/species/SpeciesComparator.java | 6 +-
.../species/TruncatedProteinComparator.java | 3 +-
.../model/map/species/UnknownComparator.java | 3 +-
.../field/AbstractSiteModification.java | 5 +-
.../map/species/field/BindingRegion.java | 3 +-
.../model/map/species/field/CodingRegion.java | 8 +-
.../species/field/ModificationResidue.java | 19 +-
.../map/species/field/ModificationSite.java | 5 +-
.../map/species/field/ModificationState.java | 32 +-
.../species/field/PositionToCompartment.java | 18 +-
.../species/field/ProteinBindingDomain.java | 7 +-
.../map/species/field/RegulatoryRegion.java | 3 +-
.../field/SpeciesWithModificationSite.java | 2 +-
.../map/species/field/SpeciesWithResidue.java | 3 +-
.../model/map/species/field/Structure.java | 8 +-
.../map/species/field/TranscriptionSite.java | 27 +-
.../map/species/field/UniprotRecord.java | 40 +-
.../model/map/statistics/SearchHistory.java | 8 +-
.../model/map/statistics/package-info.java | 1 -
.../lcsb/mapviewer/model/package-info.java | 13 +-
.../lcsb/mapviewer/model/plugin/Plugin.java | 25 +-
.../model/plugin/PluginDataEntry.java | 8 +-
.../mapviewer/model/security/Privilege.java | 20 +-
.../model/user/ConfigurationElementType.java | 3 +-
.../model/user/ConfigurationOption.java | 7 +-
.../java/lcsb/mapviewer/model/user/User.java | 2 +-
.../model/user/UserAnnotationSchema.java | 21 +-
.../model/user/UserClassAnnotators.java | 28 +-
.../user/UserClassRequiredAnnotations.java | 44 +-
.../model/user/UserClassValidAnnotations.java | 39 +-
.../model/user/UserGuiPreference.java | 9 +-
.../annotator/AnnotatorConfigParameter.java | 5 +-
.../model/user/annotator/AnnotatorData.java | 9 +-
.../annotator/AnnotatorInputParameter.java | 5 +-
.../annotator/AnnotatorOutputParameter.java | 17 +-
.../user/annotator/AnnotatorParameter.java | 11 +-
.../model/user/annotator/BioEntityField.java | 2 +-
.../mapviewer/model/user/package-info.java | 1 -
.../modelutils/map/ElementUtils.java | 56 +-
.../modelutils/map/RequireAnnotationMap.java | 9 +-
.../modelutils/map/package-info.java | 1 -
.../test/java/lcsb/mapviewer/AllTests.java | 6 +-
.../mapviewer/model/ProjectStatusTest.java | 34 +-
.../lcsb/mapviewer/model/ProjectTest.java | 3 +-
.../mapviewer/model/cache/AllCacheTests.java | 8 +-
.../model/cache/BigFileEntryTest.java | 2 +-
.../mapviewer/model/cache/CacheQueryTest.java | 3 +-
.../mapviewer/model/cache/CacheTypeTest.java | 3 +-
.../model/graphics/AllGraphicsTests.java | 10 +-
.../graphics/ArrowTypeDataComparatorTest.java | 3 +-
.../model/graphics/ArrowTypeDataTest.java | 3 +-
.../model/graphics/ArrowTypeTest.java | 34 +-
.../model/graphics/LineTypeTest.java | 34 +-
.../graphics/PolylineDataComparatorTest.java | 5 +-
.../model/graphics/PolylineDataTest.java | 2 +-
.../lcsb/mapviewer/model/map/CommentTest.java | 2 +-
.../model/map/MiriamRelationTypeTest.java | 44 +-
.../map/MiriamTypeNameComparatorTest.java | 3 +-
.../map/OverviewImageComparatorTest.java | 4 +-
.../map/OverviewImageLinkComparatorTest.java | 4 +-
.../model/map/OverviewImageLinkTest.java | 3 +-
.../model/map/OverviewImageTest.java | 4 +-
.../model/map/OverviewLinkComparatorTest.java | 3 +-
.../mapviewer/model/map/OverviewLinkTest.java | 3 +-
.../map/OverviewModelLinkComparatorTest.java | 3 +-
.../model/map/OverviewSearchLinkTest.java | 3 +-
.../mapviewer/model/map/SearchIndexTest.java | 3 +-
.../map/compartment/AllCompartmentTests.java | 16 +-
.../BottomSquareCompartmentTest.java | 2 +-
.../CompartmentComparatorTest.java | 5 +-
.../LeftSquareCompartmentTest.java | 2 +-
.../map/compartment/OvalCompartmentTest.java | 2 +-
.../compartment/PathwayCompartmentTest.java | 3 +-
.../RightSquareCompartmentTest.java | 3 +-
.../compartment/SquareCompartmentTest.java | 3 +-
.../compartment/TopSquareCompartmentTest.java | 2 +-
.../model/map/kinetics/AllKineticsTests.java | 2 +-
.../model/map/kinetics/SbmlFunctionTest.java | 2 +-
.../model/map/kinetics/SbmlKineticsTest.java | 12 +-
.../kinetics/SbmlParameterComparatorTest.java | 3 +-
.../model/map/kinetics/SbmlParameterTest.java | 2 +-
.../map/kinetics/SbmlUnitComparatorTest.java | 6 +-
.../map/kinetics/SbmlUnitTypeFactorTest.java | 2 +-
.../model/map/layout/AllLayoutTests.java | 22 +-
.../model/map/layout/ColorSchemaTest.java | 5 +-
.../model/map/layout/ElementGroupTest.java | 2 +-
.../layout/GeneVariationColorSchemaTest.java | 3 +-
.../model/map/layout/GeneVariationTest.java | 3 +-
.../map/layout/GenericColorSchemaTest.java | 2 +-
.../InvalidColorSchemaExceptionTest.java | 2 +-
.../model/map/layout/LayoutStatusTest.java | 34 +-
.../model/map/layout/LayoutTest.java | 1 -
.../ReferenceGenomeGeneMappingTest.java | 2 +-
.../model/map/layout/ReferenceGenomeTest.java | 2 +-
.../map/layout/ReferenceGenomeTypeTest.java | 43 +-
.../map/layout/graphics/AllGraphicsTests.java | 14 +-
.../layout/graphics/LayerComparatorTest.java | 3 +-
.../graphics/LayerOvalComparatorTest.java | 5 +-
.../map/layout/graphics/LayerOvalTest.java | 2 +-
.../graphics/LayerRectComparatorTest.java | 5 +-
.../map/layout/graphics/LayerRectTest.java | 2 +-
.../graphics/LayerTextComparatorTest.java | 5 +-
.../model/map/model/AllModelTests.java | 18 +-
...ementSubmodelConnectionComparatorTest.java | 5 +-
.../model/ElementSubmodelConnectionTest.java | 3 +-
.../model/map/model/ModelComparatorTest.java | 5 +-
.../model/map/model/ModelFullIndexedTest.java | 56 +-
...ModelSubmodelConnectionComparatorTest.java | 3 +-
.../model/ModelSubmodelConnectionTest.java | 4 +-
.../SubmodelConnectionComparatorTest.java | 3 +-
.../model/map/model/SubmodelTypeTest.java | 34 +-
.../model/map/modifier/AllModifierTests.java | 12 +-
.../model/map/modifier/CatalysisTest.java | 2 +-
.../model/map/modifier/InhibitionTest.java | 2 +-
.../model/map/modifier/ModulationTest.java | 2 +-
.../map/modifier/PhysicalStimulationTest.java | 2 +-
.../model/map/modifier/TriggerTest.java | 2 +-
.../map/modifier/UnknownCatalysisTest.java | 2 +-
.../map/modifier/UnknownInhibitionTest.java | 2 +-
.../reaction/AbstractNodeComparatorTest.java | 3 +-
.../model/map/reaction/AllReactionTests.java | 38 +-
.../map/reaction/AssociationOperatorTest.java | 3 +-
.../reaction/DissociationOperatorTest.java | 3 +-
.../model/map/reaction/ModifierTest.java | 2 +-
.../model/map/reaction/NandOperatorTest.java | 3 +-
.../reaction/NodeOperatorComparatorTest.java | 3 +-
.../model/map/reaction/NodeOperatorMock.java | 44 +-
.../model/map/reaction/OrOperatorTest.java | 3 +-
.../model/map/reaction/ProductTest.java | 2 +-
.../model/map/reaction/ReactantTest.java | 2 +-
.../map/reaction/ReactionComparatorTest.java | 3 +-
.../reaction/ReactionNodeComparatorTest.java | 3 +-
.../model/map/reaction/SplitOperatorTest.java | 2 +-
.../map/reaction/TruncationOperatorTest.java | 2 +-
.../map/reaction/UnknownOperatorTest.java | 3 +-
.../type/DissociationReactionTest.java | 2 +-
.../HeterodimerAssociationReactionTest.java | 2 +-
.../KnownTransitionOmittedReactionTest.java | 2 +-
.../type/NegativeInfluenceReactionTest.java | 3 +-
.../type/PositiveInfluenceReactionTest.java | 3 +-
.../map/reaction/type/ReactionRectTest.java | 34 +-
.../type/ReducedModulationReactionTest.java | 3 +-
...educedPhysicalStimulationReactionTest.java | 3 +-
.../type/ReducedTriggerReactionTest.java | 3 +-
.../type/StateTransitionReactionTest.java | 2 +-
.../type/TranscriptionReactionTest.java | 2 +-
.../type/TranslationReactionTest.java | 2 +-
.../reaction/type/TransportReactionTest.java | 2 +-
.../reaction/type/TruncationReactionTest.java | 2 +-
.../UnknownNegativeInfluenceReactionTest.java | 3 +-
.../UnknownPositiveInfluenceReactionTest.java | 3 +-
.../UnknownReducedModulationReactionTest.java | 3 +-
...educedPhysicalStimulationReactionTest.java | 3 +-
.../UnknownReducedTriggerReactionTest.java | 3 +-
.../type/UnknownTransitionReactionTest.java | 2 +-
.../model/map/species/AllSpeciesTests.java | 70 +-
.../species/AntisenseRnaComparatorTest.java | 3 +-
.../model/map/species/AntisenseRnaTest.java | 3 +-
.../map/species/ChemicalComparatorTest.java | 3 +-
.../map/species/ComplexComparatorTest.java | 7 +-
.../model/map/species/ComplexTest.java | 3 +-
.../map/species/DegradedComparatorTest.java | 3 +-
.../model/map/species/DegradedTest.java | 2 +-
.../model/map/species/DrugComparatorTest.java | 3 +-
.../mapviewer/model/map/species/DrugTest.java | 2 +-
.../map/species/ElementComparatorTest.java | 6 +-
.../model/map/species/GeneComparatorTest.java | 3 +-
.../mapviewer/model/map/species/GeneTest.java | 3 +-
.../species/GenericProteinComparatorTest.java | 3 +-
.../model/map/species/GenericProteinTest.java | 2 +-
.../IonChannelProteinComparatorTest.java | 3 +-
.../map/species/IonChannelProteinTest.java | 2 +-
.../model/map/species/IonComparatorTest.java | 3 +-
.../mapviewer/model/map/species/IonTest.java | 2 +-
.../map/species/PhenotypeComparatorTest.java | 3 +-
.../model/map/species/PhenotypeTest.java | 3 +-
.../map/species/ProteinComparatorTest.java | 3 +-
.../model/map/species/ProteinTest.java | 3 +-
.../ReceptorProteinComparatorTest.java | 3 +-
.../map/species/ReceptorProteinTest.java | 2 +-
.../model/map/species/RnaComparatorTest.java | 5 +-
.../mapviewer/model/map/species/RnaTest.java | 3 +-
.../species/SimpleMoleculeComparatorTest.java | 3 +-
.../model/map/species/SimpleMoleculeTest.java | 2 +-
.../map/species/SpeciesComparatorTest.java | 7 +-
.../model/map/species/SpeciesTest.java | 2 +-
.../TruncatedProteinComparatorTest.java | 3 +-
.../map/species/TruncatedProteinTest.java | 2 +-
.../map/species/UnknownComparatorTest.java | 3 +-
.../model/map/species/UnknownTest.java | 2 +-
.../map/species/field/AllFieldTests.java | 12 +-
.../map/species/field/CodingRegionTest.java | 3 +-
.../species/field/ModificationStateTest.java | 56 +-
.../field/PositionToCompartmentTest.java | 54 +-
.../model/map/species/field/ResidueTest.java | 5 +-
.../map/species/field/StructureTest.java | 3 +-
.../map/species/field/UniprotRecordTest.java | 3 +-
.../map/statistics/AllStatisticsTests.java | 2 +-
.../map/statistics/SearchHistoryTest.java | 2 +-
.../model/map/statistics/SearchTypeTest.java | 32 +-
.../model/security/PrivilegeTypeTest.java | 35 +-
.../ConfigurationElementEditTypeTest.java | 37 +-
.../user/ConfigurationElementTypeTest.java | 38 +-
.../model/user/ConfigurationTest.java | 2 +-
.../model/user/UserAnnotationSchemaTest.java | 2 +-
.../model/user/UserClassAnnotatorsTest.java | 2 +-
.../lcsb/mapviewer/model/user/UserTest.java | 5 +-
.../annotator/AnnotatorParameterTest.java | 12 +-
.../modelutils/map/AllMapUtilTests.java | 4 +-
.../modelutils/map/ClassTreeNodeTest.java | 2 +-
.../map/RequireAnnotationMapTest.java | 32 +-
.../lcsb/mapviewer/wikipathway/Activator.java | 30 +-
.../mapviewer/wikipathway/ImportExport.java | 362 ++--
.../wikipathway/XML/BiopaxParser.java | 454 +++--
.../wikipathway/XML/CyclicEdgeException.java | 26 +-
.../wikipathway/XML/DataNodeParser.java | 333 ++--
.../wikipathway/XML/EdgeLineParser.java | 132 +-
.../mapviewer/wikipathway/XML/EdgeParser.java | 1103 ++++++-----
.../wikipathway/XML/ElementGpmlParser.java | 221 ++-
.../wikipathway/XML/GPMLToModel.java | 66 +-
.../mapviewer/wikipathway/XML/GpmlParser.java | 1258 ++++++------
.../XML/GraphicalPathwayElementParser.java | 112 +-
.../XML/InvalidElbowConnectorException.java | 26 +-
.../wikipathway/XML/LabelParser.java | 292 +--
.../wikipathway/XML/ModelContructor.java | 207 +-
.../wikipathway/XML/ModelToGPML.java | 48 +-
.../wikipathway/XML/PointDataParser.java | 89 +-
.../wikipathway/XML/ReferenceParser.java | 265 ++-
.../wikipathway/XML/ShapeParser.java | 329 ++--
.../wikipathway/XML/StateParser.java | 280 ++-
.../XML/UnknownAttributeValueException.java | 30 +-
.../XML/UnknownChildClassException.java | 27 +-
.../XML/UnknownMergingMethodException.java | 26 +-
.../wikipathway/XML/package-info.java | 1 -
.../mapviewer/wikipathway/model/DataNode.java | 392 ++--
.../wikipathway/model/Direction.java | 118 +-
.../mapviewer/wikipathway/model/Edge.java | 893 ++++-----
.../model/GpmlInteractionType.java | 248 +--
.../model/GpmlLineConnectorType.java | 110 +-
.../wikipathway/model/GpmlLineType.java | 134 +-
.../model/GpmlModificationType.java | 245 ++-
.../wikipathway/model/GpmlStateType.java | 139 +-
.../mapviewer/wikipathway/model/Graph.java | 1126 ++++++-----
.../model/GraphicalPathwayElement.java | 465 ++---
.../mapviewer/wikipathway/model/Group.java | 242 +--
.../wikipathway/model/Interaction.java | 742 ++++---
.../wikipathway/model/InteractionMapping.java | 966 +++++----
.../mapviewer/wikipathway/model/Label.java | 320 +--
.../wikipathway/model/MergeMapping.java | 370 ++--
.../wikipathway/model/PathwayElement.java | 292 ++-
.../wikipathway/model/PointData.java | 374 ++--
.../wikipathway/model/ReferenceMapping.java | 510 ++---
.../mapviewer/wikipathway/model/Shape.java | 424 ++--
.../mapviewer/wikipathway/model/State.java | 478 ++---
.../model/UnknownTypeException.java | 26 +-
.../wikipathway/model/biopax/BiopaxData.java | 133 +-
.../BiopaxOpenControlledVocabulary.java | 129 +-
.../model/biopax/BiopaxPublication.java | 319 ++-
.../model/biopax/package-info.java | 1 -
.../wikipathway/model/package-info.java | 7 +-
.../mapviewer/wikipathway/package-info.java | 8 +-
.../lcsb/mapviewer/wikipathway/utils/Geo.java | 617 +++---
.../wikipathway/utils/package-info.java | 1 -
.../wikipathway/AllWikipathwaysTests.java | 14 +-
.../ComplexReactionToModelTest.java | 2 +-
.../wikipathway/ReactionElbowsTest.java | 3 +-
.../WikipathwaysTestFunctions.java | 43 +-
.../wikipathway/XML/AllXmlTests.java | 20 +-
.../mapviewer/wikipathway/XML/BugTest.java | 5 +-
.../XML/ElementGpmlParserTest.java | 8 +-
.../wikipathway/XML/LabelParserTest.java | 2 +-
.../wikipathway/XML/ModelContructorTest.java | 3 +-
.../wikipathway/XML/ReferenceParserTest.java | 3 +-
.../wikipathway/XML/ShapeParserTest.java | 2 +-
.../wikipathway/XML/StateParserTest.java | 3 +-
.../wikipathway/model/AllModelTests.java | 22 +-
.../persist/ApplicationContextLoader.java | 91 +-
.../persist/ConfigurationHolder.java | 52 +-
.../persist/CustomImplicitNamingStrategy.java | 7 +-
.../java/lcsb/mapviewer/persist/DbUtils.java | 15 +-
.../persist/SpringApplicationContext.java | 93 +-
.../persist/SpringPersistConfig.java | 102 +-
.../lcsb/mapviewer/persist/dao/BaseDao.java | 23 +-
.../persist/dao/ConfigurationDao.java | 76 +-
.../persist/dao/cache/BigFileEntryDao.java | 5 +-
.../persist/dao/cache/CacheQueryDao.java | 86 +-
.../persist/dao/cache/CacheTypeDao.java | 57 +-
.../dao/cache/UploadedFileEntryDao.java | 37 +-
.../persist/dao/cache/package-info.java | 1 -
.../persist/dao/graphics/PolylineDao.java | 15 +-
.../persist/dao/graphics/package-info.java | 1 -
.../mapviewer/persist/dao/map/CommentDao.java | 221 +--
.../mapviewer/persist/dao/map/LayoutDao.java | 4 +-
.../mapviewer/persist/dao/map/ModelDao.java | 177 +-
.../persist/dao/map/ReactionDao.java | 15 +-
.../dao/map/layout/ReferenceGenomeDao.java | 35 +-
.../layout/ReferenceGenomeGeneMappingDao.java | 15 +-
.../persist/dao/map/layout/package-info.java | 1 -
.../persist/dao/map/package-info.java | 1 -
.../persist/dao/map/species/ElementDao.java | 15 +-
.../persist/dao/map/species/package-info.java | 1 -
.../dao/map/statistics/SearchHistoryDao.java | 29 +-
.../dao/map/statistics/package-info.java | 1 -
.../mapviewer/persist/dao/package-info.java | 1 -
.../persist/dao/plugin/PluginDao.java | 3 +-
.../dao/plugin/PluginDataEntryDao.java | 3 +-
.../persist/dao/security/PrivilegeDao.java | 8 +-
.../mapviewer/persist/dao/user/UserDao.java | 3 +-
.../persist/dao/user/package-info.java | 1 -
.../persist/mapper/ArrowTypeDataMapper.java | 62 +-
.../persist/mapper/Point2DMapper.java | 34 +-
.../persist/mapper/package-info.java | 1 -
.../V14_0_0_20190701__bcrypt_passwords.java | 6 +-
.../lcsb/mapviewer/persist/package-info.java | 1 -
.../persist/ApplicationContextLoaderTest.java | 3 +-
.../lcsb/mapviewer/persist/DbUtilsTest.java | 3 +-
.../mapviewer/persist/InitialStateTest.java | 4 +-
.../persist/PersistTestFunctions.java | 16 +-
.../persist/SpringApplicationContextTest.java | 40 +-
.../persist/dao/ConfigurationDaoTest.java | 4 +-
.../persist/dao/cache/AllCacheDbTests.java | 6 +-
.../dao/cache/BigFileEntryDaoTest.java | 3 +-
.../persist/dao/cache/CacheQueryDaoTest.java | 3 +-
.../dao/cache/UploadedFileEntryDaoTest.java | 2 +-
.../dao/graphics/PolylineDataTest.java | 14 +-
.../persist/dao/map/CommentDaoTest.java | 5 +-
.../persist/dao/map/LayoutDaoTest.java | 3 +-
.../persist/dao/map/ModelDaoTest.java | 2 +-
.../dao/map/layout/AllLayoutTests.java | 4 +-
.../map/layout/ReferenceGenomeDaoTest.java | 2 +-
.../ReferenceGenomeGeneMappingDaoTest.java | 2 +-
.../map/statistics/SearchHistoryDaoTest.java | 2 +-
.../persist/dao/plugin/PluginDaoTest.java | 4 +-
.../dao/plugin/PluginDataEntryDaoTest.java | 14 +-
.../persist/dao/user/UserDaoTest.java | 3 +-
.../mapper/ArrowTypeDataMapperTest.java | 13 +-
.../persist/mapper/Point2DMapperTest.java | 4 +-
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 47 +-
.../api/ContentNegotiationConfig.java | 14 +-
.../mapviewer/api/ElementIdentifierType.java | 24 +-
.../api/ObjectNotFoundException.java | 48 +-
.../lcsb/mapviewer/api/QueryException.java | 48 +-
.../mapviewer/api/SpringRestApiConfig.java | 12 +-
.../configuration/ConfigurationRestImpl.java | 20 +-
.../api/convert/ConvertController.java | 76 +-
.../api/convert/ConvertRestImpl.java | 288 ++-
.../mapviewer/api/files/FileController.java | 2 +-
.../genomics/ReferenceGenomeController.java | 15 +-
.../api/genomics/ReferenceGenomeRestImpl.java | 23 +-
.../mapviewer/api/mesh/MeshController.java | 7 +-
.../lcsb/mapviewer/api/mesh/MeshRestImpl.java | 5 +-
.../api/minervanet/MinervaNetController.java | 20 +-
.../minervanet/ReportSubmissionException.java | 3 +-
.../api/plugins/PluginController.java | 19 +-
.../mapviewer/api/plugins/PluginRestImpl.java | 6 +-
.../api/projects/ProjectRestImpl.java | 56 +-
.../chemicals/ChemicalController.java | 7 +-
.../projects/chemicals/ChemicalRestImpl.java | 106 +-
.../projects/comments/CommentController.java | 35 +-
.../api/projects/drugs/DrugController.java | 7 +-
.../api/projects/drugs/DrugRestImpl.java | 9 +-
.../api/projects/mirnas/MiRnaRestImpl.java | 35 +-
.../api/projects/models/ModelController.java | 23 +-
.../api/projects/models/ModelRestImpl.java | 45 +-
.../bioEntities/BioEntitiesController.java | 12 +-
.../bioEntities/BioEntitiesRestImpl.java | 11 +-
.../elements/ElementsController.java | 46 +-
.../elements/ElementsRestImpl.java | 206 +-
.../reactions/ReactionsController.java | 41 +-
.../reactions/ReactionsRestImpl.java | 135 +-
.../models/functions/FunctionsController.java | 6 +-
.../models/functions/FunctionsRestImpl.java | 21 +-
.../parameters/ParametersController.java | 9 +-
.../models/parameters/ParametersRestImpl.java | 14 +-
.../publications/PublicationsController.java | 42 +-
.../publications/PublicationsRestImpl.java | 49 +-
.../models/units/UnitsController.java | 6 +-
.../projects/models/units/UnitsRestImpl.java | 14 +-
.../projects/overlays/OverlayController.java | 3 +-
.../api/taxonomy/TaxonomyController.java | 7 +-
.../api/taxonomy/TaxonomyRestImpl.java | 3 +-
.../mapviewer/api/users/UserController.java | 7 +-
.../mapviewer/api/users/UserRestImpl.java | 26 +-
.../mapviewer/api/BaseControllerTest.java | 5 +-
.../lcsb/mapviewer/api/BaseRestImplTest.java | 2 +-
.../lcsb/mapviewer/api/RestTestFunctions.java | 9 +-
.../api/SpringRestApiTestConfig.java | 7 +-
.../ConfigurationRestImplTest.java | 5 +-
.../api/convert/ConvertRestImplTest.java | 5 +-
.../mapviewer/api/files/FileRestImplTest.java | 8 +-
.../ReferenceGenomeControllerTest.java | 6 +-
.../mapviewer/api/mesh/MeshRestImplTest.java | 3 +-
.../api/projects/ProjectRestImplTest.java | 4 +-
.../chemicals/ChemicalRestImplTest.java | 4 +-
.../comments/CommentRestImplTest.java | 5 +-
.../api/projects/drugs/DrugRestImplTest.java | 2 +-
.../projects/mirnas/MiRnaRestImplTest.java | 2 +-
.../projects/models/ModelRestImplTest.java | 6 +-
.../BioEntitiesControllerTest.java | 5 +-
.../elements/ElementRestImplTest.java | 2 +-
.../reactions/ReactionsRestImplTest.java | 4 +-
.../functions/FunctionsRestImplTest.java | 9 +-
.../PublicationsRestImplTest.java | 18 +-
.../overlays/OverlayRestImplTest.java | 2 +-
.../mapviewer/api/users/UserRestImplTest.java | 3 +-
.../AuthenticationTokenExpireException.java | 16 +-
.../services/InvalidTokenException.java | 16 +-
.../services/SpringServiceConfig.java | 14 +-
.../services/UserAccessException.java | 16 +-
.../services/impl/CommentService.java | 157 +-
.../services/impl/ConfigurationService.java | 51 +-
.../impl/CustomMd5PasswordEncoder.java | 70 +-
.../mapviewer/services/impl/FileService.java | 7 +-
.../services/impl/LayoutService.java | 628 +++---
.../mapviewer/services/impl/LdapService.java | 52 +-
.../services/impl/MiriamService.java | 82 +-
.../mapviewer/services/impl/ModelService.java | 81 +-
.../services/impl/PrivilegeService.java | 7 +-
.../services/impl/ProjectService.java | 542 +++---
.../services/impl/ReferenceGenomeService.java | 48 +-
.../services/impl/SearchHistoryService.java | 76 +-
.../services/impl/SearchService.java | 476 +++--
.../mapviewer/services/impl/UserService.java | 64 +-
.../mapviewer/services/impl/package-info.java | 1 -
.../services/interfaces/ILayoutService.java | 268 ++-
.../services/interfaces/IMiriamService.java | 32 +-
.../interfaces/IReferenceGenomeService.java | 4 +-
.../interfaces/ISearchHistoryService.java | 26 +-
.../services/interfaces/IUserService.java | 23 +-
.../services/interfaces/package-info.java | 1 -
.../overlay/AnnotatedObjectTreeRow.java | 555 +++---
.../services/overlay/package-info.java | 1 -
.../services/search/DbSearchService.java | 54 +-
.../services/search/ElementMatcher.java | 18 +-
.../services/search/IDbSearchService.java | 64 +-
.../search/chemical/ChemicalService.java | 55 +-
.../services/search/drug/DrugService.java | 119 +-
.../services/search/mirna/MiRNAService.java | 76 +-
.../services/utils/ColorSchemaReader.java | 31 +-
.../services/utils/CreateProjectParams.java | 22 +-
.../mapviewer/services/utils/EmailSender.java | 38 +-
.../utils/InvalidPrivilegeException.java | 26 +-
.../utils/ReferenceGenomeExistsException.java | 26 +-
.../services/utils/SearchIndexer.java | 318 ++-
.../services/utils/data/BuildInLayout.java | 180 +-
.../utils/data/ColorSchemaColumn.java | 38 +-
.../services/utils/data/ExportColumn.java | 197 +-
.../services/utils/data/ExportFileType.java | 64 +-
.../services/utils/data/package-info.java | 1 -
.../services/utils/package-info.java | 1 -
.../services/ServiceTestFunctions.java | 13 +-
.../services/SpringServiceTestConfig.java | 9 +-
.../impl/CustomMd5PasswordEncoderTest.java | 3 +-
.../services/impl/FailServiceMock.java | 16 +-
.../services/impl/LayoutServiceTest.java | 7 +-
.../services/impl/OkServiceMock.java | 16 +-
.../services/impl/ProjectServiceTest.java | 8 +-
.../services/search/DbSearchServiceTest.java | 1 -
.../services/search/ElementMatcherTest.java | 13 +-
.../search/mirna/MiRNAServiceTest.java | 6 +-
.../services/utils/ColorSchemaReaderTest.java | 3 +-
.../mapviewer/web/bean/utils/CORSFilter.java | 10 +-
.../mapviewer/web/bean/utils/CacheFilter.java | 12 +-
.../web/bean/utils/CustomFilter.java | 59 +-
.../CustomHttpServletResponseWrapper.java | 439 +++--
.../mapviewer/web/bean/utils/StartupBean.java | 10 +-
.../bean/utils/VersionResourceHandler.java | 41 +-
.../web/bean/utils/XFrameFilter.java | 10 +-
.../web/bean/utils/package-info.java | 1 -
.../AuthenticationFailureHandlerImpl.java | 11 +-
.../AuthenticationSuccessHandlerImpl.java | 6 +-
.../config/LdapAuthenticationProvider.java | 4 +-
.../config/LocalAuthenticationProvider.java | 12 +-
.../web/config/LogoutSuccessHandlerImpl.java | 9 +-
.../config/RefreshAuthoritiesInterceptor.java | 23 +-
.../web/config/SpringSecurityConfig.java | 12 +-
.../mapviewer/web/config/SpringWebConfig.java | 24 +-
.../web/config/UserDetailsServiceImpl.java | 2 +-
.../web/config/WebAppInitializer.java | 19 +-
.../web/converter/MiriamTypeConverter.java | 72 +-
.../mapviewer/web/converter/package-info.java | 1 -
.../java/lcsb/mapviewer/web/events/Event.java | 1 -
.../lcsb/mapviewer/web/events/Listener.java | 94 +-
.../web/events/ObjectAddedEvent.java | 48 +-
.../web/events/ObjectModifiedEvent.java | 48 +-
.../web/events/ObjectRemovedEvent.java | 48 +-
.../mapviewer/web/events/package-info.java | 1 -
.../ChemicalControllerIntegrationTest.java | 8 +-
.../web/CommentControllerIntegrationTest.java | 9 +-
...llerIntegrationTestWithoutTransaction.java | 7 +-
...onfigurationControllerIntegrationTest.java | 15 +-
.../web/ControllerIntegrationTest.java | 14 +-
.../web/DrugControllerIntegrationTest.java | 8 +-
.../web/EndPointsInputValidationTests.java | 8 +-
.../web/FileControllerIntegrationTest.java | 6 +-
...llerIntegrationTestWithoutTransaction.java | 4 +-
.../web/LdapServiceTestConfiguration.java | 8 +-
.../web/MapControllerIntegrationTest.java | 7 +-
.../web/MiRnaControllerIntegrationTest.java | 8 +-
.../web/OverlayControllerIntegrationTest.java | 22 +-
...llerIntegrationTestWithoutTransaction.java | 9 +-
.../web/PluginControllerIntegrationTest.java | 23 +-
.../web/ProjectControllerIntegrationTest.java | 11 +-
...ontrollerIntegrationTestForAsyncCalls.java | 12 +-
...PublicationsControllerIntegrationTest.java | 4 +-
.../ReactionControllerIntegrationTest.java | 6 +-
.../SpringSecurityGeneralIntegrationTest.java | 7 +-
.../SpringSecurityLdapIntegrationTest.java | 9 +-
.../TaxonomiesControllerIntegrationTest.java | 8 +-
...serControllerAnonymousIntegrationTest.java | 8 +-
.../web/UserControllerIntegrationTest.java | 14 +-
...llerIntegrationTestWithoutTransaction.java | 22 +-
1206 files changed, 33651 insertions(+), 36667 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 9d55234612..9f9e088de4 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
@@ -1,18 +1,15 @@
package lcsb.mapviewer.cdplugin.copypaste;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-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 jp.sbi.celldesigner.plugin.*;
import lcsb.mapviewer.common.SystemClipboard;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
/**
- * CD Plugin action responsible for translating annotation stored in notes to xml
- * format stored in annotations.
+ * CD Plugin action responsible for translating annotation stored in notes to
+ * xml format stored in annotations.
*
* @author Piotr Gawron
*
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 176851f392..8514450eb4 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
@@ -3,14 +3,13 @@ package lcsb.mapviewer.cdplugin.copypaste;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Pair;
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;
+import lcsb.mapviewer.model.map.*;
/**
* This abstract class defines common function for {@link CopyAction} and
@@ -20,17 +19,16 @@ import lcsb.mapviewer.model.map.MiriamType;
*
*/
public class CopyPasteAbstractAction {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(CopyPasteAbstractAction.class);
-
/**
* Prefix used for serialization/deserialization of {@link MiriamData} to string
* stored in system clipboard.
*/
private static final String PREFIX = "[MIRIAM]";
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.getLogger(CopyPasteAbstractAction.class);
/**
* Serializes {@link MiriamData} into string that will be stored into system
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 c14384bf52..8b881dd562 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
@@ -1,10 +1,10 @@
package lcsb.mapviewer.cdplugin.copypaste;
-import java.awt.KeyEventDispatcher;
-import java.awt.KeyboardFocusManager;
+import java.awt.*;
import java.awt.event.KeyEvent;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
@@ -94,6 +94,10 @@ public class CopyPastePlugin extends CellDesignerPlugin {
};
}
+ @Override
+ public void addPluginMenu() {
+ }
+
// CHECKSTYLE:OFF
@Override
public void SBaseAdded(PluginSBase arg0) {
@@ -105,28 +109,24 @@ public class CopyPastePlugin extends CellDesignerPlugin {
}
- @Override
- public void SBaseDeleted(PluginSBase arg0) {
- }
-
// CHECKSTYLE:ON
@Override
- public void addPluginMenu() {
+ public void SBaseDeleted(PluginSBase arg0) {
}
@Override
- public void modelClosed(PluginSBase arg0) {
+ public void modelOpened(PluginSBase arg0) {
}
@Override
- public void modelOpened(PluginSBase arg0) {
+ public void modelSelectChanged(PluginSBase arg0) {
}
@Override
- public void modelSelectChanged(PluginSBase arg0) {
+ public void modelClosed(PluginSBase arg0) {
}
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 fa0f5126a9..ac2a954872 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.event.ActionEvent;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginAction;
@@ -18,15 +19,13 @@ import jp.sbi.celldesigner.plugin.PluginListOf;
public class CopyPluginAction extends PluginAction {
/**
- * Default class logger.
+ *
*/
- private Logger logger = LogManager.getLogger(PasteAction.class.getName());
-
+ private static final long serialVersionUID = 1L;
/**
- *
+ * Default class logger.
*/
- private static final long serialVersionUID = 1L;
-
+ private Logger logger = LogManager.getLogger(PasteAction.class.getName());
/**
* Plugin that access this action.
*/
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 2cc400ea97..c200f0e7a0 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
@@ -2,13 +2,10 @@ package lcsb.mapviewer.cdplugin.copypaste;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-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 jp.sbi.celldesigner.plugin.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.SystemClipboard;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
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 f69c2f31e4..f8ef0d8abf 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.event.ActionEvent;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginAction;
@@ -18,13 +19,13 @@ import jp.sbi.celldesigner.plugin.PluginListOf;
public class PastePluginAction extends PluginAction {
/**
- * Default class logger.
+ *
*/
- private Logger logger = LogManager.getLogger(PasteAction.class.getName());
+ private static final long serialVersionUID = 1L;
/**
- *
+ * Default class logger.
*/
- private static final long serialVersionUID = 1L;
+ private Logger logger = LogManager.getLogger(PasteAction.class.getName());
/**
* Plugin that access this action.
*/
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 050427adde..fc8f9cffa7 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
@@ -1,24 +1,13 @@
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.awt.*;
import java.util.ArrayList;
import java.util.List;
-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 javax.swing.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
@@ -61,24 +50,20 @@ public final class InfoFrame {
* Font size of the caption label.
*/
private static final int CAPTION_FONT_SIZE = 18;
-
+ /**
+ * Singleton instance of this class (there can be only one instance of the
+ * frame).
+ */
+ private static InfoFrame instance = null;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private final Logger logger = LogManager.getLogger(InfoFrame.class);
-
/**
* 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.
*/
@@ -130,27 +115,6 @@ public final class 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(List<PluginSpeciesAlias> species) {
- this.species = species;
- updateSpecies();
- }
-
/**
* Updates information about species in the form.
*/
@@ -186,7 +150,7 @@ public final class InfoFrame {
/**
* 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
@@ -225,16 +189,26 @@ public final class InfoFrame {
/**
* Returns info if the frame is visible.
- *
+ *
* @return info if the frame is visible
*/
public boolean isVisible() {
return frame.isVisible();
}
+ /**
+ * Set visible flag for {@link #frame}.
+ *
+ * @param visible
+ * should the frame be visible or not
+ */
+ public void setVisible(boolean visible) {
+ frame.setVisible(visible);
+ }
+
/**
* Sets frame title.
- *
+ *
* @param title
* title of the frame
*/
@@ -244,7 +218,7 @@ public final class InfoFrame {
/**
* Returns frame title.
- *
+ *
* @return frame title
*/
public JFrame getFrame() {
@@ -253,7 +227,7 @@ public final class InfoFrame {
/**
* Set {@link JFrame#defaultCloseOperation}.
- *
+ *
* @param type
* new {@link JFrame#defaultCloseOperation} value
*/
@@ -263,7 +237,7 @@ public final class InfoFrame {
/**
* Set {@link JFrame#setAlwaysOnTop(boolean)}.
- *
+ *
* @param always
* new {@link JFrame#isAlwaysOnTop()} value
*/
@@ -275,4 +249,15 @@ public final class InfoFrame {
return species;
}
+ /**
+ * This method assign a set of species to this form.
+ *
+ * @param species
+ * - species to be shown in the form
+ */
+ public void setSpecies(List<PluginSpeciesAlias> species) {
+ this.species = species;
+ updateSpecies();
+ }
+
}
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 92fa61f158..9243d57fd8 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
@@ -1,21 +1,16 @@
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.awt.*;
+import java.awt.event.*;
import java.util.ArrayList;
import java.util.List;
-import javax.swing.Timer;
+import javax.swing.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-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 jp.sbi.celldesigner.plugin.*;
/**
* This class represent a plugin to CellDesigner that add info text box with
@@ -127,6 +122,10 @@ public class InfoPlugin extends CellDesignerPlugin {
}
}
+ @Override
+ public void addPluginMenu() {
+ }
+
// CHECKSTYLE:OFF
@Override
public void SBaseAdded(PluginSBase arg0) {
@@ -138,28 +137,24 @@ public class InfoPlugin extends CellDesignerPlugin {
}
- @Override
- public void SBaseDeleted(PluginSBase arg0) {
- }
-
// CHECKSTYLE:ON
@Override
- public void addPluginMenu() {
+ public void SBaseDeleted(PluginSBase arg0) {
}
@Override
- public void modelClosed(PluginSBase arg0) {
+ public void modelOpened(PluginSBase arg0) {
}
@Override
- public void modelOpened(PluginSBase arg0) {
+ public void modelSelectChanged(PluginSBase arg0) {
}
@Override
- public void modelSelectChanged(PluginSBase arg0) {
+ public void modelClosed(PluginSBase arg0) {
}
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java
index e1b62ea3aa..75859c684c 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java
@@ -6,10 +6,7 @@ import org.apache.logging.log4j.core.LogEvent;
import org.junit.*;
import org.mockito.Mockito;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-import jp.sbi.celldesigner.plugin.PluginReaction;
-import jp.sbi.celldesigner.plugin.PluginSpecies;
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+import jp.sbi.celldesigner.plugin.*;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.UnitTestFailedWatcher;
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
index d4ce487f08..4f16d2b0d1 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.cdplugin.copypaste;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import org.mockito.Mockito;
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
index ddde8a7350..d4c8612f4a 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
@@ -38,7 +38,7 @@ public class CopyPastePluginTest extends CdPluginFunctions {
PluginListOf list = createPluginListWithSpecies(1);
when(copyPastePlugin.getSelectedAllNode()).thenReturn(list);
plugin.getCopyPluginAction().setPlugin(copyPastePlugin);
-
+
plugin.createKeyEventDispatcher().dispatchKeyEvent(event);
String newData = cp.getClipboardContents();
@@ -60,7 +60,7 @@ public class CopyPastePluginTest extends CdPluginFunctions {
PluginListOf list = createPluginListWithSpecies(1);
when(copyPastePlugin.getSelectedAllNode()).thenReturn(list);
plugin.getPastePluginAction().setPlugin(copyPastePlugin);
-
+
plugin.createKeyEventDispatcher().dispatchKeyEvent(event);
}
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
index 0094f211ba..6027c65078 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
@@ -8,10 +8,7 @@ import static org.mockito.Mockito.times;
import org.junit.Test;
import org.mockito.Mockito;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-import jp.sbi.celldesigner.plugin.PluginReaction;
-import jp.sbi.celldesigner.plugin.PluginSpecies;
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+import jp.sbi.celldesigner.plugin.*;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.SystemClipboard;
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java
index 29dd1d8ba5..fe277a1212 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java
@@ -2,11 +2,10 @@ package lcsb.mapviewer.cdplugin.info;
import static org.junit.Assert.assertEquals;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoPluginTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoPluginTest.java
index 6a5190e039..1408d25997 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoPluginTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoPluginTest.java
@@ -5,7 +5,8 @@ import static org.junit.Assert.assertEquals;
import java.util.Arrays;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/SpringAnnotationConfig.java b/annotation/src/main/java/lcsb/mapviewer/annotation/SpringAnnotationConfig.java
index 5f829e5c27..7b3ec73faf 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/SpringAnnotationConfig.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/SpringAnnotationConfig.java
@@ -4,6 +4,6 @@ import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
@Configuration
-@ComponentScan(basePackages = {"lcsb.mapviewer.annotation"})
+@ComponentScan(basePackages = { "lcsb.mapviewer.annotation" })
public class SpringAnnotationConfig {
}
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 ac69ec6114..fc7fa4a55b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.annotation.cache;
import java.util.HashMap;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
@@ -48,9 +49,16 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
*/
private static ApplicationLevelCache cache = null;
+ /**
+ * Default constructor. Prevents instantiation.
+ */
+ private ApplicationLevelCache() {
+
+ }
+
/**
* Returns single instance of global application cache (singleton pattern).
- *
+ *
* @return single instance of global application cache
*/
public static ApplicationLevelCache getInstance() {
@@ -64,13 +72,6 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
}
}
- /**
- * Default constructor. Prevents instantiation.
- */
- private ApplicationLevelCache() {
-
- }
-
@Override
public synchronized Node getXmlNodeByQuery(String query, CacheType type) {
Node result = null;
@@ -89,7 +90,7 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
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();
@@ -105,6 +106,24 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
}
}
+ @Override
+ public synchronized void clearCache() {
+ logger.info("Clearing application cache");
+ cachedQueryNodes.clear();
+ cachedQueryString.clear();
+ }
+
+ @Override
+ public synchronized void removeByQuery(String query, CacheType type) {
+ cachedQueryString.remove(type.getId() + "\n" + query);
+ cachedQueryNodes.remove(type.getId() + "\n" + query);
+ }
+
+ @Override
+ public void invalidateByQuery(String query, CacheType type) {
+ removeByQuery(query, type);
+ }
+
/**
* Method that clean cache if memory usage is too high.
*/
@@ -129,22 +148,4 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
}
}
- @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/BigFileCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java
index 44c205e061..21ba35a919 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java
@@ -1,34 +1,19 @@
package lcsb.mapviewer.annotation.cache;
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.net.HttpURLConnection;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.net.URL;
+import java.io.*;
+import java.net.*;
import java.util.Calendar;
import java.util.List;
-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 java.util.concurrent.*;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.output.CountingOutputStream;
-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.logging.log4j.*;
+import org.apache.commons.net.ftp.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -38,7 +23,6 @@ import lcsb.mapviewer.model.user.ConfigurationElementType;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.ConfigurationDao;
import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
-import org.springframework.stereotype.Service;
/**
* Interface for accessing and storing big files. They are stored in local file
@@ -254,244 +238,11 @@ public class BigFileCache {
return entry;
}
- /**
- * Task that will be able to fetch file from ftp server.
- *
- * @author Piotr Gawron
- *
- */
- private final class GetFtpFileTask 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;
-
- /**
- * Default constructor.
- *
- * @param url
- * {@link #url}
- * @param updater
- * {@link #updater}
- */
- private GetFtpFileTask(String url, IProgressUpdater updater) {
- this.url = url;
- if (updater != null) {
- this.updater = updater;
- } else {
- this.updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
- }
- }
-
- @Override
- public Void call() throws Exception {
- dbUtils.createSessionForCurrentThread();
- FTPClient ftp = ftpClientFactory.createFtpClient();
- try {
- try {
- if (getAbsolutePathForFile(url) != null) {
- logger.warn("File already downloaded. Skipping...");
- return null;
- }
- } catch (FileNotFoundException e) {
- removeFile(url);
- }
-
- BigFileEntry entry = createEntryForBigFile(url);
- entry.setDownloadThreadId(Thread.currentThread().getId());
- bigFileEntryDao.update(entry);
-
- String server = getDomainName(url);
- 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 IOException("FTP server refused connection.");
- }
- ftp.enterLocalPassiveMode();
- ftp.login("anonymous", "");
- ftp.setFileType(FTP.BINARY_FILE_TYPE);
-
- long fileSize = -1;
- String remotePath = getFilePath(url);
- FTPFile[] files = ftp.listFiles(remotePath);
- if (files.length == 1 && files[0].isFile()) {
- fileSize = files[0].getSize();
- }
- final long size = fileSize;
-
- OutputStream output = new FileOutputStream(Configuration.getWebAppDir() + entry.getLocalPath());
- CountingOutputStream cos = new CountingOutputStream(output) {
- private double lastProgress = -1;
-
- protected void beforeWrite(int n) {
- super.beforeWrite(n);
- double newProgress = ((double) getCount()) / ((double) size) * IProgressUpdater.MAX_PROGRESS;
- if (newProgress - lastProgress >= IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION) {
- lastProgress = newProgress;
- entry.setDownloadProgress(lastProgress);
- bigFileEntryDao.update(entry);
- bigFileEntryDao.commit();
- updater.setProgress(lastProgress);
- }
- }
- };
- ftp.retrieveFile(remotePath, cos);
-
- entry.setDownloadProgress(IProgressUpdater.MAX_PROGRESS);
- bigFileEntryDao.update(entry);
- bigFileEntryDao.commit();
- updater.setProgress(IProgressUpdater.MAX_PROGRESS);
-
- output.close();
-
- ftp.logout();
-
- return null;
- } finally {
- bigFileEntryDao.commit();
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- if (ftp.isConnected()) {
- ftp.disconnect();
- }
-
- }
- }
-
- }
-
- /**
- * Class that describes task of downloading http file.
- *
- * @author Piotr Gawron
- *
- */
- private final class GetHttpFileTask 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;
-
- /**
- * Default constructor.
- *
- * @param url
- * {@link #url}
- * @param updater
- * {@link #updater}
- */
- private GetHttpFileTask(String url, IProgressUpdater updater) {
- this.url = url;
- if (updater != null) {
- this.updater = updater;
- } else {
- this.updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
- }
- }
-
- @Override
- public Void call() throws Exception {
- dbUtils.createSessionForCurrentThread();
- BufferedInputStream in = null;
- CountingOutputStream cos = null;
- try {
- try {
- if (getAbsolutePathForFile(url) != null) {
- logger.warn("File already downloaded. Skipping...");
- return null;
- }
- } catch (FileNotFoundException e) {
- removeFile(url);
- }
- BigFileEntry entry = createEntryForBigFile(url);
- entry.setDownloadThreadId(Thread.currentThread().getId());
- bigFileEntryDao.update(entry);
-
- final long size = getRemoteHttpFileSize(url);
-
- OutputStream output = new FileOutputStream(Configuration.getWebAppDir() + entry.getLocalPath());
- cos = new CountingOutputStream(output) {
- private double lastProgress = -1;
-
- protected void beforeWrite(int n) {
- super.beforeWrite(n);
- double newProgress = ((double) getCount()) / ((double) size) * IProgressUpdater.MAX_PROGRESS;
- if (newProgress - lastProgress >= IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION) {
- lastProgress = newProgress;
- entry.setDownloadProgress(lastProgress);
- bigFileEntryDao.update(entry);
- bigFileEntryDao.commit();
- updater.setProgress(lastProgress);
- }
- }
- };
- URL website = new URL(url);
- in = new BufferedInputStream(website.openStream());
-
- final byte[] data = new byte[DOWNLOAD_BUFFER_SIZE];
- int count;
- while ((count = in.read(data, 0, DOWNLOAD_BUFFER_SIZE)) != -1) {
- cos.write(data, 0, count);
- }
-
- entry.setDownloadProgress(IProgressUpdater.MAX_PROGRESS);
- bigFileEntryDao.update(entry);
- bigFileEntryDao.commit();
- updater.setProgress(IProgressUpdater.MAX_PROGRESS);
-
- output.close();
-
- return null;
- } catch (Exception e) {
- logger.error(e, e);
- throw e;
- } finally {
- bigFileEntryDao.commit();
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- // close opened streams
- if (in != null) {
- in.close();
- }
- if (cos != null) {
- cos.close();
- }
- }
- }
- }
-
/**
* Checks if local file for given url is up to date. The check is based on file
* size check (ftp doesn't provide checksums for files, so we cannot compare it
* differently without downloading file).
- *
+ *
* @param url
* url to ftp file
* @return <code>true</code> if file is up to date, <code>false</code> in other
@@ -513,7 +264,7 @@ public class BigFileCache {
/**
* Checks if local file fetched from ftp is up to date.
- *
+ *
* @param url
* url to remote file
* @return <code>true</code> if file is up to date, <code>false</code> otherwise
@@ -571,7 +322,7 @@ public class BigFileCache {
/**
* Checks if local file fetched from http is up to date.
- *
+ *
* @param url
* url to remote file
* @return <code>true</code> if file is up to date, <code>false</code> otherwise
@@ -600,7 +351,7 @@ public class BigFileCache {
/**
* Returns size of the remote file access via http url.
- *
+ *
* @param url
* url address to the file
* @return size of the remote file access via http url
@@ -626,7 +377,7 @@ public class BigFileCache {
/**
* Removes local file copy of a file given in a parameter.
- *
+ *
* @param url
* ftp url of a file
* @throws IOException
@@ -649,105 +400,18 @@ public class BigFileCache {
}
/**
- * Task that describes updating file from ftp.
- *
- * @author Piotr Gawron
+ * Updates local copy of a file that can be downloaded from a url given in
+ * parameter.
*
- */
- private final class UpdateFtpFileTask implements Callable<Void> {
-
- /**
- * Url to file.
- */
- private String url;
-
- /**
- * Default constructor.
- *
- * @param url
- * {@link #url}
- */
- private UpdateFtpFileTask(String url) {
- this.url = url;
- }
-
- @Override
- public Void call() throws Exception {
- dbUtils.createSessionForCurrentThread();
- FTPClient ftp = ftpClientFactory.createFtpClient();
- try {
- BigFileEntry localEntryCopy = bigFileEntryDao.getByUrl(url);
- localEntryCopy.setDownloadThreadId(Thread.currentThread().getId());
- localEntryCopy.setDownloadProgress(0.0);
- bigFileEntryDao.update(localEntryCopy);
-
- // remove current version
- new File(Configuration.getWebAppDir() + localEntryCopy.getLocalPath()).delete();
-
- String server = getDomainName(url);
- 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 IOException("FTP server refused connection.");
- }
- ftp.enterLocalPassiveMode();
- ftp.login("anonymous", "");
- ftp.setFileType(FTP.BINARY_FILE_TYPE);
-
- long fileSize = -1;
- String remotePath = getFilePath(url);
- FTPFile[] files = ftp.listFiles(remotePath);
- if (files.length == 1 && files[0].isFile()) {
- fileSize = files[0].getSize();
- }
- final long size = fileSize;
-
- OutputStream output = new FileOutputStream(localEntryCopy.getLocalPath());
- CountingOutputStream cos = new CountingOutputStream(output) {
- private double lastProgress = -1;
-
- protected void beforeWrite(int n) {
- super.beforeWrite(n);
- double newProgress = ((double) getCount()) / ((double) size) * IProgressUpdater.MAX_PROGRESS;
- if (newProgress - lastProgress >= IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION) {
- lastProgress = newProgress;
- localEntryCopy.setDownloadProgress(lastProgress);
- bigFileEntryDao.update(localEntryCopy);
- }
- }
- };
- ftp.retrieveFile(remotePath, cos);
-
- output.close();
-
- ftp.logout();
- return null;
- } finally {
- dbUtils.closeSessionForCurrentThread();
- if (ftp.isConnected()) {
- ftp.disconnect();
- }
- }
- }
-
- }
-
- /**
- * Updates local copy of a file that can be downloaded from a url given in
- * parameter.
- *
- * @param url
- * url to an ftp file to be updated
- * @param async
- * <code>true</code> if update should be done asynchronously,
- * <code>false</code> otherwise
- * @throws IOException
- * thrown when there is a problem with accessing remote file
- * @throws URISyntaxException
- * thrown when url is invalid
+ * @param url
+ * url to an ftp file to be updated
+ * @param async
+ * <code>true</code> if update should be done asynchronously,
+ * <code>false</code> otherwise
+ * @throws IOException
+ * thrown when there is a problem with accessing remote file
+ * @throws URISyntaxException
+ * thrown when url is invalid
*/
public void updateFile(String url, boolean async) throws URISyntaxException, IOException {
if (isLocalFileUpToDate(url)) {
@@ -765,7 +429,7 @@ public class BigFileCache {
/**
* Executes download/update task.
- *
+ *
* @param task
* task to be executed
* @throws URISyntaxException
@@ -791,7 +455,7 @@ public class BigFileCache {
/**
* Returns server domain name from url.
- *
+ *
* @param url
* url to be processed
* @return server domain name from url
@@ -810,7 +474,7 @@ public class BigFileCache {
/**
* Returns path to file on server without server domain name from url.
- *
+ *
* @param url
* url to be processed
* @return path to file on server without server domain name from url
@@ -824,7 +488,7 @@ public class BigFileCache {
/**
* Returns simple file name from url.
- *
+ *
* @param url
* url to be processed
* @return simple file name from url
@@ -838,7 +502,7 @@ public class BigFileCache {
/**
* Checks if the file identified by url is cached.
- *
+ *
* @param sourceUrl
* url that identifies file
* @return <code>true</code> if the file is cached, <code>false</code> otherwise
@@ -870,7 +534,7 @@ public class BigFileCache {
/**
* 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() {
@@ -906,4 +570,324 @@ public class BigFileCache {
this.configurationDao = configurationDao;
}
+ /**
+ * Task that will be able to fetch file from ftp server.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class GetFtpFileTask 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;
+
+ /**
+ * Default constructor.
+ *
+ * @param url
+ * {@link #url}
+ * @param updater
+ * {@link #updater}
+ */
+ private GetFtpFileTask(String url, IProgressUpdater updater) {
+ this.url = url;
+ if (updater != null) {
+ this.updater = updater;
+ } else {
+ this.updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+ }
+ }
+
+ @Override
+ public Void call() throws Exception {
+ dbUtils.createSessionForCurrentThread();
+ FTPClient ftp = ftpClientFactory.createFtpClient();
+ try {
+ try {
+ if (getAbsolutePathForFile(url) != null) {
+ logger.warn("File already downloaded. Skipping...");
+ return null;
+ }
+ } catch (FileNotFoundException e) {
+ removeFile(url);
+ }
+
+ BigFileEntry entry = createEntryForBigFile(url);
+ entry.setDownloadThreadId(Thread.currentThread().getId());
+ bigFileEntryDao.update(entry);
+
+ String server = getDomainName(url);
+ 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 IOException("FTP server refused connection.");
+ }
+ ftp.enterLocalPassiveMode();
+ ftp.login("anonymous", "");
+ ftp.setFileType(FTP.BINARY_FILE_TYPE);
+
+ long fileSize = -1;
+ String remotePath = getFilePath(url);
+ FTPFile[] files = ftp.listFiles(remotePath);
+ if (files.length == 1 && files[0].isFile()) {
+ fileSize = files[0].getSize();
+ }
+ final long size = fileSize;
+
+ OutputStream output = new FileOutputStream(Configuration.getWebAppDir() + entry.getLocalPath());
+ CountingOutputStream cos = new CountingOutputStream(output) {
+ private double lastProgress = -1;
+
+ protected void beforeWrite(int n) {
+ super.beforeWrite(n);
+ double newProgress = ((double) getCount()) / ((double) size) * IProgressUpdater.MAX_PROGRESS;
+ if (newProgress - lastProgress >= IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION) {
+ lastProgress = newProgress;
+ entry.setDownloadProgress(lastProgress);
+ bigFileEntryDao.update(entry);
+ bigFileEntryDao.commit();
+ updater.setProgress(lastProgress);
+ }
+ }
+ };
+ ftp.retrieveFile(remotePath, cos);
+
+ entry.setDownloadProgress(IProgressUpdater.MAX_PROGRESS);
+ bigFileEntryDao.update(entry);
+ bigFileEntryDao.commit();
+ updater.setProgress(IProgressUpdater.MAX_PROGRESS);
+
+ output.close();
+
+ ftp.logout();
+
+ return null;
+ } finally {
+ bigFileEntryDao.commit();
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ if (ftp.isConnected()) {
+ ftp.disconnect();
+ }
+
+ }
+ }
+
+ }
+
+ /**
+ * Class that describes task of downloading http file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class GetHttpFileTask 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;
+
+ /**
+ * Default constructor.
+ *
+ * @param url
+ * {@link #url}
+ * @param updater
+ * {@link #updater}
+ */
+ private GetHttpFileTask(String url, IProgressUpdater updater) {
+ this.url = url;
+ if (updater != null) {
+ this.updater = updater;
+ } else {
+ this.updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+ }
+ }
+
+ @Override
+ public Void call() throws Exception {
+ dbUtils.createSessionForCurrentThread();
+ BufferedInputStream in = null;
+ CountingOutputStream cos = null;
+ try {
+ try {
+ if (getAbsolutePathForFile(url) != null) {
+ logger.warn("File already downloaded. Skipping...");
+ return null;
+ }
+ } catch (FileNotFoundException e) {
+ removeFile(url);
+ }
+ BigFileEntry entry = createEntryForBigFile(url);
+ entry.setDownloadThreadId(Thread.currentThread().getId());
+ bigFileEntryDao.update(entry);
+
+ final long size = getRemoteHttpFileSize(url);
+
+ OutputStream output = new FileOutputStream(Configuration.getWebAppDir() + entry.getLocalPath());
+ cos = new CountingOutputStream(output) {
+ private double lastProgress = -1;
+
+ protected void beforeWrite(int n) {
+ super.beforeWrite(n);
+ double newProgress = ((double) getCount()) / ((double) size) * IProgressUpdater.MAX_PROGRESS;
+ if (newProgress - lastProgress >= IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION) {
+ lastProgress = newProgress;
+ entry.setDownloadProgress(lastProgress);
+ bigFileEntryDao.update(entry);
+ bigFileEntryDao.commit();
+ updater.setProgress(lastProgress);
+ }
+ }
+ };
+ URL website = new URL(url);
+ in = new BufferedInputStream(website.openStream());
+
+ final byte[] data = new byte[DOWNLOAD_BUFFER_SIZE];
+ int count;
+ while ((count = in.read(data, 0, DOWNLOAD_BUFFER_SIZE)) != -1) {
+ cos.write(data, 0, count);
+ }
+
+ entry.setDownloadProgress(IProgressUpdater.MAX_PROGRESS);
+ bigFileEntryDao.update(entry);
+ bigFileEntryDao.commit();
+ updater.setProgress(IProgressUpdater.MAX_PROGRESS);
+
+ output.close();
+
+ return null;
+ } catch (Exception e) {
+ logger.error(e, e);
+ throw e;
+ } finally {
+ bigFileEntryDao.commit();
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ // close opened streams
+ if (in != null) {
+ in.close();
+ }
+ if (cos != null) {
+ cos.close();
+ }
+ }
+ }
+ }
+
+ /**
+ * Task that describes updating file from ftp.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class UpdateFtpFileTask implements Callable<Void> {
+
+ /**
+ * Url to file.
+ */
+ private String url;
+
+ /**
+ * Default constructor.
+ *
+ * @param url
+ * {@link #url}
+ */
+ private UpdateFtpFileTask(String url) {
+ this.url = url;
+ }
+
+ @Override
+ public Void call() throws Exception {
+ dbUtils.createSessionForCurrentThread();
+ FTPClient ftp = ftpClientFactory.createFtpClient();
+ try {
+ BigFileEntry localEntryCopy = bigFileEntryDao.getByUrl(url);
+ localEntryCopy.setDownloadThreadId(Thread.currentThread().getId());
+ localEntryCopy.setDownloadProgress(0.0);
+ bigFileEntryDao.update(localEntryCopy);
+
+ // remove current version
+ new File(Configuration.getWebAppDir() + localEntryCopy.getLocalPath()).delete();
+
+ String server = getDomainName(url);
+ 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 IOException("FTP server refused connection.");
+ }
+ ftp.enterLocalPassiveMode();
+ ftp.login("anonymous", "");
+ ftp.setFileType(FTP.BINARY_FILE_TYPE);
+
+ long fileSize = -1;
+ String remotePath = getFilePath(url);
+ FTPFile[] files = ftp.listFiles(remotePath);
+ if (files.length == 1 && files[0].isFile()) {
+ fileSize = files[0].getSize();
+ }
+ final long size = fileSize;
+
+ OutputStream output = new FileOutputStream(localEntryCopy.getLocalPath());
+ CountingOutputStream cos = new CountingOutputStream(output) {
+ private double lastProgress = -1;
+
+ protected void beforeWrite(int n) {
+ super.beforeWrite(n);
+ double newProgress = ((double) getCount()) / ((double) size) * IProgressUpdater.MAX_PROGRESS;
+ if (newProgress - lastProgress >= IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION) {
+ lastProgress = newProgress;
+ localEntryCopy.setDownloadProgress(lastProgress);
+ bigFileEntryDao.update(localEntryCopy);
+ }
+ }
+ };
+ ftp.retrieveFile(remotePath, cos);
+
+ output.close();
+
+ ftp.logout();
+ return null;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ if (ftp.isConnected()) {
+ ftp.disconnect();
+ }
+ }
+ }
+
+ }
+
}
\ No newline at end of file
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 53b8eef6c2..01b15a9d52 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
@@ -25,35 +25,6 @@ public abstract class CachableInterface {
* Default class logger.
*/
private static Logger logger = LogManager.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
@@ -61,24 +32,20 @@ public abstract class CachableInterface {
* 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.
*/
@@ -86,7 +53,7 @@ public abstract class CachableInterface {
/**
* Default constructor.
- *
+ *
* @param clazz
* type that defines this interface
*/
@@ -94,6 +61,34 @@ public abstract class CachableInterface {
this.cacheIdentifier = clazz.getCanonicalName();
}
+ /**
+ * 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;
+ }
+
/**
* Puts some string value into cache.
*
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 b171e2a1cc..1f3701d9b0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CacheException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CacheException.java
@@ -7,19 +7,19 @@ package lcsb.mapviewer.annotation.cache;
*
*/
public class CacheException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 1d18378679..38ad4b0141 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/FtpClientFactory.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/FtpClientFactory.java
@@ -10,12 +10,12 @@ import org.apache.commons.net.ftp.FTPClient;
*/
public class FtpClientFactory {
- /**
- * Creates new instance of {@link FTPClient}.
- *
- * @return new instance of {@link FTPClient}
- */
- public FTPClient createFtpClient() {
- return new FTPClient();
- }
+ /**
+ * 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 360a50c391..97031ec889 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCache.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.cache;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.stereotype.Service;
@@ -48,16 +49,6 @@ public class GeneralCache implements GeneralCacheInterface {
this.cache2 = 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) {
@@ -116,6 +107,16 @@ public class GeneralCache implements GeneralCacheInterface {
}
}
+ @Override
+ public void clearCache() {
+ if (cache1 != null) {
+ cache1.clearCache();
+ }
+ if (cache2 != null) {
+ cache2.clearCache();
+ }
+ }
+
@Override
public void removeByQuery(String query, CacheType type) {
if (type == null) {
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 1a82107082..f0c2863a39 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusion.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusion.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.cache;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -74,7 +75,7 @@ public class GeneralCacheWithExclusion implements GeneralCacheInterface {
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);
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 5d5059a89a..de3f74fdbc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -1,19 +1,12 @@
package lcsb.mapviewer.annotation.cache;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.LinkedList;
-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 java.util.*;
+import java.util.concurrent.*;
import javax.annotation.PostConstruct;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.aop.framework.Advised;
import org.springframework.aop.support.AopUtils;
import org.springframework.beans.factory.annotation.Autowired;
@@ -47,6 +40,248 @@ import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
@Service
public class PermanentDatabaseLevelCache implements PermanentDatabaseLevelCacheInterface, ApplicationContextAware {
+ /**
+ * Spring application context.
+ */
+ private static ApplicationContext applicationContext;
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(PermanentDatabaseLevelCache.class);
+ /**
+ * Data access object for query entries accessed by string key.
+ */
+ private CacheQueryDao cacheQueryDao;
+ /**
+ * Utility that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ 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;
+
+ @Autowired
+ public PermanentDatabaseLevelCache(CacheQueryDao cacheQueryDao, DbUtils dbUtils) {
+ this.cacheQueryDao = cacheQueryDao;
+ this.dbUtils = dbUtils;
+ }
+
+ /**
+ * http://forum.spring.io/forum/spring-projects/aop/52011-need-to-unwrap-a-proxy-to-get-the-object-being-proxied
+ *
+ * @param bean
+ * @return
+ * @throws Exception
+ */
+ private final Object unwrapProxy(Object bean) throws Exception {
+
+ /*
+ * If the given object is a proxy, set the return value as the object being
+ * proxied, otherwise return the given object.
+ */
+ if (AopUtils.isAopProxy(bean) && bean instanceof Advised) {
+
+ Advised advised = (Advised) bean;
+
+ bean = advised.getTargetSource().getTarget();
+ }
+
+ return bean;
+ }
+
+ /**
+ * 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 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 = XmlParser.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 = XmlParser.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 clearCache() {
+ cacheQueryDao.clearTable();
+ }
+
+ @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 void waitToFinishTasks() throws InterruptedException, ExecutionException {
+ Collection<Future<?>> futures = new LinkedList<Future<?>>();
+ futures.add(cacheRefreshService.submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ return null;
+ }
+ }));
+ futures.add(service.submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ return null;
+ }
+ }));
+
+ for (Future<?> future : futures) {
+ future.get();
+ }
+ }
+
+ @Override
+ public CacheQueryDao getCacheQueryDao() {
+ return cacheQueryDao;
+ }
+
+ @Override
+ public void setCacheQueryDao(CacheQueryDao cacheQueryDao) {
+ this.cacheQueryDao = cacheQueryDao;
+ }
+
/**
* This class represents new thread task for querying database.
*
@@ -184,29 +419,6 @@ public class PermanentDatabaseLevelCache implements PermanentDatabaseLevelCacheI
}
- /**
- * http://forum.spring.io/forum/spring-projects/aop/52011-need-to-unwrap-a-proxy-to-get-the-object-being-proxied
- *
- * @param bean
- * @return
- * @throws Exception
- */
- private final Object unwrapProxy(Object bean) throws Exception {
-
- /*
- * If the given object is a proxy, set the return value as the object being
- * proxied, otherwise return the given object.
- */
- if (AopUtils.isAopProxy(bean) && bean instanceof Advised) {
-
- Advised advised = (Advised) bean;
-
- bean = advised.getTargetSource().getTarget();
- }
-
- return bean;
- }
-
/**
* This class represents new thread task for adding entry to database.
*
@@ -398,228 +610,4 @@ public class PermanentDatabaseLevelCache implements PermanentDatabaseLevelCacheI
}
- /**
- * Spring application context.
- */
- private static ApplicationContext applicationContext;
-
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger(PermanentDatabaseLevelCache.class);
-
- /**
- * Data access object for query entries accessed by string key.
- */
- private CacheQueryDao cacheQueryDao;
-
- /**
- * Utility that help to manage the sessions in custom multithreaded
- * implementation.
- */
- 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;
-
- @Autowired
- public PermanentDatabaseLevelCache(CacheQueryDao cacheQueryDao, DbUtils dbUtils) {
- this.cacheQueryDao = cacheQueryDao;
- this.dbUtils = dbUtils;
- }
-
- /**
- * 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 = XmlParser.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 = XmlParser.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 CacheQueryDao getCacheQueryDao() {
- return cacheQueryDao;
- }
-
- @Override
- public void setCacheQueryDao(CacheQueryDao cacheQueryDao) {
- this.cacheQueryDao = cacheQueryDao;
- }
-
- @Override
- public void waitToFinishTasks() throws InterruptedException, ExecutionException {
- Collection<Future<?>> futures = new LinkedList<Future<?>>();
- futures.add(cacheRefreshService.submit(new Callable<Void>() {
- @Override
- public Void call() throws Exception {
- return null;
- }
- }));
- futures.add(service.submit(new Callable<Void>() {
- @Override
- public Void call() throws Exception {
- return null;
- }
- }));
-
- for (Future<?> future : futures) {
- future.get();
- }
- }
-
}
\ 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 59099aedab..bea55aba3f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
@@ -23,8 +23,9 @@ public interface PermanentDatabaseLevelCacheInterface extends QueryCacheInterfac
/**
* Waits for all tasks in the cache to finish (refresh/get/etc).
- * @throws ExecutionException
- * @throws InterruptedException
+ *
+ * @throws ExecutionException
+ * @throws InterruptedException
*/
void waitToFinishTasks() throws InterruptedException, ExecutionException;
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 6c84091a5c..ab8a03536d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/QueryCacheInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/QueryCacheInterface.java
@@ -1,9 +1,9 @@
package lcsb.mapviewer.annotation.cache;
-import lcsb.mapviewer.model.cache.CacheType;
-
import org.w3c.dom.Node;
+import lcsb.mapviewer.model.cache.CacheType;
+
/**
* This interface describes general functionality of the cache interface.
*
@@ -47,7 +47,7 @@ public interface QueryCacheInterface {
* 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);
/**
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 29c7bf36fb..771996e563 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/SourceNotAvailable.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/SourceNotAvailable.java
@@ -9,41 +9,41 @@ package lcsb.mapviewer.annotation.cache;
*/
public class SourceNotAvailable extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
- public SourceNotAvailable(Exception e) {
- super(e);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 f22b0530b3..c6302e8ced 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
@@ -1,21 +1,12 @@
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 java.io.*;
+import java.net.*;
+import java.util.concurrent.*;
import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
@@ -33,159 +24,151 @@ import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
*/
public class WebPageDownloader {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.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;
- }
+ /**
+ * 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;
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(WebPageDownloader.class);
+
+ /**
+ * 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 3f4189908b..c9ccf48fb3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
@@ -2,13 +2,11 @@ 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 javax.xml.bind.*;
import org.apache.commons.lang3.SerializationException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
/**
@@ -21,91 +19,91 @@ import org.w3c.dom.Node;
* type of the object to serialize
*/
public class XmlSerializer<T> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(XmlSerializer.class);
- /**
- * Class of the object that DAO works on.
- */
- private Class<? extends T> clazz;
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(XmlSerializer.class);
- /**
- * Java Architecture for XML Binding (JAXB) class that allows transforming T
- * object into xml.
- */
- private Marshaller jaxbMarshaller;
+ /**
+ * Class of the object that DAO works on.
+ */
+ private Class<? extends T> clazz;
- /**
- * Java Architecture for XML Binding (JAXB) class that allows transforming xml
- * describing T into T object.
- */
- private Unmarshaller jaxbUnmarshaller;
+ /**
+ * Java Architecture for XML Binding (JAXB) class that allows transforming T
+ * object into xml.
+ */
+ private Marshaller jaxbMarshaller;
- /**
- * 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);
- }
- }
+ /**
+ * Java Architecture for XML Binding (JAXB) class that allows transforming xml
+ * describing T into T object.
+ */
+ private Unmarshaller jaxbUnmarshaller;
- /**
- * 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();
- }
+ /**
+ * 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);
+ }
+ }
- /**
- * 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;
- }
- }
+ /**
+ * 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 64f1ec2089..016987a387 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
@@ -1,20 +1,22 @@
/**
* This package contains implementation of cache utils. General interface of
- * cache is defined in {@link lcsb.mapviewer.annotation.cache.QueryCacheInterface
+ * 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
+ * <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
+ * <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>
+ * <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}
@@ -24,4 +26,3 @@
* 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 5909001a86..31f84391f8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Article.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Article.java
@@ -16,180 +16,180 @@ import javax.xml.bind.annotation.XmlRootElement;
*/
@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;
- }
+ /**
+ *
+ */
+ 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 6725ec2b98..63284f4ff5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ArticleCitationComparator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ArticleCitationComparator.java
@@ -11,9 +11,9 @@ import java.util.Comparator;
*/
public class ArticleCitationComparator implements Comparator<Article> {
- @Override
- public int compare(Article o1, Article o2) {
- return -((Integer) o1.getCitationCount()).compareTo(o2.getCitationCount());
- }
+ @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 00e4d1f0fc..282181424d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java
@@ -6,11 +6,10 @@ import java.util.List;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.*;
/**
* This class represents <a href="http://www.ebi.ac.uk/chebi/">chebi</a> object.
@@ -21,227 +20,227 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
@XmlRootElement
public class Chebi implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 c4cce63e7e..9b3aa6be01 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChebiRelation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChebiRelation.java
@@ -12,95 +12,95 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
*
*/
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;
- }
+
+ /**
+ *
+ */
+ 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 a5bb9ba78f..f2b8141847 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
@@ -1,10 +1,7 @@
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 java.util.*;
import javax.xml.bind.annotation.XmlRootElement;
@@ -22,274 +19,257 @@ import lcsb.mapviewer.model.map.MiriamData;
@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());
- }
-
- }
+ /**
+ *
+ */
+ 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;
+ }
+
+ /**
+ * @param synonyms
+ * list of all names that are synonyms.
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return list of synonyms as string.
+ */
+ public String getSynonymsString() {
+ return StringUtils.join(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();
+ }
@Override
public Collection<MiriamData> getSources() {
@@ -303,13 +283,32 @@ public class Chemical implements Serializable, TargettingStructure {
return sources;
}
- @Override
- public Collection<Target> getTargets() {
- return getInferenceNetwork();
- }
+ @Override
+ public Collection<Target> getTargets() {
+ return getInferenceNetwork();
+ }
public void addSynonyms(List<String> synonyms) {
this.synonyms.addAll(synonyms);
}
+ /**
+ * 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());
+ }
+
+ }
+
}
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 c5e3895247..754c0f65c3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidence.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidence.java
@@ -8,30 +8,31 @@ package lcsb.mapviewer.annotation.data;
*/
public enum ChemicalDirectEvidence {
- /**
- * Values.
- */
- MARKER("marker/mechanism"), THERAPEUTIC("therapeutic");
+ /**
+ * Values.
+ */
+ MARKER("marker/mechanism"),
+ THERAPEUTIC("therapeutic");
- /**
- * Value.
- */
- private String value;
+ /**
+ * Value.
+ */
+ private String value;
- /**
- * @param value
- * string to set the value.
- */
- ChemicalDirectEvidence(String value) {
+ /**
+ * @param value
+ * string to set the value.
+ */
+ ChemicalDirectEvidence(String value) {
- this.value = value;
- }
+ this.value = value;
+ }
- /**
- * @return the value
- */
- public String getValue() {
- return 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 d4e786a065..f308e36325 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
+import java.util.*;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.model.map.MiriamData;
@@ -22,315 +21,315 @@ import lcsb.mapviewer.model.map.MiriamData;
@XmlRootElement
public class Drug implements Serializable, TargettingStructure {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.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());
- }
-
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.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 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;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * @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 b826b8c412..8f5f10dfd5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/EntrezData.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/EntrezData.java
@@ -18,135 +18,136 @@ import lcsb.mapviewer.model.map.MiriamData;
@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;
- }
+ /**
+ *
+ */
+ 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;
+ }
+
+ /**
+ * @param miriamData
+ * the miriamData to set
+ * @see #miriamData
+ */
+ public void setMiriamData(List<MiriamData> miriamData) {
+ this.miriamData = 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;
+ }
}
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 8031d370f4..93ce1220e4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Go.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Go.java
@@ -12,75 +12,75 @@ import javax.xml.bind.annotation.XmlRootElement;
*/
@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;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
+ /**
+ * Human readable name.
+ */
+ private String commonName;
- /**
- * @param commonName
- * the commonName to set
- * @see #commonName
- */
- public void setCommonName(String commonName) {
- this.commonName = commonName;
- }
+ /**
+ * Description of the object.
+ */
+ private String description;
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
+ /**
+ * Go identifier.
+ */
+ private String goTerm;
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
- /**
- * @return the goTerm
- * @see #goTerm
- */
- public String getGoTerm() {
- return goTerm;
- }
+ /**
+ * @param commonName
+ * the commonName to set
+ * @see #commonName
+ */
+ public void setCommonName(String commonName) {
+ this.commonName = commonName;
+ }
- /**
- * @param goTerm
- * the goTerm to set
- * @see #goTerm
- */
- public void setGoTerm(String goTerm) {
- this.goTerm = goTerm;
- }
+ /**
+ * @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 dfe74c5eb9..6cae7710f6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import javax.xml.bind.annotation.XmlRootElement;
import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class represents <a href="http://www.nlm.nih.gov/cgi/mesh//">MeSH</a>
@@ -20,164 +19,164 @@ import org.apache.logging.log4j.*;
@XmlRootElement
public class MeSH implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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);
- }
-
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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;
+ }
+
+ /**
+ * @param meSHId
+ * database identifier
+ */
+ public void setMeSHId(String meSHId) {
+ this.meSHId = meSHId;
+ }
+
+ /**
+ * @return description of the object.
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @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 2602a1751a..aeef8f7704 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
@@ -1,10 +1,7 @@
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 java.util.*;
import javax.xml.bind.annotation.XmlRootElement;
@@ -65,21 +62,6 @@ public class MiRNA implements Serializable, TargettingStructure {
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.
*/
@@ -97,7 +79,7 @@ public class MiRNA implements Serializable, TargettingStructure {
/**
* Adds target to mirna.
- *
+ *
* @param target
* target to add.
*/
@@ -111,6 +93,21 @@ public class MiRNA implements Serializable, TargettingStructure {
return new ArrayList<>();
}
+ /**
+ * @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;
+ }
+
/**
* Comparator of the objects by their name.
*
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 20c0eaa0ad..1b2b36520c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
@@ -1,13 +1,12 @@
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
import javax.xml.bind.annotation.XmlElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
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 6b695531bb..ce2cc04d75 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargetType.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargetType.java
@@ -8,46 +8,46 @@ package lcsb.mapviewer.annotation.data;
*/
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;
- }
+ /**
+ * 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/TargettingStructure.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
index c35645c3da..6f1dbae2d3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
@@ -12,17 +12,17 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
public interface TargettingStructure {
- /**
- *
- * @return list of {@link MiriamData annotations} that describe source of this
- * object
- */
- Collection<MiriamData> getSources();
+ /**
+ *
+ * @return list of {@link MiriamData annotations} that describe source of this
+ * object
+ */
+ Collection<MiriamData> getSources();
- /**
- *
- * @return list of {@link Target targets} with which object is interacting
- */
- Collection<Target> getTargets();
+ /**
+ *
+ * @return list of {@link Target targets} with which object is interacting
+ */
+ Collection<Target> getTargets();
}
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 1473f561a5..edfa64fa1f 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
@@ -2,4 +2,3 @@
* 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 4791f2adb2..37a429c6f0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -2,30 +2,18 @@ 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 java.util.*;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
-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 org.w3c.dom.*;
+
+import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.data.*;
+import lcsb.mapviewer.annotation.services.annotators.*;
+import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -43,54 +31,45 @@ import lcsb.mapviewer.model.map.MiriamType;
@Service
public class ChEMBLParser extends DrugAnnotation implements IExternalService {
+ /**
+ * Prefix used in key for storing data by name.
+ */
+ static final String NAME_PREFIX = "drug:";
/**
* 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.
*/
@@ -122,30 +101,9 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
this.hgncAnnotator = hgncAnnotator;
}
- @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
@@ -244,7 +202,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* 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
@@ -272,7 +230,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Returns list of targets for given drug.
- *
+ *
* @param drugId
* identifier of a drug for which targets are looked
* @throws DrugSearchException
@@ -321,7 +279,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Parse xml node with references.
- *
+ *
* @param referenceNode
* node with references
* @return list of references obtained from xml node
@@ -396,10 +354,94 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
}
+ @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 = XmlParser.getXmlDocumentFromString(page);
+
+ Node response = XmlParser.getNode("response", document);
+ Node targets = XmlParser.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 = XmlParser.getNode("organism", node).getTextContent();
+ if (organismMatch(organismName, organisms)) {
+ Node chemblTargetIdNode = XmlParser.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;
+
+ }
+
+ @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;
+ }
+
/**
* 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">
@@ -432,7 +474,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Get targets for chembl children nodes.
- *
+ *
* @param drugId
* id of the parent drug
* @return list of drug targets for children molecules in chembl ontology
@@ -474,7 +516,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Parse xml node with synonyms.
- *
+ *
* @param synonymsNode
* xml node with synonyms
* @return list of synonyms obtained from the input xml
@@ -498,7 +540,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Returns information about drug by chembl drug identifier.
- *
+ *
* @param drugId
* {@link MiriamType#CHEMBL_COMPOUND chembl drug identifier}
* @return drug by chembl drug identifier
@@ -556,69 +598,6 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
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 = XmlParser.getXmlDocumentFromString(page);
-
- Node response = XmlParser.getNode("response", document);
- Node targets = XmlParser.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 = XmlParser.getNode("organism", node).getTextContent();
- if (organismMatch(organismName, organisms)) {
- Node chemblTargetIdNode = XmlParser.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.
*
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 3519a430ba..381c637811 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -1,33 +1,20 @@
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.*;
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.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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.cache.*;
+import lcsb.mapviewer.annotation.data.*;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -47,108 +34,89 @@ import lcsb.mapviewer.persist.dao.ProjectDao;
@Service
public class ChemicalParser extends CachableInterface implements IExternalService {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.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 = URL + "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 = URL + "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;
-
+ /**
+ * 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:";
+ /**
+ * Prefix used for caching elements with chemical identifier as a key.
+ */
+ static final String CHEMICAL_PREFIX = "chemical:";
+ /**
+ * 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 = URL + "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 = URL + "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;
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(ChemicalParser.class);
/**
* Object that allows to serialize {@link Chemical} elements into xml string and
* deserialize xml into {@link Chemical} objects.
@@ -367,6 +335,16 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
}
}
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
/**
* @param diseaseID
* the Mesh id of the disease.
@@ -669,16 +647,6 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
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<>();
@@ -687,7 +655,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
String cachedData = getCacheValue(cacheQuery);
List<String> result;
if (cachedData == null) {
-// result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
+ // result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
result = new ArrayList<>();
cachedData = StringUtils.join(result, "\n");
setCacheValue(cacheQuery, cachedData);
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 6c06b5320f..e1f6b6d39a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalSearchException.java
@@ -8,41 +8,41 @@ package lcsb.mapviewer.annotation.services;
*/
public class ChemicalSearchException extends Exception {
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public ChemicalSearchException(String string) {
- super(string);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public ChemicalSearchException(Exception e) {
- super(e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public ChemicalSearchException(String string) {
+ super(string);
+ }
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public ChemicalSearchException(String message, Exception e) {
- super(message, e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public ChemicalSearchException(Exception e) {
+ super(e);
+ }
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public ChemicalSearchException(String message, Exception e) {
+ super(message, e);
+ }
}
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 5cc8c49bbd..e05925aedc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
@@ -1,20 +1,14 @@
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 java.util.*;
import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.cache.*;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
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 f52c229c3e..b5332ce490 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugSearchException.java
@@ -8,41 +8,41 @@ package lcsb.mapviewer.annotation.services;
*/
public class DrugSearchException extends Exception {
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public DrugSearchException(String string) {
- super(string);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public DrugSearchException(Exception e) {
- super(e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public DrugSearchException(String string) {
+ super(string);
+ }
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public DrugSearchException(String message, Exception e) {
- super(message, e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public DrugSearchException(Exception e) {
+ super(e);
+ }
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public DrugSearchException(String message, Exception e) {
+ super(message, e);
+ }
}
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 b377b95434..51cab1bc64 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -3,11 +3,7 @@ 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.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -18,18 +14,12 @@ import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
-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.cache.*;
+import lcsb.mapviewer.annotation.data.*;
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;
+import lcsb.mapviewer.model.map.*;
/**
* Class used for parsing and accessing data from html interfaces of drugbank
@@ -42,63 +32,52 @@ import lcsb.mapviewer.model.map.MiriamType;
@Service
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}.
- */
- 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 = LogManager.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/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=bio_entities&query=";
-
/**
* Url that helps finding drug name for given target identifier.
*/
static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/bio_entities/";
-
+ /**
+ * Maximum available length of the pubmed identifiers.
+ */
+ private static final int MAX_PUBMED_IDENTIFIER_LENGTH = 9;
+ /**
+ * Pattern that extract information about drug name when accessing page about
+ * target.
+ */
+ private final Pattern drugNamePattern = Pattern.compile("(?<=<td><strong>)([\\s\\S]*?)(?=</strong></td>)");
+ /**
+ * Service used for annotation of proteins using {@link MiriamType#UNIPROT
+ * uniprot}.
+ */
+ private UniprotAnnotator uniprotAnnotator;
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(DrugbankHTMLParser.class);
/**
* Pattern used to get information about {@link Drug#bloodBrainBarrier blood
* brain barrier}.
@@ -120,30 +99,9 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
this.uniprotAnnotator = uniprotAnnotator;
}
- @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
@@ -161,7 +119,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* 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
@@ -178,7 +136,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* 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
@@ -204,7 +162,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* 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
@@ -235,7 +193,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* Returns list of drug synonyms from drugbank database.
- *
+ *
* @param page
* web page content with drug information
* @return list of drug synonyms
@@ -264,7 +222,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* 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}
@@ -298,7 +256,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* Returns targets parsed from page content.
- *
+ *
* @param page
* webpage content from which data are extracted
* @throws DrugSearchException
@@ -358,7 +316,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* Parse html info about target into {@link Target} structure.
- *
+ *
* @param htmlPage
* string with html content
* @return {@link Target} for given html content
@@ -422,7 +380,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* Finds information about drug in drugbank database.
- *
+ *
* @param name
* name of the dug that we are looking for
* @throws DrugSearchException
@@ -482,7 +440,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* Check if drug data mateches with the search name.
- *
+ *
* @param drug
* drug to be checked
* @param name
@@ -511,10 +469,10 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* 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) {
@@ -543,10 +501,10 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* 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) {
@@ -599,27 +557,6 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
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 target, Collection<MiriamData> organisms)
throws DrugSearchException {
@@ -664,6 +601,48 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
}
}
+ @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;
+ }
+
+ @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;
+ }
+
boolean isDrugContainTarget(MiriamData targetMiriamData, Drug drug) {
boolean targets = false;
for (Target target : drug.getTargets()) {
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 dd45fbfd58..f7bd01cacd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatus.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatus.java
@@ -9,83 +9,83 @@ package lcsb.mapviewer.annotation.services;
*/
public class ExternalServiceStatus {
- /**
- * Name of the service.
- */
- private String name;
+ /**
+ * Name of the service.
+ */
+ private String name;
- /**
- * Status of the external resource.
- */
- private ExternalServiceStatusType status;
+ /**
+ * Status of the external resource.
+ */
+ private ExternalServiceStatusType status;
- /**
- * Webpage associated with external resource.
- */
- private String page;
+ /**
+ * 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);
- }
+ /**
+ * 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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 2e3092188b..c3666cd684 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusType.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusType.java
@@ -7,59 +7,59 @@ package lcsb.mapviewer.annotation.services;
*
*/
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;
+ /**
+ * Service is ok and access method is ok.
+ */
+ OK("Ok", 0),
- /**
- * 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;
- }
+ /**
+ * Service is down (we don't know anything about access method).
+ */
+ DOWN("Not available", 1),
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
+ /**
+ * Service is up, but access method changed.
+ */
+ CHANGED("Specification changed", 2);
- /**
- * @return the level
- * @see #level
- */
- public int getLevel() {
- return level;
- }
+ /**
+ * 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 a6d859ef72..764897e279 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/IExternalService.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/IExternalService.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.annotation.services;
-
/**
* Interface that should be implemented by all classes that access external
* resources.
@@ -9,22 +8,21 @@ package lcsb.mapviewer.annotation.services;
*
*/
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();
+ /**
+ * 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/ImproperAnnotations.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
index 4337be731d..65b8f1b17a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
@@ -18,60 +18,60 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class ImproperAnnotations implements ProblematicAnnotation {
- /**
- * {@link BioEntity} improperly annotated.
- */
- private BioEntity bioEntity;
+ /**
+ * {@link BioEntity} improperly annotated.
+ */
+ private BioEntity bioEntity;
- /**
- * Wrong miriam data.
- */
- private List<MiriamData> wrongAnnotations = new ArrayList<>();
+ /**
+ * Wrong miriam data.
+ */
+ private List<MiriamData> wrongAnnotations = new ArrayList<>();
- /**
- * Constructor that initializes the data with {@link #bioEntity bioEntity} and
- * list of improper {@link MiriamData}.
- *
- * @param list
- * list of improper {@link MiriamData}
- * @param bioEntity
- * bioentity
- */
- public ImproperAnnotations(BioEntity bioEntity, List<MiriamData> list) {
- if (list.size() == 0) {
- throw new InvalidArgumentException("List of improper annotations cannot be null");
- }
- this.bioEntity = bioEntity;
- wrongAnnotations.addAll(list);
- }
+ /**
+ * Constructor that initializes the data with {@link #bioEntity bioEntity} and
+ * list of improper {@link MiriamData}.
+ *
+ * @param list
+ * list of improper {@link MiriamData}
+ * @param bioEntity
+ * bioentity
+ */
+ public ImproperAnnotations(BioEntity bioEntity, List<MiriamData> list) {
+ if (list.size() == 0) {
+ throw new InvalidArgumentException("List of improper annotations cannot be null");
+ }
+ this.bioEntity = bioEntity;
+ wrongAnnotations.addAll(list);
+ }
- /**
- * Constructor that initializes the data with {@link #bioEntity bio entity}
- * and improper {@link MiriamData}.
- *
- * @param miriamData
- * invalid {@link MiriamData}
- * @param bioEntity
- * annotated object
- */
- public ImproperAnnotations(BioEntity bioEntity, MiriamData miriamData) {
- this.bioEntity = bioEntity;
- wrongAnnotations.add(miriamData);
- }
+ /**
+ * Constructor that initializes the data with {@link #bioEntity bio entity} and
+ * improper {@link MiriamData}.
+ *
+ * @param miriamData
+ * invalid {@link MiriamData}
+ * @param bioEntity
+ * annotated object
+ */
+ public ImproperAnnotations(BioEntity bioEntity, MiriamData miriamData) {
+ this.bioEntity = bioEntity;
+ wrongAnnotations.add(miriamData);
+ }
- @Override
- public String getMessage() {
- StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
- result.append("contains invalid annotations: ");
- for (MiriamData miriamData : wrongAnnotations) {
- result.append(miriamData.getDataType().getCommonName() + "(" + miriamData.getResource() + "), ");
- }
- return result.toString();
- }
+ @Override
+ public String getMessage() {
+ StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
+ result.append("contains invalid annotations: ");
+ for (MiriamData miriamData : wrongAnnotations) {
+ result.append(miriamData.getDataType().getCommonName() + "(" + miriamData.getResource() + "), ");
+ }
+ return result.toString();
+ }
- @Override
- public String toString() {
- return getMessage();
- }
+ @Override
+ public String toString() {
+ return getMessage();
+ }
}
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 f178fc9cef..e94b209278 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
@@ -1,26 +1,18 @@
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 java.util.*;
import org.apache.commons.lang3.SerializationException;
import org.apache.http.HttpStatus;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
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.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.cache.*;
import lcsb.mapviewer.annotation.data.MeSH;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -36,21 +28,18 @@ import lcsb.mapviewer.model.map.MiriamType;
@Service
public class MeSHParser extends CachableInterface implements IExternalService {
+ /**
+ * Prefix used in the DB to identify the cache entry.
+ */
+ static final String MESH_PREFIX = "mesh:";
/**
* 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.
*/
@@ -99,6 +88,16 @@ public class MeSHParser extends CachableInterface implements IExternalService {
return result;
}
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
/**
* @param meshID
* miriam type id.
@@ -189,7 +188,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
/**
* Extracts name from gson object.
- *
+ *
* @param gsonObject
* gson to process
* @return name of {@link MeSH} entry
@@ -204,7 +203,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
/**
* Extracts Mesh id name from gson object.
- *
+ *
* @param gsonObject
* gson to process
* @return id of {@link MeSH} entry
@@ -219,7 +218,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
/**
* Extracts Mesh term description from gson object.
- *
+ *
* @param gsonObject
* gson to process
* @return description of {@link MeSH} entry
@@ -231,7 +230,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
/**
* Extracts list of synonyms from gson object.
- *
+ *
* @param gsonObject
* gson to process
* @return synonyms of {@link MeSH} entry
@@ -276,7 +275,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
/**
* Checks if the mesh identifier is valid.
- *
+ *
* @param meshId
* mesh id
* @return <code>true</code> if it's valid
@@ -290,16 +289,6 @@ public class MeSHParser extends CachableInterface implements IExternalService {
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<>();
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 166a177023..bb6dec3baa 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java
@@ -1,47 +1,22 @@
package lcsb.mapviewer.annotation.services;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
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 java.util.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.poi.poifs.filesystem.NotOLE2FileException;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.CellType;
-import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.*;
import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
-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.springframework.stereotype.Service;
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.cache.*;
+import lcsb.mapviewer.annotation.data.*;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -62,65 +37,53 @@ import lcsb.mapviewer.persist.dao.ProjectDao;
@Service
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;
-
+ /**
+ * 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:";
+ /**
+ * 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";
/**
* Size of the buffer when copying files.
*/
private static final int BUFFER_SIZE = 1024;
-
+ /**
+ * Cached file with static database about miriam (right now we parse it from
+ * excel file).
+ */
+ private ByteArrayOutputStream sourceInputStream;
/**
* Default class logger.
*/
@@ -157,9 +120,9 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
*/
@Autowired
public MiRNAParser(TaxonomyBackend taxonomyBackend,
- HgncAnnotator hgncAnnotator,
- BigFileCache bigFileCache,
- ProjectDao projectDao) {
+ HgncAnnotator hgncAnnotator,
+ BigFileCache bigFileCache,
+ ProjectDao projectDao) {
super(MiRNAParser.class);
miRnaSerializer = new XmlSerializer<>(MiRNA.class);
this.taxonomyBackend = taxonomyBackend;
@@ -268,7 +231,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
String filename = bigFileCache.getAbsolutePathForFile(URL_SOURCE_DATABASE);
this.sourceInputStream = downloadedFileToInputStream(filename);
- //if downloaded file is corrupted download it again
+ // if downloaded file is corrupted download it again
try {
POIFSFileSystem element = new POIFSFileSystem(new ByteArrayInputStream(sourceInputStream.toByteArray()));
element.close();
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 e63f663df4..5090f6bff0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNASearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNASearchException.java
@@ -8,40 +8,40 @@ package lcsb.mapviewer.annotation.services;
*/
public class MiRNASearchException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public MiRNASearchException(String string) {
- super(string);
- }
+ /**
+ * 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 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);
- }
+ /**
+ * 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 c4b3c8e7d4..86bcd1aa80 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
@@ -23,21 +23,19 @@ import lcsb.mapviewer.model.map.*;
*/
@Service
public final class MiriamConnector extends CachableInterface implements IExternalService {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.getLogger(MiriamConnector.class);
-
/**
* String used to distinguish cached data for links.
*/
static final String LINK_DB_PREFIX = "Link: ";
-
/**
* 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 = LogManager.getLogger(MiriamConnector.class);
/**
* Default class constructor. Prevent initialization.
@@ -69,9 +67,19 @@ public final class MiriamConnector extends CachableInterface implements IExterna
return result;
}
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
/**
* Returns url to the web page represented by {@link MiriamData} parameter.
- *
+ *
* @param miriamData
* miriam data
* @return url to resource pointed by miriam data
@@ -160,7 +168,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
/**
* 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#getCommonName()} and IDENTIFIER is resource
@@ -179,7 +187,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
/**
* Checks if {@link MiriamType} is valid.
- *
+ *
* @param type
* type to be checked
* @return <code>true</code> if {@link MiriamType} is valid, <code>false</code>
@@ -194,7 +202,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
/**
* Returns uri to miriam resource.
- *
+ *
* @param md
* {@link MiriamData} object for which uri should be returned
* @return uri to miriam resource
@@ -202,14 +210,4 @@ public final class MiriamConnector extends CachableInterface implements IExterna
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);
- }
}
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 1dd95d2302..6f62351bd4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
@@ -12,29 +12,29 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class MissingAnnotation implements ProblematicAnnotation {
- /**
- * BioEntity improperly annotated.
- */
- private BioEntity bioEntity;
+ /**
+ * 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;
- }
+ /**
+ * 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 getMessage() {
+ return new ElementUtils().getElementTag(bioEntity) + "misses annotations.";
+ }
- @Override
- public String toString() {
- return getMessage();
- }
+ @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 bc57929783..291b370178 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
@@ -1,13 +1,9 @@
package lcsb.mapviewer.annotation.services;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
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.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -19,46 +15,46 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
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();
- }
+ /**
+ * 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/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index f2c8889279..28e51f6e7e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -1,17 +1,10 @@
package lcsb.mapviewer.annotation.services;
-import java.util.ArrayList;
-import java.util.Collection;
-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.*;
import org.apache.commons.collections4.ListUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@@ -19,9 +12,7 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
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.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -52,17 +43,14 @@ public class ModelAnnotator {
* {@link #performAnnotations(Model, IProgressUpdater)} method.
*/
private static final double COPYING_RATIO = 0.2;
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- private MiriamConnector miriamConnector;
-
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(ModelAnnotator.class);
-
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ private MiriamConnector miriamConnector;
/**
* List of all avaliable {@link ElementAnnotator} objects.
*/
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 90e41d1cfe..b2404c82d6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java
@@ -8,10 +8,10 @@ package lcsb.mapviewer.annotation.services;
*/
public interface ProblematicAnnotation {
- /**
- * Returns error message.
- *
- * @return problem error message
- */
- String getMessage();
+ /**
+ * 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 e26017f9f9..60f0c7fc60 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -1,29 +1,21 @@
package lcsb.mapviewer.annotation.services;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathExpressionException;
-import javax.xml.xpath.XPathFactory;
+import javax.xml.xpath.*;
-import lcsb.mapviewer.common.XmlParser;
import org.apache.commons.lang3.SerializationException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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.cache.*;
import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -48,19 +40,15 @@ public class PubmedParser extends CachableInterface implements IExternalService
* 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 = "6.1";
-
static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
-
+ /**
+ * Length of {@link #PUBMED_PREFIX} string.
+ */
+ private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
/**
* Connector used for accessing data from miriam registry.
*/
@@ -77,6 +65,17 @@ public class PubmedParser extends CachableInterface implements IExternalService
*/
private XmlSerializer<Article> articleSerializer;
+ /**
+ * Constructor. Initializes structures used for transforming {@link Article}
+ * from/to xml.
+ */
+ @Autowired
+ public PubmedParser(MiriamConnector miriamConnector) {
+ super(PubmedParser.class);
+ articleSerializer = new XmlSerializer<>(Article.class);
+ this.miriamConnector = miriamConnector;
+ }
+
@Override
public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
Object result = null;
@@ -99,20 +98,19 @@ public class PubmedParser extends CachableInterface implements IExternalService
return result;
}
- /**
- * Constructor. Initializes structures used for transforming {@link Article}
- * from/to xml.
- */
- @Autowired
- public PubmedParser(MiriamConnector miriamConnector) {
- super(PubmedParser.class);
- articleSerializer = new XmlSerializer<>(Article.class);
- this.miriamConnector = miriamConnector;
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
}
/**
* Returns article data for given pubmed identifier.
- *
+ *
* @param id
* pubmed identifier
* @return article data
@@ -218,7 +216,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* This method return html \< a\ > tag with link for pubmed id (with some
* additional information).
- *
+ *
* @param id
* pubmed identifier
* @param withTextPrefix
@@ -245,7 +243,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* 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
@@ -259,7 +257,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* Get the summary of the article.
- *
+ *
* @param id
* pubmed identifier
* @return summary of the article.
@@ -304,7 +302,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* 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 database
@@ -334,7 +332,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* Get the summary of the article.
- *
+ *
* @param id
* pubmed identifier
* @return summary of the article.
@@ -380,14 +378,4 @@ public class PubmedParser extends CachableInterface implements IExternalService
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 ae2d8cf115..64acc6532c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
@@ -8,31 +8,31 @@ package lcsb.mapviewer.annotation.services;
*/
public class PubmedSearchException extends Exception {
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public PubmedSearchException(Exception e) {
- super(e);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public PubmedSearchException(String message, Exception e) {
- super(message, e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public PubmedSearchException(Exception e) {
+ super(e);
+ }
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public PubmedSearchException(String message, Exception e) {
+ super(message, e);
+ }
}
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 dffc032f82..e694c4c101 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
@@ -5,16 +5,14 @@ import java.net.URLEncoder;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Service;
-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.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import org.springframework.stereotype.Service;
/**
* This class is a backend to Taxonomy.
@@ -41,6 +39,17 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
* by taxonomy id.
*/
static final String TAXONOMY_NAME_CACHE_PREFIX = "TAXONOMY_NAME_BY_ID: ";
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(TaxonomyBackend.class);
+
+ /**
+ * Default constructor.
+ */
+ public TaxonomyBackend() {
+ super(TaxonomyBackend.class);
+ }
@Override
public String refreshCacheQuery(Object query) throws SourceNotAvailable {
@@ -71,6 +80,16 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
return result;
}
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
/**
* Returns {@link MiriamData} representing taxonomy identified by name.
*
@@ -85,8 +104,8 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
return null;
}
if (term.equalsIgnoreCase("Humans")) {
- term="Human";
- }
+ term = "Human";
+ }
String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
if (res != null) {
if (res.equals("null")) {
@@ -134,18 +153,6 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
}
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.getLogger(TaxonomyBackend.class);
-
- /**
- * Default constructor.
- */
- public TaxonomyBackend() {
- super(TaxonomyBackend.class);
- }
-
@Override
public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.TAXONOMY.getCommonName(),
@@ -207,14 +214,4 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
}
}
- @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 ce90c04e61..02ec2c2031 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomySearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomySearchException.java
@@ -9,22 +9,22 @@ package lcsb.mapviewer.annotation.services;
*/
public class TaxonomySearchException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 501f7a4807..eee6f59029 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/WrongResponseCodeIOException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/WrongResponseCodeIOException.java
@@ -11,33 +11,33 @@ import java.io.IOException;
*
*/
public class WrongResponseCodeIOException extends IOException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- /**
- * Response code returned by the super {@link IOException}.
- */
- private int responseCode;
+ /**
+ *
+ */
+ 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;
- }
+ /**
+ * 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;
- }
+ /**
+ * @return the responseCode
+ * @see #responseCode
+ */
+ public int getResponseCode() {
+ return responseCode;
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
index 5c123b67d7..864f922507 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
@@ -1,28 +1,20 @@
package lcsb.mapviewer.annotation.services.annotators;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements a backend to Brenda enzyme database.
@@ -121,16 +113,6 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
return MiriamType.BRENDA.getDbHomepage();
}
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
@Override
public List<AnnotatorInputParameter> getAvailableInputParameters() {
return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
@@ -147,4 +129,14 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
return new MiriamData(MiriamType.UNIPROT, "P12345");
}
+ @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/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index c4ace692b7..7974a2a06b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
@@ -1,34 +1,24 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.annotation.services.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements a backend to CAZy.
@@ -105,9 +95,35 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
return cazyIds.size() > 0;
}
+ @Override
+ public String getCommonName() {
+ return MiriamType.CAZY.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.CAZY.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
+ new AnnotatorInputParameter(MiriamType.UNIPROT));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(new AnnotatorOutputParameter(MiriamType.CAZY));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "Q9SG95");
+ }
+
/**
* Returns URL to TAIR page about TAIR entry.
- *
+ *
* @param uniProtId
* UniProt identifier
* @return URL to CAZY UniProt accession search result page
@@ -119,7 +135,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
/**
* Parse CAZy webpage to find information about {@link MiriamType#CAZY} and
* returns them.
- *
+ *
* @param pageContent
* CAZy info page
* @return CAZy family identifier found on the page
@@ -135,7 +151,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
/**
* Transform UniProt identifier to CAZy identifier.
- *
+ *
* @param UniProt
* {@link MiriamData} with UniProt identifier
* @return {@link MiriamData} with CAZy identifier
@@ -169,16 +185,6 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
}
}
- @Override
- public String getCommonName() {
- return MiriamType.CAZY.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.CAZY.getDbHomepage();
- }
-
@Override
protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader();
@@ -189,20 +195,4 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
super.setWebPageDownloader(webPageDownloader);
}
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
- new AnnotatorInputParameter(MiriamType.UNIPROT));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(new AnnotatorOutputParameter(MiriamType.CAZY));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.UNIPROT, "Q9SG95");
- }
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
index 355a9828d7..359333328a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
@@ -1,42 +1,22 @@
package lcsb.mapviewer.annotation.services.annotators;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Queue;
-import java.util.Set;
+import java.util.*;
import javax.xml.ws.WebServiceException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.cache.*;
import lcsb.mapviewer.annotation.data.Chebi;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.*;
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.model.map.*;
import lcsb.mapviewer.model.map.species.Chemical;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.user.annotator.*;
import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
-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.LiteEntity;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntityList;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.SearchCategory;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.StarsCategory;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.*;
/**
* This is a class that implements a backend to publicly available chebi API.
@@ -47,17 +27,15 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.StarsCategory;
@Service
public class ChebiAnnotator extends ElementAnnotator implements IExternalService {
+ /**
+ * Prefix used for entries identified by chebi id.
+ */
+ public static final String ID_PREFIX = "id: ";
/**
* What is the maximum number of results that should be retrieved from chebi
* API.
*/
static final int MAX_SEARCH_RESULTS_FROM_CHEBI_API = 50;
-
- /**
- * Prefix used for entries identified by chebi id.
- */
- public static final String ID_PREFIX = "id: ";
-
/**
* Prefix used for ontology list for single chebi id.
*/
@@ -77,6 +55,28 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
* Length of the prefix used for entries identified by name.
*/
private static final int NAME_PREFIX_LENGTH = NAME_PREFIX.length();
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(ChebiAnnotator.class);
+ /**
+ * Client to chebi API.
+ */
+ private ChebiWebServiceClient client = null;
+ /**
+ * Object that allows to serialize {@link Chebi} elements into xml string and
+ * deserialize xml into {@link Chebi} objects.
+ */
+ private XmlSerializer<Chebi> chebiSerializer;
+
+ /**
+ * Default constructor. Initializes structures used for transforming
+ * {@link Chebi} from/to xml.
+ */
+ public ChebiAnnotator() {
+ super(ChebiAnnotator.class, new Class[] { Chemical.class }, true);
+ chebiSerializer = new XmlSerializer<>(Chebi.class);
+ }
@Override
public String refreshCacheQuery(Object query) throws SourceNotAvailable {
@@ -109,31 +109,6 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
return result;
}
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger(ChebiAnnotator.class);
-
- /**
- * Client to chebi API.
- */
- private ChebiWebServiceClient client = null;
-
- /**
- * Object that allows to serialize {@link Chebi} elements into xml string and
- * deserialize xml into {@link Chebi} objects.
- */
- private XmlSerializer<Chebi> chebiSerializer;
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Chebi} from/to xml.
- */
- public ChebiAnnotator() {
- super(ChebiAnnotator.class, new Class[] { Chemical.class }, true);
- chebiSerializer = new XmlSerializer<>(Chebi.class);
- }
-
/**
* Returns {@link MiriamData} for given chebi name.
*
@@ -435,21 +410,13 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
return client;
}
- @Override
- public boolean annotateElement(BioEntityProxy element, String name, AnnotatorData parameters)
- throws AnnotatorException {
- try {
- MiriamData chebi = getChebiForChebiName(name);
- if (chebi != null) {
- element.addMiriamData(chebi);
- return annotateElement(element, chebi, parameters);
- } else {
- logger.warn(element.getElementTag() + "Chemical name cannot be found in chebi: " + name);
- return false;
- }
- } catch (Exception e) {
- throw new AnnotatorException("Problem with getting information about chebi", e);
- }
+ /**
+ * @param client
+ * the client to set
+ * @see #client
+ */
+ void setClient(ChebiWebServiceClient client) {
+ this.client = client;
}
@Override
@@ -473,6 +440,23 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
}
}
+ @Override
+ public boolean annotateElement(BioEntityProxy element, String name, AnnotatorData parameters)
+ throws AnnotatorException {
+ try {
+ MiriamData chebi = getChebiForChebiName(name);
+ if (chebi != null) {
+ element.addMiriamData(chebi);
+ return annotateElement(element, chebi, parameters);
+ } else {
+ logger.warn(element.getElementTag() + "Chemical name cannot be found in chebi: " + name);
+ return false;
+ }
+ } catch (Exception e) {
+ throw new AnnotatorException("Problem with getting information about chebi", e);
+ }
+ }
+
@Override
public String getCommonName() {
return MiriamType.CHEBI.getCommonName();
@@ -483,15 +467,6 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
return MiriamType.CHEBI.getDbHomepage();
}
- /**
- * @param client
- * the client to set
- * @see #client
- */
- void setClient(ChebiWebServiceClient client) {
- this.client = client;
- }
-
@Override
public List<AnnotatorInputParameter> getAvailableInputParameters() {
return Arrays.asList(new AnnotatorInputParameter(MiriamType.CHEBI),
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index 68874cf702..a41c28d60f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -1,33 +1,21 @@
package lcsb.mapviewer.annotation.services.annotators;
-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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Chemical;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
-import lcsb.mapviewer.model.user.annotator.AnnotatorConfigParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.user.annotator.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -50,128 +38,400 @@ public abstract class ElementAnnotator extends CachableInterface {
* annotator}.
*/
private final List<Class<? extends BioEntity>> validClasses = new ArrayList<>();
-
+ /**
+ * Parameters which this annotator can be provided. Should be set in
+ * constructor.
+ */
+ protected List<AnnotatorParamDefinition> paramsDefs = new ArrayList<>();
/**
* Should be this annotator used as a default annotator.
*/
private boolean isDefault = false;
/**
- * Parameters which this annotator can be provided. Should be set in
- * constructor.
+ * Default constructor.
+ *
+ * @param validClasses
+ * list of classes for which this annotator is valid
+ * @param isDefault
+ * {@link #isDefault}
+ * @param clazz
+ * type that defines this interface
*/
- protected List<AnnotatorParamDefinition> paramsDefs = new ArrayList<>();
-
- class BioEntityProxy {
- private BioEntity originalBioEntity;
- private AnnotatorData parameters;
-
- public BioEntityProxy(BioEntity bioEntity, AnnotatorData parameters) {
- originalBioEntity = bioEntity;
- this.parameters = parameters;
-
- }
-
- public void addMiriamData(Collection<MiriamData> annotations) {
- for (MiriamData miriamData : annotations) {
- addMiriamData(miriamData);
+ @SuppressWarnings("unchecked")
+ public ElementAnnotator(Class<? extends CachableInterface> clazz, Class<?>[] validClasses, boolean isDefault) {
+ super(clazz);
+ for (Class<?> validClass : validClasses) {
+ if (BioEntity.class.isAssignableFrom(validClass)) {
+ addValidClass((Class<? extends BioEntity>) validClass);
+ } else {
+ throw new InvalidArgumentException("Cannot pass class of type: " + validClass + ". Only classes extending "
+ + BioEntity.class + " are accepted.");
}
}
+ this.isDefault = isDefault;
+ }
- public void addMiriamData(MiriamData miriamData) {
- if (!contains(miriamData)) {
- miriamData.setAnnotator(ElementAnnotator.this.getClass());
- originalBioEntity.addMiriamData(miriamData);
+ /**
+ * Annotate element.
+ *
+ * @param element
+ * object to be annotated
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating not related to data
+ */
+ public void annotateElement(BioEntity element) throws AnnotatorException {
+ annotateElement(element, createAnnotatorData());
+ }
+
+ /**
+ * Annotate element using parameters.
+ *
+ * @param bioEntity
+ * object to be annotated
+ * @param parameters
+ * list of parameters passed to the annotator which is expected to be
+ * in the same order as its {@link this#parameterDefs}
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating not related to data
+ */
+ public final void annotateElement(BioEntity bioEntity, AnnotatorData parameters) throws AnnotatorException {
+ if (isAnnotatable(bioEntity)) {
+ BioEntityProxy proxy = new BioEntityProxy(bioEntity, parameters);
+ List<AnnotatorInputParameter> inputParameters = parameters.getInputParameters();
+ if (inputParameters.size() == 0) {
+ inputParameters = getAvailableInputParameters();
+ }
+ if (parameters.getOutputParameters().size() == 0) {
+ parameters.addAnnotatorParameters(this.getAvailableOuputProperties());
+ }
+ List<Set<Object>> inputs = getInputsParameters(bioEntity, inputParameters);
+ for (Set<Object> inputSet : inputs) {
+ boolean annotated = false;
+ for (Object object : inputSet) {
+ if (object instanceof MiriamData) {
+ if (annotateElement(proxy, (MiriamData) object, parameters)) {
+ annotated = true;
+ }
+ } else if (object instanceof String) {
+ if (annotateElement(proxy, (String) object, parameters)) {
+ annotated = true;
+ }
+ } else {
+ throw new NotImplementedException();
+ }
+ }
+ if (annotated) {
+ break;
+ }
}
}
+ }
- public boolean contains(MiriamData identifier) {
- MiriamData copy = new MiriamData(identifier);
- copy.setAnnotator(null);
- MiriamData copy2 = new MiriamData(identifier);
- copy.setAnnotator(ElementAnnotator.this.getClass());
- return originalBioEntity.getMiriamData().contains(copy) || originalBioEntity.getMiriamData().contains(copy2);
- }
+ public abstract boolean annotateElement(BioEntityProxy element, MiriamData identifier,
+ AnnotatorData parameters)
+ throws AnnotatorException;
- public String getElementTag() {
- return new ElementUtils().getElementTag(originalBioEntity, ElementAnnotator.this);
- }
+public boolean annotateElement(BioEntityProxy element, String name, AnnotatorData parameters)
+ throws AnnotatorException {
+ throw new NotImplementedException();
+ }
- public boolean isElement() {
- return originalBioEntity instanceof Element;
- }
+ /**
+ * Returns a list of all classes that can be annotated using this annotator.
+ *
+ * @return a list of all classes that can be annotated using this annotator
+ */
+ public List<Class<? extends BioEntity>> getValidClasses() {
+ return validClasses;
+ };
- public void addUniprot(UniprotRecord ur) {
- if (originalBioEntity instanceof Species) {
- Species species = ((Species) originalBioEntity);
- species.getUniprots().add(ur);
- ur.setSpecies(species);
- } else {
- logger.warn("Cannot add uniprot object to: " + originalBioEntity.getClass().getSimpleName());
+ /**
+ * Returns <code>true</code> if this annotator can annotate the object given in
+ * the parameter.
+ *
+ * @param object
+ * object to be tested if can be annotated
+ * @return <code>true</code> if object can be annotated by this annotator,
+ * <code>false</code> otherwise
+ */
+ public boolean isAnnotatable(BioEntity object) {
+ Class<?> clazz = object.getClass();
+ for (Class<?> validClazz : getValidClasses()) {
+ if (validClazz.isAssignableFrom(clazz)) {
+ return true;
}
}
+ return false;
+ }
- public boolean isReaction() {
- return originalBioEntity instanceof Reaction;
- }
+ /**
+ * Adds a class to list of classes that can be annotated by the annotator.
+ *
+ * @param clazz
+ * class to add
+ */
+ private void addValidClass(Class<? extends BioEntity> clazz) {
+ validClasses.add(clazz);
+ }
- /**
- * Sets synonyms to the element.
- *
- * @param synonyms
- * new synonyms list
- */
- public void setSynonyms(Collection<String> synonyms) {
- if (canAssignStringSet(synonyms, originalBioEntity.getSynonyms(), BioEntityField.SYNONYMS)) {
- List<String> sortedSynonyms = new ArrayList<>(synonyms);
- Collections.sort(sortedSynonyms);
+ /**
+ * Returns the common name that should be presented to user.
+ *
+ * @return the common name
+ */
+ public abstract String getCommonName();
- originalBioEntity.setSynonyms(sortedSynonyms);
- }
- }
+ /**
+ * Returns url to the external resource used for annotation.
+ *
+ * @return url
+ */
+ public abstract String getUrl();
- private boolean canAssignStringSet(Collection<String> newCollection, Collection<String> oldCollection,
- BioEntityField field) {
- if (!parameters.hasOutputField(field)) {
- return false;
- }
- if (oldCollection == null || oldCollection.size() == 0) {
- return true;
- } else if (newCollection == null || newCollection.size() == 0) {
- return false;
- } else {
- StringSetComparator stringSetComparator = new StringSetComparator();
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
+ /**
+ * Provides description of the extraction process for {@link ElementAnnotator}
+ * to be used in the front end.
+ *
+ * @return the description
+ */
+ public String getDescription() {
+ return "";
+ }
- set1.addAll(newCollection);
- set2.addAll(oldCollection);
+ /**
+ * Returns list with definitions of the parameters available for this annotator.
+ *
+ * @return the parameters {@link AnnotatorParamDefinition} list
+ */
+ public Collection<AnnotatorParamDefinition> getParametersDefinitions() {
+ return paramsDefs;
+ }
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.warn(getElementTag() + field.getCommonName() + " don't match: \"" + set1 + "\", \"" + set2 + "\"");
- return false;
- }
+ /**
+ * Sets definitions of parameters for given annotator.
+ *
+ * @param paramDefs
+ * definitions to be set
+ */
+ public void setParametersDefinitions(List<AnnotatorParamDefinition> paramDefs) {
+ this.paramsDefs = paramDefs;
+ }
+
+ /**
+ * Returns <code>true</code> if this annotator can annotate the object of given
+ * class type.
+ *
+ * @param clazz
+ * class to be tested if can be annotated
+ * @return <code>true</code> if class can be annotated by this annotator,
+ * <code>false</code> otherwise
+ */
+ public boolean isAnnotatable(Class<?> clazz) {
+ for (Class<?> clazz2 : validClasses) {
+ if (clazz2.isAssignableFrom(clazz)) {
return true;
}
}
+ return false;
+ }
- /**
- * Sets symbol value to the element.
- *
- * @param symbol
- * new symbol
- */
- public void setSymbol(String symbol) {
- if (canAssign(symbol, originalBioEntity.getSymbol(), BioEntityField.SYMBOL)) {
- originalBioEntity.setSymbol(symbol);
- }
- }
+ /**
+ *
+ * @return {@link #isDefault}
+ */
+ public boolean isDefault() {
+ return isDefault;
+ }
- public void setName(String nam) {
- if (canAssign(nam, originalBioEntity.getName(), BioEntityField.NAME)) {
- originalBioEntity.setName(nam);
- }
- }
+ /**
+ * Adds parameter definition to the definitions of parameters for given
+ * annotator
+ *
+ * @param paramDef
+ * parameter definition to be added
+ */
+ public void addParameterDefinition(AnnotatorParamDefinition paramDef) {
+ this.paramsDefs.add(paramDef);
+ }
+
+ /**
+ * Returns list of available {@link AnnotatorInputParameter}. Order indicates
+ * the default order that should be considered when extracting identifier.
+ *
+ * @return list of available {@link AnnotatorInputParameter} for class
+ */
+ public abstract List<AnnotatorInputParameter> getAvailableInputParameters();
+
+ /**
+ * Returns list of available {@link AnnotatorOutputParameter}. Order indicates
+ * the default order that should be considered when extracting identifier.
+ *
+ * @return list of available {@link AnnotatorOutputParameter} for class
+ */
+ public abstract List<AnnotatorOutputParameter> getAvailableOuputProperties();
+
+ public List<Set<Object>> getInputsParameters(BioEntity bioEntity, List<AnnotatorInputParameter> inputParameters) {
+ List<Set<Object>> result = new ArrayList<>();
+ for (AnnotatorInputParameter parameter : inputParameters) {
+ Set<Object> inputs = new HashSet<>();
+ if (parameter.getField() != null && parameter.getIdentifierType() == null) {
+ inputs.add(BioEntityField.getFieldValueForBioEntity(bioEntity, parameter.getField()));
+ } else if (parameter.getField() != null && parameter.getIdentifierType() != null) {
+ String value = BioEntityField.getFieldValueForBioEntity(bioEntity, parameter.getField());
+ if (value != null && !value.isEmpty()) {
+ inputs.add(new MiriamData(parameter.getIdentifierType(),
+ BioEntityField.getFieldValueForBioEntity(bioEntity, parameter.getField())));
+ }
+ } else if (parameter.getField() == null && parameter.getIdentifierType() != null) {
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(parameter.getIdentifierType())) {
+ inputs.add(md);
+ }
+ }
+ } else {
+ throw new InvalidArgumentException("Input parameter must have either field or identifierType defined");
+ }
+ result.add(inputs);
+ }
+
+ return result;
+ }
+
+ public abstract MiriamData getExampleValidAnnotation();
+
+ public List<AnnotatorConfigParameter> getExampleValidParameters() {
+ return new ArrayList<>();
+ }
+
+ /**
+ * Creates default {@link AnnotatorData} for this {@link ElementAnnotator}.
+ *
+ * @return
+ */
+ public AnnotatorData createAnnotatorData() {
+ AnnotatorData result = new AnnotatorData(this.getClass());
+ // by default use everything as input
+ result.addAnnotatorParameters(getAvailableInputParameters());
+ // and provide all available output
+ result.addAnnotatorParameters(getAvailableOuputProperties());
+ // and provide all available output
+ for (AnnotatorParamDefinition type : getParametersDefinitions()) {
+ result.addAnnotatorParameter(type, "");
+ }
+ return result;
+ }
+
+ class BioEntityProxy {
+ private BioEntity originalBioEntity;
+ private AnnotatorData parameters;
+
+ public BioEntityProxy(BioEntity bioEntity, AnnotatorData parameters) {
+ originalBioEntity = bioEntity;
+ this.parameters = parameters;
+
+ }
+
+ public void addMiriamData(Collection<MiriamData> annotations) {
+ for (MiriamData miriamData : annotations) {
+ addMiriamData(miriamData);
+ }
+ }
+
+ public void addMiriamData(MiriamData miriamData) {
+ if (!contains(miriamData)) {
+ miriamData.setAnnotator(ElementAnnotator.this.getClass());
+ originalBioEntity.addMiriamData(miriamData);
+ }
+ }
+
+ public boolean contains(MiriamData identifier) {
+ MiriamData copy = new MiriamData(identifier);
+ copy.setAnnotator(null);
+ MiriamData copy2 = new MiriamData(identifier);
+ copy.setAnnotator(ElementAnnotator.this.getClass());
+ return originalBioEntity.getMiriamData().contains(copy) || originalBioEntity.getMiriamData().contains(copy2);
+ }
+
+ public String getElementTag() {
+ return new ElementUtils().getElementTag(originalBioEntity, ElementAnnotator.this);
+ }
+
+ public boolean isElement() {
+ return originalBioEntity instanceof Element;
+ }
+
+ public void addUniprot(UniprotRecord ur) {
+ if (originalBioEntity instanceof Species) {
+ Species species = ((Species) originalBioEntity);
+ species.getUniprots().add(ur);
+ ur.setSpecies(species);
+ } else {
+ logger.warn("Cannot add uniprot object to: " + originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public boolean isReaction() {
+ return originalBioEntity instanceof Reaction;
+ }
+
+ /**
+ * Sets synonyms to the element.
+ *
+ * @param synonyms
+ * new synonyms list
+ */
+ public void setSynonyms(Collection<String> synonyms) {
+ if (canAssignStringSet(synonyms, originalBioEntity.getSynonyms(), BioEntityField.SYNONYMS)) {
+ List<String> sortedSynonyms = new ArrayList<>(synonyms);
+ Collections.sort(sortedSynonyms);
+
+ originalBioEntity.setSynonyms(sortedSynonyms);
+ }
+ }
+
+ private boolean canAssignStringSet(Collection<String> newCollection, Collection<String> oldCollection,
+ BioEntityField field) {
+ if (!parameters.hasOutputField(field)) {
+ return false;
+ }
+ if (oldCollection == null || oldCollection.size() == 0) {
+ return true;
+ } else if (newCollection == null || newCollection.size() == 0) {
+ return false;
+ } else {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ set1.addAll(newCollection);
+ set2.addAll(oldCollection);
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.warn(getElementTag() + field.getCommonName() + " don't match: \"" + set1 + "\", \"" + set2 + "\"");
+ return false;
+ }
+ return true;
+ }
+ }
+
+ /**
+ * Sets symbol value to the element.
+ *
+ * @param symbol
+ * new symbol
+ */
+ public void setSymbol(String symbol) {
+ if (canAssign(symbol, originalBioEntity.getSymbol(), BioEntityField.SYMBOL)) {
+ originalBioEntity.setSymbol(symbol);
+ }
+ }
+
+ public void setName(String nam) {
+ if (canAssign(nam, originalBioEntity.getName(), BioEntityField.NAME)) {
+ originalBioEntity.setName(nam);
+ }
+ }
private boolean canAssign(String newValue, String oldValue, BioEntityField field) {
if (!parameters.hasOutputField(field)) {
@@ -220,7 +480,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets name to the element.
- *
+ *
* @param name
* new name
*/
@@ -238,7 +498,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Adds description to {@link BioEntity#getNotes()}.
- *
+ *
* @param description
* value to set
*/
@@ -269,7 +529,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link CellDesignerChemical#inChI}.
- *
+ *
* @param inchi
* value to set
*/
@@ -286,7 +546,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link CellDesignerChemical#inChIKey}.
- *
+ *
* @param inchiKey
* value to set
*/
@@ -304,7 +564,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link CellDesignerChemical#smiles}.
- *
+ *
* @param smile
* value to set
*/
@@ -326,7 +586,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link Species#charge}.
- *
+ *
* @param charge
* value to set
*/
@@ -344,7 +604,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link Reaction#subsystem}.
- *
+ *
* @param subsystem
* value to set
*/
@@ -362,7 +622,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link BioEntity#getFormula()}.
- *
+ *
* @param formula
* value to set
*/
@@ -374,7 +634,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link BioEntity#getAbbreviation()}.
- *
+ *
* @param value
* value to set
*/
@@ -386,7 +646,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Sets {@link Reaction#getMechanicalConfidenceScore()}.
- *
+ *
* @param value
* value to set
*/
@@ -481,278 +741,4 @@ public abstract class ElementAnnotator extends CachableInterface {
}
- /**
- * Default constructor.
- *
- * @param validClasses
- * list of classes for which this annotator is valid
- * @param isDefault
- * {@link #isDefault}
- * @param clazz
- * type that defines this interface
- */
- @SuppressWarnings("unchecked")
- public ElementAnnotator(Class<? extends CachableInterface> clazz, Class<?>[] validClasses, boolean isDefault) {
- super(clazz);
- for (Class<?> validClass : validClasses) {
- if (BioEntity.class.isAssignableFrom(validClass)) {
- addValidClass((Class<? extends BioEntity>) validClass);
- } else {
- throw new InvalidArgumentException("Cannot pass class of type: " + validClass + ". Only classes extending "
- + BioEntity.class + " are accepted.");
- }
- }
- this.isDefault = isDefault;
- }
-
- /**
- * Annotate element.
- *
- * @param element
- * object to be annotated
- * @throws AnnotatorException
- * thrown when there is a problem with annotating not related to data
- */
- public void annotateElement(BioEntity element) throws AnnotatorException {
- annotateElement(element, createAnnotatorData());
- }
-
- /**
- * Annotate element using parameters.
- *
- * @param bioEntity
- * object to be annotated
- * @param parameters
- * list of parameters passed to the annotator which is expected to be
- * in the same order as its {@link this#parameterDefs}
- * @throws AnnotatorException
- * thrown when there is a problem with annotating not related to data
- */
- public final void annotateElement(BioEntity bioEntity, AnnotatorData parameters) throws AnnotatorException {
- if (isAnnotatable(bioEntity)) {
- BioEntityProxy proxy = new BioEntityProxy(bioEntity, parameters);
- List<AnnotatorInputParameter> inputParameters = parameters.getInputParameters();
- if (inputParameters.size() == 0) {
- inputParameters = getAvailableInputParameters();
- }
- if (parameters.getOutputParameters().size() == 0) {
- parameters.addAnnotatorParameters(this.getAvailableOuputProperties());
- }
- List<Set<Object>> inputs = getInputsParameters(bioEntity, inputParameters);
- for (Set<Object> inputSet : inputs) {
- boolean annotated = false;
- for (Object object : inputSet) {
- if (object instanceof MiriamData) {
- if (annotateElement(proxy, (MiriamData) object, parameters)) {
- annotated = true;
- }
- } else if (object instanceof String) {
- if (annotateElement(proxy, (String) object, parameters)) {
- annotated = true;
- }
- } else {
- throw new NotImplementedException();
- }
- }
- if (annotated) {
- break;
- }
- }
- }
- }
-
- public abstract boolean annotateElement(BioEntityProxy element, MiriamData identifier,
- AnnotatorData parameters)
- throws AnnotatorException;
-
- public boolean annotateElement(BioEntityProxy element, String name, AnnotatorData parameters)
- throws AnnotatorException {
- throw new NotImplementedException();
- };
-
- /**
- * Returns a list of all classes that can be annotated using this annotator.
- *
- * @return a list of all classes that can be annotated using this annotator
- */
- public List<Class<? extends BioEntity>> getValidClasses() {
- return validClasses;
- }
-
- /**
- * Returns <code>true</code> if this annotator can annotate the object given in
- * the parameter.
- *
- * @param object
- * object to be tested if can be annotated
- * @return <code>true</code> if object can be annotated by this annotator,
- * <code>false</code> otherwise
- */
- public boolean isAnnotatable(BioEntity object) {
- Class<?> clazz = object.getClass();
- for (Class<?> validClazz : getValidClasses()) {
- if (validClazz.isAssignableFrom(clazz)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Adds a class to list of classes that can be annotated by the annotator.
- *
- * @param clazz
- * class to add
- */
- private void addValidClass(Class<? extends BioEntity> clazz) {
- validClasses.add(clazz);
- }
-
- /**
- * Returns the common name that should be presented to user.
- *
- * @return the common name
- */
- public abstract String getCommonName();
-
- /**
- * Returns url to the external resource used for annotation.
- *
- * @return url
- */
- public abstract String getUrl();
-
- /**
- * Provides description of the extraction process for {@link ElementAnnotator}
- * to be used in the front end.
- *
- * @return the description
- */
- public String getDescription() {
- return "";
- }
-
- /**
- * Returns list with definitions of the parameters available for this annotator.
- *
- * @return the parameters {@link AnnotatorParamDefinition} list
- */
- public Collection<AnnotatorParamDefinition> getParametersDefinitions() {
- return paramsDefs;
- }
-
- /**
- * Returns <code>true</code> if this annotator can annotate the object of given
- * class type.
- *
- * @param clazz
- * class to be tested if can be annotated
- * @return <code>true</code> if class can be annotated by this annotator,
- * <code>false</code> otherwise
- */
- public boolean isAnnotatable(Class<?> clazz) {
- for (Class<?> clazz2 : validClasses) {
- if (clazz2.isAssignableFrom(clazz)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- *
- * @return {@link #isDefault}
- */
- public boolean isDefault() {
- return isDefault;
- }
-
- /**
- * Sets definitions of parameters for given annotator.
- *
- * @param paramDefs
- * definitions to be set
- */
- public void setParametersDefinitions(List<AnnotatorParamDefinition> paramDefs) {
- this.paramsDefs = paramDefs;
- }
-
- /**
- * Adds parameter definition to the definitions of parameters for given
- * annotator
- *
- * @param paramDef
- * parameter definition to be added
- */
- public void addParameterDefinition(AnnotatorParamDefinition paramDef) {
- this.paramsDefs.add(paramDef);
- }
-
- /**
- * Returns list of available {@link AnnotatorInputParameter}. Order indicates
- * the default order that should be considered when extracting identifier.
- *
- * @return list of available {@link AnnotatorInputParameter} for class
- */
- public abstract List<AnnotatorInputParameter> getAvailableInputParameters();
-
- /**
- * Returns list of available {@link AnnotatorOutputParameter}. Order indicates
- * the default order that should be considered when extracting identifier.
- *
- * @return list of available {@link AnnotatorOutputParameter} for class
- */
- public abstract List<AnnotatorOutputParameter> getAvailableOuputProperties();
-
- public List<Set<Object>> getInputsParameters(BioEntity bioEntity, List<AnnotatorInputParameter> inputParameters) {
- List<Set<Object>> result = new ArrayList<>();
- for (AnnotatorInputParameter parameter : inputParameters) {
- Set<Object> inputs = new HashSet<>();
- if (parameter.getField() != null && parameter.getIdentifierType() == null) {
- inputs.add(BioEntityField.getFieldValueForBioEntity(bioEntity, parameter.getField()));
- } else if (parameter.getField() != null && parameter.getIdentifierType() != null) {
- String value = BioEntityField.getFieldValueForBioEntity(bioEntity, parameter.getField());
- if (value != null && !value.isEmpty()) {
- inputs.add(new MiriamData(parameter.getIdentifierType(),
- BioEntityField.getFieldValueForBioEntity(bioEntity, parameter.getField())));
- }
- } else if (parameter.getField() == null && parameter.getIdentifierType() != null) {
- for (MiriamData md : bioEntity.getMiriamData()) {
- if (md.getDataType().equals(parameter.getIdentifierType())) {
- inputs.add(md);
- }
- }
- } else {
- throw new InvalidArgumentException("Input parameter must have either field or identifierType defined");
- }
- result.add(inputs);
- }
-
- return result;
- }
-
- public abstract MiriamData getExampleValidAnnotation();
-
- public List<AnnotatorConfigParameter> getExampleValidParameters() {
- return new ArrayList<>();
- }
-
- /**
- * Creates default {@link AnnotatorData} for this {@link ElementAnnotator}.
- *
- * @return
- */
- public AnnotatorData createAnnotatorData() {
- AnnotatorData result = new AnnotatorData(this.getClass());
- // by default use everything as input
- result.addAnnotatorParameters(getAvailableInputParameters());
- // and provide all available output
- result.addAnnotatorParameters(getAvailableOuputProperties());
- // and provide all available output
- for (AnnotatorParamDefinition type : getParametersDefinitions()) {
- result.addAnnotatorParameter(type, "");
- }
- return result;
- }
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index d38d2e2807..6f01d674e5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -1,35 +1,24 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.annotation.services.*;
+import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This class is responsible for connecting to
@@ -43,10 +32,10 @@ import lcsb.mapviewer.model.user.annotator.BioEntityField;
@Service
public class EnsemblAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Version of the rest API that is supported by this annotator.
- */
- static final String SUPPORTED_VERSION = "11.0";
+ /**
+ * Version of the rest API that is supported by this annotator.
+ */
+ static final String SUPPORTED_VERSION = "11.0";
/**
* Url address of ensembl restful service.
@@ -63,6 +52,10 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
* Url used for retrieving version of the restful API.
*/
private static final String REST_SERVICE_VERSION_URL = "https://rest.ensembl.org/info/rest?content-type=text/xml";
+ /**
+ * Standard class logger.
+ */
+ private final Logger logger = LogManager.getLogger(EnsemblAnnotator.class);
/**
* Default constructor.
@@ -71,21 +64,6 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
super(EnsemblAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
}
- /**
- * Standard class logger.
- */
- private final Logger logger = LogManager.getLogger(EnsemblAnnotator.class);
-
- @Override
- public String getCommonName() {
- return MiriamType.ENSEMBL.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.ENSEMBL.getDbHomepage();
- }
-
@Override
public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
@@ -222,13 +200,13 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
+ public String getCommonName() {
+ return MiriamType.ENSEMBL.getCommonName();
}
@Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
+ public String getUrl() {
+ return MiriamType.ENSEMBL.getDbHomepage();
}
@Override
@@ -251,4 +229,14 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
return new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
}
+ @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/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 6ae860d282..9fceeda97a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -2,42 +2,24 @@ package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
import java.net.HttpURLConnection;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import org.apache.commons.text.StringEscapeUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
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.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.cache.*;
import lcsb.mapviewer.annotation.data.EntrezData;
-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.annotation.services.*;
import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.exception.*;
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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This class is responsible for connecting to
@@ -51,17 +33,19 @@ import lcsb.mapviewer.model.user.annotator.BioEntityField;
@Service
public class EntrezAnnotator extends ElementAnnotator implements IExternalService {
+ /**
+ * Prefix used in cache key to indicate that cached value contains
+ * {@link EntrezData} object for a given entrez id.
+ */
+ static final String ENTREZ_DATA_PREFIX = "ENTREZ_DATA:";
/**
* Address of Entrez API that should be used for retrieving data.
*/
private static final String REST_API_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&rettype=xml&id=";
-
/**
- * Prefix used in cache key to indicate that cached value contains
- * {@link EntrezData} object for a given entrez id.
+ * Standard class logger.
*/
- static final String ENTREZ_DATA_PREFIX = "ENTREZ_DATA:";
-
+ private final Logger logger = LogManager.getLogger(EntrezAnnotator.class);
/**
* Object that allows to serialize {@link EntrezData} elements into xml string
* and deserialize xml into {@link EntrezData} objects.
@@ -102,19 +86,14 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
return result;
}
- /**
- * Standard class logger.
- */
- private final Logger logger = LogManager.getLogger(EntrezAnnotator.class);
-
@Override
- public String getCommonName() {
- return MiriamType.ENTREZ.getCommonName();
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
}
@Override
- public String getUrl() {
- return MiriamType.ENTREZ.getDbHomepage();
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
}
@Override
@@ -164,6 +143,36 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
}
}
+ @Override
+ public String getCommonName() {
+ return MiriamType.ENTREZ.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.ENTREZ.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.ENTREZ));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(new AnnotatorOutputParameter(MiriamType.ENSEMBL),
+ new AnnotatorOutputParameter(MiriamType.HGNC),
+ new AnnotatorOutputParameter(BioEntityField.FULL_NAME),
+ new AnnotatorOutputParameter(BioEntityField.DESCRIPTION),
+ new AnnotatorOutputParameter(BioEntityField.SYMBOL),
+ new AnnotatorOutputParameter(BioEntityField.SYNONYMS));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.ENTREZ, "6621");
+ }
+
/**
* Returns preprocessed data for entrez identifier.
*
@@ -264,7 +273,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
Node node = list.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equals("Gene-ref_syn_E")) {
- synonyms.add(StringEscapeUtils.unescapeHtml4(node.getTextContent()));
+ synonyms.add(StringEscapeUtils.unescapeHtml4(node.getTextContent()));
}
}
}
@@ -298,16 +307,6 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
return result;
}
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
/**
* @return the entrezSerializer
* @see #entrezSerializer
@@ -325,24 +324,4 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
this.entrezSerializer = entrezSerializer;
}
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.ENTREZ));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(new AnnotatorOutputParameter(MiriamType.ENSEMBL),
- new AnnotatorOutputParameter(MiriamType.HGNC),
- new AnnotatorOutputParameter(BioEntityField.FULL_NAME),
- new AnnotatorOutputParameter(BioEntityField.DESCRIPTION),
- new AnnotatorOutputParameter(BioEntityField.SYMBOL),
- new AnnotatorOutputParameter(BioEntityField.SYNONYMS));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.ENTREZ, "6621");
- }
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index 53669eecb7..78077388e8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -1,38 +1,25 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import com.google.gson.Gson;
-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.cache.*;
import lcsb.mapviewer.annotation.data.Go;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
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.*;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This class is a backend to Gene Ontology API.
@@ -99,6 +86,16 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
return result;
}
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
@Override
public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotatorData parameters)
throws AnnotatorException {
@@ -120,6 +117,33 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
}
+ @Override
+ public String getCommonName() {
+ return MiriamType.GO.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.GO.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.GO));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(
+ new AnnotatorOutputParameter(BioEntityField.FULL_NAME),
+ new AnnotatorOutputParameter(BioEntityField.DESCRIPTION));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.GO, "GO:0046902");
+ }
+
/**
* Returns go entry from the Gene Ontology database for the goTerm (identifier).
*
@@ -210,41 +234,4 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
this.mc = mc;
}
- @Override
- public String getCommonName() {
- return MiriamType.GO.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.GO.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.GO));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(
- new AnnotatorOutputParameter(BioEntityField.FULL_NAME),
- new AnnotatorOutputParameter(BioEntityField.DESCRIPTION));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.GO, "GO:0046902");
- }
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index 36aa9fb4a2..e7af4a9ce6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -1,36 +1,23 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.MiriamConnector;
-import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.annotation.services.*;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.*;
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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This class is responsible for connecting to
@@ -48,7 +35,10 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
* Address of HGNC API that should be used for retrieving data.
*/
private static final String REST_API_URL = "https://rest.genenames.org/fetch/";
-
+ /**
+ * Standard class logger.
+ */
+ private final Logger logger = LogManager.getLogger(HgncAnnotator.class);
private MiriamConnector miriamConnector;
/**
@@ -59,21 +49,6 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
this.miriamConnector = miriamConnector;
}
- /**
- * Standard class logger.
- */
- private final Logger logger = LogManager.getLogger(HgncAnnotator.class);
-
- @Override
- public String getCommonName() {
- return MiriamType.HGNC.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.HGNC.getDbHomepage();
- }
-
@Override
public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
@@ -205,6 +180,43 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
}
+ @Override
+ public String getCommonName() {
+ return MiriamType.HGNC.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.HGNC.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.HGNC_SYMBOL),
+ new AnnotatorInputParameter(MiriamType.HGNC),
+ new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.HGNC_SYMBOL));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(
+ new AnnotatorOutputParameter(MiriamType.ENSEMBL),
+ new AnnotatorOutputParameter(MiriamType.ENTREZ),
+ new AnnotatorOutputParameter(MiriamType.HGNC),
+ new AnnotatorOutputParameter(MiriamType.HGNC_SYMBOL),
+ new AnnotatorOutputParameter(MiriamType.REFSEQ),
+ new AnnotatorOutputParameter(MiriamType.UNIPROT),
+ new AnnotatorOutputParameter(BioEntityField.SYMBOL),
+ new AnnotatorOutputParameter(BioEntityField.SYNONYMS),
+ new AnnotatorOutputParameter(BioEntityField.NAME),
+ new AnnotatorOutputParameter(BioEntityField.FULL_NAME));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ }
+
/**
* Creates query url for given {@link MiriamType#HGNC} identifier.
*
@@ -425,31 +437,4 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
super.setWebPageDownloader(webPageDownloader);
}
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.HGNC_SYMBOL),
- new AnnotatorInputParameter(MiriamType.HGNC),
- new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.HGNC_SYMBOL));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(
- new AnnotatorOutputParameter(MiriamType.ENSEMBL),
- new AnnotatorOutputParameter(MiriamType.ENTREZ),
- new AnnotatorOutputParameter(MiriamType.HGNC),
- new AnnotatorOutputParameter(MiriamType.HGNC_SYMBOL),
- new AnnotatorOutputParameter(MiriamType.REFSEQ),
- new AnnotatorOutputParameter(MiriamType.UNIPROT),
- new AnnotatorOutputParameter(BioEntityField.SYMBOL),
- new AnnotatorOutputParameter(BioEntityField.SYNONYMS),
- new AnnotatorOutputParameter(BioEntityField.NAME),
- new AnnotatorOutputParameter(BioEntityField.FULL_NAME));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- }
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
index 3d53b59497..813d56f3a0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
@@ -1,36 +1,23 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.annotation.services.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.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.*;
import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
-import lcsb.mapviewer.model.user.annotator.AnnotatorConfigParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements KEGG annotator which extract from KEGG PUBMED
@@ -153,17 +140,56 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
} catch (IOException exception) {
throw new AnnotatorException(exception);
} catch (UniprotSearchException e) {
- logger.warn(e, e);
- return false;
+ logger.warn(e, e);
+ return false;
}
}
object.addMiriamData(annotations);
return annotations.size() > 0;
}
+ @Override
+ public String getCommonName() {
+ return "KEGG";
+ }
+
+ @Override
+ public String getUrl() {
+ return "http://www.genome.jp/kegg/";
+ }
+
+ @Override
+ public String getDescription() {
+ return "Annotations extracted from KEGG ENZYME Database based on species EC numbers. "
+ + "Annotation include relevant publications and homologous genes for given EC numbers.";
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
+ new AnnotatorInputParameter(MiriamType.UNIPROT),
+ new AnnotatorInputParameter(MiriamType.EC));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(new AnnotatorOutputParameter(MiriamType.PUBMED),
+ new AnnotatorOutputParameter(MiriamType.TAIR_LOCUS));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.EC, "3.1.2.14");
+ }
+
+ @Override
+ public List<AnnotatorConfigParameter> getExampleValidParameters() {
+ return Arrays.asList(new AnnotatorConfigParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "ATH"));
+ }
+
/**
* Returns url to KEGG restful API about enzyme classification.
- *
+ *
* @param ecId
* enzyme classification
* @return url to KEGG restful API about given EC
@@ -175,7 +201,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
/**
* Parse KEGG webpage to find information about {@link MiriamType#PUBMED}s and
* returns them.
- *
+ *
* @param pageContent
* Kegg page
* @param params
@@ -184,7 +210,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
* organisms names. If the value has not been set by the user, null
* will be passed.
* @return {@link MiriamType#PUBMED}s found on the page
- * @throws UniprotSearchException
+ * @throws UniprotSearchException
*/
private Collection<MiriamData> parseKegg(String pageContent, AnnotatorData params) throws UniprotSearchException {
@@ -207,11 +233,11 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
if (m.find()) {
String[] tairLocusNames = m.group(1).trim().split(" ");
for (String tairLocusName : tairLocusNames) {
- tairLocusName = tairLocusName.split("\\(")[0]; // some codes are in the form AT1G08510(FATB)
- MiriamData md = uniprotAnnotator.uniprotTairLocusNameToId(tairLocusName);
- if (!md.equals(new MiriamData())){
- result.add(md);
- }
+ tairLocusName = tairLocusName.split("\\(")[0]; // some codes are in the form AT1G08510(FATB)
+ MiriamData md = uniprotAnnotator.uniprotTairLocusNameToId(tairLocusName);
+ if (!md.equals(new MiriamData())) {
+ result.add(md);
+ }
}
}
}
@@ -221,22 +247,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
return result;
}
- @Override
- public String getCommonName() {
- return "KEGG";
- }
-
- @Override
- public String getUrl() {
- return "http://www.genome.jp/kegg/";
- }
-
- @Override
- public String getDescription() {
- return "Annotations extracted from KEGG ENZYME Database based on species EC numbers. "
- + "Annotation include relevant publications and homologous genes for given EC numbers.";
- }
-
@Override
protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader();
@@ -246,27 +256,4 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
super.setWebPageDownloader(webPageDownloader);
}
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
- new AnnotatorInputParameter(MiriamType.UNIPROT),
- new AnnotatorInputParameter(MiriamType.EC));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(new AnnotatorOutputParameter(MiriamType.PUBMED),
- new AnnotatorOutputParameter(MiriamType.TAIR_LOCUS));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.EC, "3.1.2.14");
- }
-
- @Override
- public List<AnnotatorConfigParameter> getExampleValidParameters() {
- return Arrays.asList(new AnnotatorConfigParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "ATH"));
- }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index 65b1a8a5ba..96d96d4d32 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -1,15 +1,10 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@@ -18,23 +13,14 @@ import com.google.gson.reflect.TypeToken;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.annotation.services.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-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.model.map.*;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.Structure;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements a backend to the EBI's PDB SIFTS REST API
@@ -59,6 +45,24 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
super(PdbAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
}
+ /**
+ * Tests if given input string is a valid JSON document.
+ *
+ * @param json
+ * Input document as a string.
+ * @return True or false dependent on whether the input string is a valid JSON
+ * document
+ */
+ public static boolean isJson(String json) {
+ Gson gson = new Gson();
+ try {
+ gson.fromJson(json, Object.class);
+ return true;
+ } catch (com.google.gson.JsonSyntaxException ex) {
+ return false;
+ }
+ }
+
@Override
public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
@@ -139,9 +143,34 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
}
}
+ @Override
+ public String getCommonName() {
+ return MiriamType.PDB.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.PDB.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.UNIPROT));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(new AnnotatorOutputParameter(MiriamType.PDB));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "P29373");
+ }
+
/**
* Returns url to JSON with best mapping PDB entries given the UniProt entry.
- *
+ *
* @param uniprotId
* uniprot identifier
* @return url with best mapping PDB entries to the UniProt entry
@@ -153,7 +182,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
/**
* Parse UniProt-to-PDB mapping JSON file. {@link MiriamType#PDB} and returns
* them.
- *
+ *
* @param pageContentJson
* JSON file with the UniProt to PDB mapping
* @return set of PDB identifiers found on the webpage
@@ -178,27 +207,9 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
return result;
}
- /**
- * Tests if given input string is a valid JSON document.
- *
- * @param json
- * Input document as a string.
- * @return True or false dependent on whether the input string is a valid JSON
- * document
- */
- public static boolean isJson(String json) {
- Gson gson = new Gson();
- try {
- gson.fromJson(json, Object.class);
- return true;
- } catch (com.google.gson.JsonSyntaxException ex) {
- return false;
- }
- }
-
/**
* Transform UniProt identifier into PDB IDs.
- *
+ *
* @param uniprot
* {@link MiriamData} with UniProt identifier
* @return JSON String with mapping. thrown when there is a problem with
@@ -219,16 +230,6 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
return isJson(json) ? processMappingData(json) : new ArrayList<>();
}
- @Override
- public String getCommonName() {
- return MiriamType.PDB.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.PDB.getDbHomepage();
- }
-
@Override
protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader();
@@ -239,19 +240,4 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
super.setWebPageDownloader(webPageDownloader);
}
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.UNIPROT));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(new AnnotatorOutputParameter(MiriamType.PDB));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.UNIPROT, "P29373");
- }
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 4bd99f0f05..e2335ab292 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -1,25 +1,18 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
import java.util.Map.Entry;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
-import com.google.gson.JsonArray;
-import com.google.gson.JsonElement;
-import com.google.gson.JsonObject;
-import com.google.gson.JsonParser;
+import com.google.gson.*;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.*;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -27,10 +20,7 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements a backend to RECON database.
@@ -317,45 +307,6 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
}
}
- public MiriamData createKeggMiriam(BioEntityProxy element, String value) {
- MiriamData md = null;
- if (value.startsWith("C")) {
- md = new MiriamData(MiriamType.KEGG_COMPOUND, value);
- } else if (value.startsWith("R")) {
- md = new MiriamData(MiriamType.KEGG_REACTION, value);
- } else if (value.startsWith("K")) {
- md = new MiriamData(MiriamType.KEGG_ORTHOLOGY, value);
- } else {
- logger.warn(element.getElementTag()
- + "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
- }
- return md;
- }
-
- private JsonObject getBestMatchForAbbreviation(String id, JsonArray asJsonArray) {
- String match = null;
- JsonObject result = null;
- for (JsonElement element : asJsonArray) {
- if (((JsonObject) element).get("abbreviation") != null) {
- String objAbreviation = ((JsonObject) element).get("abbreviation").getAsString();
- if (match == null) {
- match = objAbreviation;
- result = (JsonObject) element;
- } else if (match.length() > objAbreviation.length()) {
- match = objAbreviation;
- result = (JsonObject) element;
- } else if (id.equalsIgnoreCase(objAbreviation)) {
- match = objAbreviation;
- result = (JsonObject) element;
- }
- } else if (match == null) {
- logger.warn("No abbreviation found for element: " + element);
- result = (JsonObject) element;
- }
- }
- return result;
- }
-
@Override
public String getCommonName() {
return "Recon annotator";
@@ -366,16 +317,6 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
return "https://www.vmh.life/";
}
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
@Override
public List<AnnotatorInputParameter> getAvailableInputParameters() {
return Arrays.asList(new AnnotatorInputParameter(BioEntityField.ABBREVIATION, MiriamType.VMH_METABOLITE),
@@ -420,4 +361,53 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
return null;
}
+ public MiriamData createKeggMiriam(BioEntityProxy element, String value) {
+ MiriamData md = null;
+ if (value.startsWith("C")) {
+ md = new MiriamData(MiriamType.KEGG_COMPOUND, value);
+ } else if (value.startsWith("R")) {
+ md = new MiriamData(MiriamType.KEGG_REACTION, value);
+ } else if (value.startsWith("K")) {
+ md = new MiriamData(MiriamType.KEGG_ORTHOLOGY, value);
+ } else {
+ logger.warn(element.getElementTag()
+ + "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
+ }
+ return md;
+ }
+
+ private JsonObject getBestMatchForAbbreviation(String id, JsonArray asJsonArray) {
+ String match = null;
+ JsonObject result = null;
+ for (JsonElement element : asJsonArray) {
+ if (((JsonObject) element).get("abbreviation") != null) {
+ String objAbreviation = ((JsonObject) element).get("abbreviation").getAsString();
+ if (match == null) {
+ match = objAbreviation;
+ result = (JsonObject) element;
+ } else if (match.length() > objAbreviation.length()) {
+ match = objAbreviation;
+ result = (JsonObject) element;
+ } else if (id.equalsIgnoreCase(objAbreviation)) {
+ match = objAbreviation;
+ result = (JsonObject) element;
+ }
+ } else if (match == null) {
+ logger.warn("No abbreviation found for element: " + element);
+ result = (JsonObject) element;
+ }
+ }
+ return result;
+ }
+
+ @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/StitchAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
index 553b202ce2..b2239ef737 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.annotation.services.annotators;
import java.util.Arrays;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -14,9 +15,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements STITCH annotation which is derived from
@@ -100,16 +99,6 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
return MiriamType.STITCH.getDbHomepage();
}
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
@Override
public List<AnnotatorInputParameter> getAvailableInputParameters() {
return Arrays.asList(new AnnotatorInputParameter(MiriamType.CHEBI));
@@ -125,4 +114,14 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
return new MiriamData(MiriamType.CHEBI, "CHEBI:35697");
}
+ @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/StringAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
index f32e7904ef..32511bc1db 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.annotation.services.annotators;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@@ -13,12 +11,8 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements a mapping to STRING database.
@@ -31,13 +25,11 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
/**
* Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
- * TAIR}.
- * Note that STRING annotation process will annotate only
- * records which have a TAIR ID assigned by a human annotator.
- * Otherwise, it would generate UniProt miriam records also for
- * TAIR IDs generated from, e.g., KEGG annotator, i.e. for homologues
- * and these UniProt IDs would be indistinguishable from the
- * UniProt IDs describing the molecule.
+ * TAIR}. Note that STRING annotation process will annotate only records which
+ * have a TAIR ID assigned by a human annotator. Otherwise, it would generate
+ * UniProt miriam records also for TAIR IDs generated from, e.g., KEGG
+ * annotator, i.e. for homologues and these UniProt IDs would be
+ * indistinguishable from the UniProt IDs describing the molecule.
*/
private TairAnnotator tairAnnotator;
@@ -60,9 +52,9 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
throws AnnotatorException {
List<MiriamData> mdUniprots = new ArrayList<>();
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- if (identifier.getAnnotator() == null) {
- mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
- }
+ if (identifier.getAnnotator() == null) {
+ mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
+ }
} else if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
mdUniprots.add(identifier);
} else {
@@ -80,27 +72,6 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
return stringIds.size() > 0;
}
- /**
- * Transform UniProt {@link MiriamData} data to STRING {@link MiriamData}.
- *
- * @param UniProt
- * {@link MiriamData} with UniProt identifier
- * @return {@link MiriamData} with STRING identifier
- * @throws AnnotatorException
- * thrown when there is a problem with accessing external database
- */
- public MiriamData uniprotToString(MiriamData uniprot) throws AnnotatorException {
- if (uniprot == null) {
- return null;
- }
-
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
-
- return new MiriamData(MiriamType.STRING, uniprot.getResource());
- }
-
@Override
public String getCommonName() {
return MiriamType.STRING.getCommonName();
@@ -126,4 +97,25 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
public MiriamData getExampleValidAnnotation() {
return new MiriamData(MiriamType.UNIPROT, "P53350");
}
+
+ /**
+ * Transform UniProt {@link MiriamData} data to STRING {@link MiriamData}.
+ *
+ * @param UniProt
+ * {@link MiriamData} with UniProt identifier
+ * @return {@link MiriamData} with STRING identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing external database
+ */
+ public MiriamData uniprotToString(MiriamData uniprot) throws AnnotatorException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ return new MiriamData(MiriamType.STRING, uniprot.getResource());
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index cf28f3f734..13c12430f8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -1,41 +1,31 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.annotation.services.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
- * This is a class that implements a backend to TAIR.
- * Note that TAIR annotation process will annotate only
- * records which have a TAIR ID assigned by a human annotator.
- * Otherwise, it would generate UniProt miriam records also for
- * TAIR IDs generated from, e.g., KEGG annotator, i.e. for homologues
- * and these UniProt IDs would be indistinguishable from the
- * UniProt IDs describing the molecule.
+ * This is a class that implements a backend to TAIR. Note that TAIR annotation
+ * process will annotate only records which have a TAIR ID assigned by a human
+ * annotator. Otherwise, it would generate UniProt miriam records also for TAIR
+ * IDs generated from, e.g., KEGG annotator, i.e. for homologues and these
+ * UniProt IDs would be indistinguishable from the UniProt IDs describing the
+ * molecule.
*
*
* @author David Hoksza
@@ -50,18 +40,17 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
private static Logger logger = LogManager.getLogger(TairAnnotator.class);
/**
- * Pattern used for getting Tair Locus ID symbol from UniProt result page.
+ * Default constructor.
*/
- private Pattern getUniprotIdParsePattern(String tairId) {
- return Pattern.compile("(\\w*)\\tlocus:" + tairId);
+ public TairAnnotator() {
+ super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
}
-
/**
- * Default constructor.
+ * Pattern used for getting Tair Locus ID symbol from UniProt result page.
*/
- public TairAnnotator() {
- super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ private Pattern getUniprotIdParsePattern(String tairId) {
+ return Pattern.compile("(\\w*)\\tlocus:" + tairId);
}
@Override
@@ -92,12 +81,13 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotatorData parameters)
throws AnnotatorException {
- if (identifier.getAnnotator() != null) {
- return false;
- }
+ if (identifier.getAnnotator() != null) {
+ return false;
+ }
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- //UniProt are only obained from TAIR's which were provided by the annotator (otherwise we would get
- //also UniProt IDs for, e.g., homologous genes' TAIR IDs obtained from KEGG
+ // UniProt are only obained from TAIR's which were provided by the annotator
+ // (otherwise we would get
+ // also UniProt IDs for, e.g., homologous genes' TAIR IDs obtained from KEGG
Collection<MiriamData> collection = tairToUniprot(identifier);
if (collection.size() > 0) {
object.addMiriamData(collection);
@@ -111,24 +101,51 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
}
+ @Override
+ public String getCommonName() {
+ return "TAIR";
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.TAIR_LOCUS.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(new AnnotatorOutputParameter(MiriamType.UNIPROT));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.TAIR_LOCUS, "2200950");
+ }
+
/**
* Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR
* entry.
- *
+ *
* @param tairId
* TAIR identifier
* @return URL to UniProt result page with the TAIR mapping
*/
private String getUniProtUrl(String tairId) {
- return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+" + tairId + "&format=tab&columns=id,database(tair)";
-// return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair+"+tairId+"%29&format=list&columns=id";
+ return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+" + tairId
+ + "&format=tab&columns=id,database(tair)";
+ // return
+ // "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair+"+tairId+"%29&format=list&columns=id";
}
/**
* Parse UniProt result page which contains list of Uniprot ids mapped to
* submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT} and
* returns it.
- *
+ *
* @param pageContent
* uniprot REST API result page
* @return uniprot identifier found on the page
@@ -136,22 +153,22 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
private Collection<MiriamData> parseUniprotUniprot(String pageContent, String tairId) {
Collection<MiriamData> result = new HashSet<MiriamData>();
if (!pageContent.isEmpty()) {
- //the query returns a list of possible matches which needs to be pruned
- Matcher m = getUniprotIdParsePattern(tairId).matcher(pageContent);
- if (m.find()) {
- result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
- }
+ // the query returns a list of possible matches which needs to be pruned
+ Matcher m = getUniprotIdParsePattern(tairId).matcher(pageContent);
+ if (m.find()) {
+ result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
+ }
}
return result;
}
/**
* Transform TAIR identifier into uniprot identifier.
- *
+ *
* Used to use the TAIR record page, but that tends to change and moreover TAIR
* limits number of accesses from an address. So now the transformation queries
* directly UniProt from which the mapping can be obtained as well.
- *
+ *
* @param tair
* {@link MiriamData} with TAIR identifier
* @return {@link MiriamData} with UniProt identifier
@@ -179,16 +196,6 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
}
- @Override
- public String getCommonName() {
- return "TAIR";
- }
-
- @Override
- public String getUrl() {
- return MiriamType.TAIR_LOCUS.getDbHomepage();
- }
-
@Override
protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader();
@@ -199,19 +206,4 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
super.setWebPageDownloader(webPageDownloader);
}
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(new AnnotatorOutputParameter(MiriamType.UNIPROT));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.TAIR_LOCUS, "2200950");
- }
-
}
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 58aa9b9366..ff87b55ac5 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
@@ -1,34 +1,23 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
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.annotation.services.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.user.annotator.*;
/**
* This is a class that implements a backend to uniprot restfull API.
@@ -59,7 +48,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
*/
private Pattern uniprotToEC = Pattern
.compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
-
+
/**
* Pattern used for getting Tair Locus ID symbol from UniProt result page.
*/
@@ -132,9 +121,38 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
}
}
+ @Override
+ public String getCommonName() {
+ return MiriamType.UNIPROT.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.UNIPROT.getDbHomepage();
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.UNIPROT),
+ new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.UNIPROT));
+ }
+
+ @Override
+ public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
+ return Arrays.asList(new AnnotatorOutputParameter(MiriamType.HGNC_SYMBOL),
+ new AnnotatorOutputParameter(MiriamType.UNIPROT),
+ new AnnotatorOutputParameter(MiriamType.EC),
+ new AnnotatorOutputParameter(MiriamType.ENTREZ));
+ }
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "Q5S007");
+ }
+
/**
* Returns url to uniprot restfull API about uniprot entry.
- *
+ *
* @param uniprotId
* uniprot identifier
* @return url to uniprot restfull API about uniprot entry
@@ -142,23 +160,24 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
private String getUniprotUrl(String uniprotId) {
return "https://www.uniprot.org/uniprot/" + uniprotId + ".txt";
}
-
+
/**
* Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR
* entry.
- *
+ *
* @param tairId
* TAIR identifier
* @return URL to UniProt result page with the TAIR mapping
*/
private String getUniProtTairLocus2IdUrl(String tairLocusName) {
- return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair+" + tairLocusName + "%29&format=tab&columns=id,database(tair)";
+ return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair+" + tairLocusName
+ + "%29&format=tab&columns=id,database(tair)";
}
/**
* 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
@@ -175,7 +194,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
/**
* 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
@@ -192,7 +211,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
/**
* 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
@@ -208,7 +227,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
/**
* Transform uniprot identifier into hgnc name.
- *
+ *
* @param uniprot
* {@link MiriamData} with uniprot identifier
* @return {@link MiriamData} with hgnc name
@@ -241,7 +260,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
/**
* Transform uniprot identifier into EC identifiers.
- *
+ *
* @param uniprot
* {@link MiriamData} with uniprot identifier
* @return ArrayList of {@link MiriamData} with EC codes
@@ -268,12 +287,12 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
}
}
-
+
/**
- * Transform TAIR Locus name into TAIR Locus identifier.
- * UniProt is used for this task because TAIR i) does not have
- * an API and ii) restricts the number of accesses.
- *
+ * Transform TAIR Locus name into TAIR Locus identifier. UniProt is used for
+ * this task because TAIR i) does not have an API and ii) restricts the number
+ * of accesses.
+ *
* @param tairLocus
* String with the TAIR Locus name.
* @return {@link MiriamData} with TAIR Locus ID
@@ -281,29 +300,19 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
* thrown when there is a problem with accessing external database
*/
public MiriamData uniprotTairLocusNameToId(String tairLocus) throws UniprotSearchException {
- String accessUrl = getUniProtTairLocus2IdUrl(tairLocus);
- try {
- String pageContent = getWebPageContent(accessUrl);
- Matcher m = uniprotTairLocusToId.matcher(pageContent);
- if (m.find()) {
- return new MiriamData(MiriamType.TAIR_LOCUS, m.group(1));
- } else {
- logger.warn("No TAIR ID found for locus: " + tairLocus);
- return new MiriamData();
- }
- } 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();
+ String accessUrl = getUniProtTairLocus2IdUrl(tairLocus);
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Matcher m = uniprotTairLocusToId.matcher(pageContent);
+ if (m.find()) {
+ return new MiriamData(MiriamType.TAIR_LOCUS, m.group(1));
+ } else {
+ logger.warn("No TAIR ID found for locus: " + tairLocus);
+ return new MiriamData();
+ }
+ } catch (IOException e) {
+ throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
+ }
}
@Override
@@ -315,23 +324,4 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
super.setWebPageDownloader(webPageDownloader);
}
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.UNIPROT),
- new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.UNIPROT));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- return Arrays.asList(new AnnotatorOutputParameter(MiriamType.HGNC_SYMBOL),
- new AnnotatorOutputParameter(MiriamType.UNIPROT),
- new AnnotatorOutputParameter(MiriamType.EC),
- new AnnotatorOutputParameter(MiriamType.ENTREZ));
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- return new MiriamData(MiriamType.UNIPROT, "Q5S007");
- }
}
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 25b66c7be1..1d74ee6fff 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
@@ -6,4 +6,3 @@
*
*/
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 f46251b46d..281a9d4bb5 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
@@ -2,15 +2,10 @@ 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.logging.log4j.*;
+import java.util.concurrent.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.cache.BigFileCache;
@@ -32,365 +27,369 @@ import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeGeneMappingDao;
*/
public abstract class AbstractReferenceGenomeConnector extends CachableInterface implements ReferenceGenomeConnector {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.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}
- * @throws ReferenceGenomeConnectorException
- */
- private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) throws ReferenceGenomeConnectorException {
- 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.setName(name);
- mapping.setSourceUrl(url);
- referenceGenome.addReferenceGenomeGeneMapping(mapping);
- getReferenceGenomeDao().update(referenceGenome);
- getReferenceGenomeDao().commit();
- getReferenceGenomeDao().flush();
- 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 thread
- 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);
- }
- }
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.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;
+ }
+ });
+ }
+
+ @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);
+ }
+ }
+
+ @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 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;
+ }
+
+ /**
+ * @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);
+ }
+ }
+ }
+
+ /**
+ * 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}
+ * @throws ReferenceGenomeConnectorException
+ */
+ private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url,
+ IProgressUpdater updater) throws ReferenceGenomeConnectorException {
+ 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.setName(name);
+ mapping.setSourceUrl(url);
+ referenceGenome.addReferenceGenomeGeneMapping(mapping);
+ getReferenceGenomeDao().update(referenceGenome);
+ getReferenceGenomeDao().commit();
+ getReferenceGenomeDao().flush();
+ 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 thread
+ 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();
+ }
+ }
+
+ }
}
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 0a11c19a4b..9a358e7326 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
@@ -9,40 +9,40 @@ package lcsb.mapviewer.annotation.services.genome;
*/
public class FileNotAvailableException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public FileNotAvailableException(String message) {
- super(message);
- }
+ /**
+ * 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 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);
- }
+ /**
+ * 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 0eeb5101a6..5bf0554bb1 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
@@ -17,142 +17,142 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
*/
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 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 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;
+ /**
+ * 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
+ * @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 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;
+ /**
+ * 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;
+ /**
+ * 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;
+ /**
+ * 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
- */
+ /**
+ * 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;
+ 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 58253f8b61..84cc441980 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
@@ -10,41 +10,41 @@ package lcsb.mapviewer.annotation.services.genome;
*/
public class ReferenceGenomeConnectorException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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
+ * @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 message
+ * message associated with exception
+ */
+ public ReferenceGenomeConnectorException(String message) {
+ super(message);
+ }
- /**
- * Default constructor.
- *
- * @param cause
- * original exception
- */
- public ReferenceGenomeConnectorException(Exception cause) {
- super(cause);
- }
+ /**
+ * 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 e58e376800..a8f94a0215 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
@@ -2,23 +2,17 @@ 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.*;
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.logging.log4j.*;
+import org.apache.commons.net.ftp.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -29,10 +23,7 @@ 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 org.springframework.stereotype.Service;
+import lcsb.mapviewer.model.map.layout.*;
/**
* Implementeation of reference genome connector accessing
@@ -44,17 +35,15 @@ import org.springframework.stereotype.Service;
@Service
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:";
-
+ /**
+ * Server domain name.
+ */
+ private static final String SERVER = "hgdownload.cse.ucsc.edu";
/**
* Default class logger.
*/
@@ -186,6 +175,92 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
}
}
+ @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);
+ }
+ }
+
+ @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);
+ }
+ }
+ }
+
+ @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) {
+ 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;
+ }
+
@Override
public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
String result = null;
@@ -212,22 +287,13 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
}
@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);
- }
- }
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
}
/**
@@ -247,9 +313,66 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
this.taxonomyBackend = taxonomyBackend;
}
+ /**
+ * 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/";
+ }
+
+ /**
+ * 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));
+ }
+ }
+
/**
* Task that will be able to fetch genome file from ftp server.
- *
+ *
* @author Piotr Gawron
*
*/
@@ -257,13 +380,13 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
/**
* Url to the file that we want to download.
- *
+ *
*/
private String url;
/**
* Callback listener that will receive information about upload progress.
- *
+ *
*/
private IProgressUpdater updater;
@@ -279,7 +402,7 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
/**
* Default constructor.
- *
+ *
* @param url
* {@link #url}
* @param updater
@@ -339,138 +462,4 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
}
- @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) {
- 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/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/package-info.java
index 4ada42b53e..3a7a415d56 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
@@ -3,4 +3,3 @@
* 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 90e78c71dd..51cf2c586e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
@@ -1,17 +1,17 @@
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;
+import lcsb.mapviewer.annotation.cache.AllCacheTests;
+import lcsb.mapviewer.annotation.data.AllDataTests;
+import lcsb.mapviewer.annotation.services.AllServicesTests;
+
@RunWith(Suite.class)
@SuiteClasses({ AllCacheTests.class,
- AllDataTests.class,
- AllServicesTests.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 85396c4660..f76fa0a60d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -1,34 +1,17 @@
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.io.*;
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 java.util.*;
+
+import javax.xml.parsers.*;
+import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.junit.*;
import org.junit.runner.RunWith;
@@ -37,14 +20,11 @@ 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.w3c.dom.*;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.UnitTestFailedWatcher;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -59,20 +39,16 @@ import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
+ private static Map<String, Model> models = new HashMap<String, Model>();
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
@Autowired
protected PermanentDatabaseLevelCacheInterface cache;
-
@Autowired
protected CacheTypeDao cacheTypeDao;
-
@Autowired
protected DbUtils dbUtils;
-
private Logger logger = LogManager.getLogger(AnnotationTestFunctions.class);
-
private MinervaLoggerAppender appender;
@Before
@@ -156,8 +132,6 @@ public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit
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);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/SpringAnnotationTestConfig.java b/annotation/src/test/java/lcsb/mapviewer/annotation/SpringAnnotationTestConfig.java
index e29d521622..447d16adc4 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/SpringAnnotationTestConfig.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/SpringAnnotationTestConfig.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.annotation;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.*;
import lcsb.mapviewer.annotation.cache.MockCacheInterface;
import lcsb.mapviewer.persist.SpringPersistConfig;
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 99707b056d..f1d84ab021 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
@@ -6,13 +6,13 @@ 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,
+ 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/BigFileCacheTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
index 0e0b7f5305..826e7498f1 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.cache;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.when;
import java.io.*;
import java.net.URISyntaxException;
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 f58f0a89cc..54d45f3f3b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceMock.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceMock.java
@@ -2,13 +2,13 @@ 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;
- }
+ 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 eb6f03d3ed..fe5428d0d8 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.annotation.cache;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.when;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
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 31d47d8a99..08d20c049c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java
@@ -9,25 +9,25 @@ package lcsb.mapviewer.annotation.cache;
*/
public final class MockCacheInterface extends CachableInterface {
- public static RuntimeException exceptionToThrow = null;
- public static Error errorToThrow;
+ public static RuntimeException exceptionToThrow = null;
+ public static Error errorToThrow;
- /**
- * Defsault constructor.
- */
- public MockCacheInterface() {
- super(MockCacheInterface.class);
- }
+ /**
+ * 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>";
- }
+ @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 a20da355c6..580b5b5c7e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.annotation.cache;
import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.util.Calendar;
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 ac982ca9ff..bdd47bf8d9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/SourceNotAvailableTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/SourceNotAvailableTest.java
@@ -2,29 +2,26 @@ 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;
+import org.junit.*;
public class SourceNotAvailableTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testConstructor() {
- Exception e = new SourceNotAvailable("meessage");
- assertTrue(e.getMessage().contains("meessage"));
- }
+ @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 ab41debd38..c1b09b568f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.io.IOException;
import java.net.HttpURLConnection;
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 b4a981f759..ccec50eb8b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
@@ -6,18 +6,18 @@ 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,
+ 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 7d12657ef9..dff11ad93e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleCitationComparatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleCitationComparatorTest.java
@@ -5,43 +5,40 @@ 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;
+import org.junit.*;
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));
- }
+ @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/ChebiTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java
index 66427fec89..2cf2947c0b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.data;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 157d62127c..2065be34bf 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidenceTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidenceTest.java
@@ -2,30 +2,27 @@ 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;
+import org.junit.*;
public class ChemicalDirectEvidenceTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValues() {
- for (ChemicalDirectEvidence value : ChemicalDirectEvidence.values()) {
- assertNotNull(ChemicalDirectEvidence.valueOf(value.toString()));
- }
- }
+ @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 b89bfb937a..01d006c6e0 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalTest.java
@@ -6,62 +6,59 @@ 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 org.junit.*;
import lcsb.mapviewer.model.map.MiriamData;
public class ChemicalTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() 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);
+ @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());
-
- }
+ 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());
- }
+ @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/EntrezDataTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java
index 8d51c5853d..45d8c54a64 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java
@@ -6,46 +6,43 @@ 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 org.junit.*;
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());
- }
+ @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/MeSHTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java
index 5a99ef7c1e..12ddc0ee56 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.data;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.util.ArrayList;
import java.util.List;
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 bff4c92797..ebfbb2493a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/MiRNATest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MiRNATest.java
@@ -6,40 +6,37 @@ 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 org.junit.*;
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);
- }
+ @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 c1f4d752ac..9aa043d6e6 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.data;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 5cd268ced9..14bd965ca9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTypeTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTypeTest.java
@@ -2,31 +2,28 @@ 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;
+import org.junit.*;
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()));
- }
- }
+ @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 228a4b67c7..cde00bdf33 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
@@ -1,32 +1,32 @@
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;
+import lcsb.mapviewer.annotation.services.annotators.AllAnnotatorTests;
+import lcsb.mapviewer.annotation.services.genome.AllGenomeTests;
+
@RunWith(Suite.class)
@SuiteClasses({ AllAnnotatorTests.class,
- AllGenomeTests.class,
- ChEMBLParserTest.class,
- ChemicalParserTest.class,
- ChemicalSearchExceptionTest.class,
- DrugAnnotationTest.class,
- DrugbankHTMLParserTest.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,
+ AllGenomeTests.class,
+ ChEMBLParserTest.class,
+ ChemicalParserTest.class,
+ ChemicalSearchExceptionTest.class,
+ DrugAnnotationTest.class,
+ DrugbankHTMLParserTest.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 ab6a62d96f..dfe8729b8f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.*;
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 bb82811c85..01df6e958b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.*;
@@ -28,11 +28,9 @@ import lcsb.mapviewer.model.map.model.Model;
@Ignore("ctd decided to block us due to too many requests")
public class ChemicalParserTest extends AnnotationTestFunctions {
- Logger logger = LogManager.getLogger(ChemicalParserTest.class);
-
final MiriamData parkinsonDiseaseId = new MiriamData(MiriamType.MESH_2012, "D010300");
final MiriamData dystoniaDisease = new MiriamData(MiriamType.MESH_2012, "C538007");
-
+ Logger logger = LogManager.getLogger(ChemicalParserTest.class);
MiriamData glutathioneDisulfideChemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
MiriamData stilbeneOxideChemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C025906");
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 48e93bd829..3c58cb2741 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 +1,27 @@
package lcsb.mapviewer.annotation.services;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ChemicalSearchExceptionTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testConstructor() {
- ChemicalSearchException e = new ChemicalSearchException("msg");
- assertEquals("msg", e.getMessage());
- }
+ @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 3ba3717a96..3a1e5e52a8 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.services;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.Collection;
import java.util.List;
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 e5e204064e..21451bcdb8 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.ArrayList;
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 7953bf1799..d8f7938bd8 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 +1,31 @@
package lcsb.mapviewer.annotation.services;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ExternalServiceStatusTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testGetters() {
- String name = "b";
- String page = "page";
+ @Test
+ public void testGetters() {
+ String name = "b";
+ String page = "page";
- ExternalServiceStatus status = new ExternalServiceStatus(name, page);
- assertEquals(name, status.getName());
- assertEquals(page, status.getPage());
- }
+ 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 1eb86e29c9..bb363bd747 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTypeTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTypeTest.java
@@ -2,32 +2,29 @@ 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;
+import org.junit.*;
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()));
- }
- }
+ @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/ImproperAnnotationsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
index b7316ecc36..6d21ec34b4 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.services;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 2232a229ca..896b49de79 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.List;
@@ -182,7 +183,7 @@ public class MeSHParserTest extends AnnotationTestFunctions {
meshParser.refreshCacheQuery(query);
}
- @Test(expected=SourceNotAvailable.class)
+ @Test(expected = SourceNotAvailable.class)
public void testRefreshWhenProblemWithSourceDb() throws Exception {
WebPageDownloader downloader = meshParser.getWebPageDownloader();
GeneralCacheInterface cache = meshParser.getCache();
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 ba35eb5f63..d6d84474f9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.when;
import java.util.*;
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 9e191033dc..8bcc30754a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNASearchExceptionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNASearchExceptionTest.java
@@ -5,35 +5,32 @@ 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;
+import org.junit.*;
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());
- }
+ @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 7231d20416..ed031f64d7 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.lang.reflect.Field;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
index 84490b1219..0978edf024 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
@@ -2,31 +2,28 @@ package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.assertTrue;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingAnnotationTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void test() {
- MissingAnnotation annotation = new MissingAnnotation(new GenericProtein("id"));
- assertTrue(annotation.toString().contains("misses annotations"));
- }
+ @Test
+ public void test() {
+ MissingAnnotation annotation = new MissingAnnotation(new GenericProtein("id"));
+ assertTrue(annotation.toString().contains("misses annotations"));
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
index 9b901b6e7b..0e901ee712 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
@@ -5,10 +5,7 @@ import static org.junit.Assert.assertTrue;
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.junit.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamType;
@@ -16,37 +13,37 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingRequiredAnnotationsTest {
- @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 MissingRequiredAnnotations(new GenericProtein("id"), new ArrayList<>());
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
- }
- }
-
- @Test
- public void testGetMessage() {
- try {
- List<MiriamType> list = new ArrayList<>();
- list.add(MiriamType.CAS);
- MissingRequiredAnnotations mre = new MissingRequiredAnnotations(new GenericProtein("id"), list);
- assertTrue(mre.toString().contains("misses one of the following annotations"));
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
- }
- }
+ @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 MissingRequiredAnnotations(new GenericProtein("id"), new ArrayList<>());
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
+ }
+ }
+
+ @Test
+ public void testGetMessage() {
+ try {
+ List<MiriamType> list = new ArrayList<>();
+ list.add(MiriamType.CAS);
+ MissingRequiredAnnotations mre = new MissingRequiredAnnotations(new GenericProtein("id"), list);
+ assertTrue(mre.toString().contains("misses one of the following annotations"));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
+ }
+ }
}
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 83aa54626c..bc984854dd 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.ArrayList;
@@ -22,18 +23,15 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
public class PubmedParserTest extends AnnotationTestFunctions {
+ @Autowired
+ protected PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCacheInterface;
Logger logger = LogManager.getLogger(PubmedParserTest.class);
- private boolean status2;
-
@Autowired
PubmedParser pubmedParser;
-
+ private boolean status2;
@Autowired
private GeneralCacheInterface cache;
- @Autowired
- protected PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCacheInterface;
-
@Before
public void setUp() throws Exception {
status2 = Configuration.isApplicationCacheOn();
@@ -96,7 +94,8 @@ public class PubmedParserTest extends AnnotationTestFunctions {
/**
* This case was problematic with old API used to retrieve data from pubmed
- * @throws PubmedSearchException
+ *
+ * @throws PubmedSearchException
*/
@Test
public void testProblematicCase() throws PubmedSearchException {
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 6c90220d69..d0b73d3eab 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
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 29befabb84..9b3ff91e0c 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
@@ -2,10 +2,7 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class AnnotatorExceptionTest {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
index 153d02adcc..fd3483f31f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
@@ -8,11 +8,9 @@ import static org.mockito.Mockito.when;
import java.io.IOException;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
index feea977aa6..fe852a34f3 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
index 4af51cf203..19cbd5b90f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.util.List;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorImplementationsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorImplementationsTest.java
index 9fc4231272..41a17b548a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorImplementationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorImplementationsTest.java
@@ -4,11 +4,10 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
@@ -23,23 +22,19 @@ import lcsb.mapviewer.annotation.SpringAnnotationTestConfig;
import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator.BioEntityProxy;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
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.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.user.annotator.*;
import lcsb.mapviewer.persist.DbUtils;
@RunWith(Parameterized.class)
public class ElementAnnotatorImplementationsTest extends AnnotationTestFunctions {
+ static ApplicationContext applicationContext;
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(ElementAnnotatorImplementationsTest.class);
-
@Parameter
public String testName;
@Parameter(1)
@@ -49,8 +44,6 @@ public class ElementAnnotatorImplementationsTest extends AnnotationTestFunctions
@Parameter(3)
public BioEntity bioEntity;
- static ApplicationContext applicationContext;
-
@Parameters(name = "{0}")
public static Collection<Object[]> data() throws IOException {
List<Object[]> result = new ArrayList<>();
@@ -126,7 +119,7 @@ public class ElementAnnotatorImplementationsTest extends AnnotationTestFunctions
parameters.addAnnotatorParameter(parameter);
}
}
- for (MiriamType type: MiriamType.values()) {
+ for (MiriamType type : MiriamType.values()) {
AnnotatorOutputParameter parameter = new AnnotatorOutputParameter(type);
if (!annotator.getAvailableOuputProperties().contains(parameter)) {
parameters.addAnnotatorParameter(parameter);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
index c2b91fbff5..405f213e31 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
@@ -1,8 +1,10 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.Arrays;
@@ -23,12 +25,11 @@ import lcsb.mapviewer.model.user.annotator.*;
public class ElementAnnotatorTest extends AnnotationTestFunctions {
+ static AnnotatorData allOutputFieldsAndAnnotations = new AnnotatorData(Object.class);
ElementAnnotator annotator = Mockito.mock(ElementAnnotator.class, Mockito.CALLS_REAL_METHODS);
-
@Autowired
HgncAnnotator autowiredAnnotator;
- static AnnotatorData allOutputFieldsAndAnnotations = new AnnotatorData(Object.class);
{
for (BioEntityField field : BioEntityField.values()) {
allOutputFieldsAndAnnotations.addAnnotatorParameter(new AnnotatorOutputParameter(field));
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
index 78a2dd104c..e511d41685 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
index 819b0363c3..0029230e3d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.io.IOException;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
index e907c37532..e441d8b257 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index a57e8f255c..42af972fe9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.List;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
index 6609554d4c..cb535e502c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
@@ -1,8 +1,10 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.*;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java
index e2b2294988..adf9801d94 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
index b73292ab9f..568f3583c5 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.util.Set;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
index 475f7d55ad..51d7680d4a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
@@ -2,7 +2,8 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.when;
import java.io.IOException;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
index 0ad50e1a8e..827f624a06 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
index e39e0d2732..b3313bc2c3 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
index d2d97a1103..0a123f4b7f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
index a85c04eceb..85e746031d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.Collection;
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 6d5a6e730b..ce2fae9fa4 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
@@ -2,7 +2,7 @@ package lcsb.mapviewer.annotation.services.genome;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.net.URISyntaxException;
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
index f1ac82c46a..7dd64a8a0a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
@@ -4,7 +4,7 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Configuration.java b/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
index f4f5352500..36532d2444 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
@@ -1,14 +1,11 @@
package lcsb.mapviewer.common;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
+import java.io.*;
import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
/**
* Basic configuration parameters of the system (these values cannot be modified
@@ -20,24 +17,6 @@ import org.apache.logging.log4j.*;
*/
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 = LogManager.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
@@ -47,61 +26,65 @@ public final class Configuration {
* 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;
-
/**
* 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";
-
/**
* Guest account.
*/
public static final String ANONYMOUS_LOGIN = "anonymous";
-
+ /**
+ * Epsilon used for different types of comparisons.
+ */
+ public static final double EPSILON = 1e-6;
+ /**
+ * 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;
+ /**
+ * How many elements should be visible in auto-complete lists.
+ */
+ private static final int DEFAULT_AUTOCOMPLETE_SIZE = 5;
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(Configuration.class);
/**
* Max session length in seconds.
*/
private static int sessionLength = 60 * 120;
-
/**
* Should the application cache be turned on.
*/
private static boolean applicationCacheOn = 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.
*/
@@ -341,6 +324,13 @@ public final class Configuration {
Configuration.xFrametDomain = xFrametDomains;
}
+ /**
+ * @return the {@link #webAppDir}
+ */
+ public static String getWebAppDir() {
+ return Configuration.webAppDir;
+ }
+
/**
* @param path
* the path to webapps to set
@@ -350,13 +340,6 @@ public final class Configuration {
Configuration.webAppDir = path;
}
- /**
- * @return the {@link #webAppDir}
- */
- public static String getWebAppDir() {
- return Configuration.webAppDir;
- }
-
/**
* @return the memorySaturationRatioTriggerClean
* @see #memorySaturationRatioTriggerClean
diff --git a/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java b/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java
index f59648ac18..00bff73803 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java
@@ -10,82 +10,82 @@ import java.io.Serializable;
*
*/
public class FrameworkVersion implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Version of the framework.
- */
- private String version;
+ /**
+ * Version of the framework.
+ */
+ private String version;
- /**
- * When this version was committed to git.
- */
- private String gitVersion;
+ /**
+ * When this version was committed to git.
+ */
+ private String gitVersion;
- /**
- * When the framework was built.
- */
- private String time;
+ /**
+ * When the framework was built.
+ */
+ private String time;
- /**
- * Default constructor.
- *
- */
- public FrameworkVersion() {
- }
+ /**
+ * Default constructor.
+ *
+ */
+ public FrameworkVersion() {
+ }
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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/IProgressUpdater.java b/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java
index a74aa0557a..89ac9aef9f 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java
@@ -8,20 +8,20 @@ package lcsb.mapviewer.common;
*
*/
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;
+ /**
+ * 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);
+ /**
+ * 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/MinervaLoggerAppender.java b/commons/src/main/java/lcsb/mapviewer/common/MinervaLoggerAppender.java
index 5fc9f78100..6cf1094c34 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/MinervaLoggerAppender.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/MinervaLoggerAppender.java
@@ -5,10 +5,7 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.Level;
-import org.apache.logging.log4j.core.Filter;
-import org.apache.logging.log4j.core.Layout;
-import org.apache.logging.log4j.core.LogEvent;
-import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.*;
import org.apache.logging.log4j.core.appender.AbstractAppender;
import org.apache.logging.log4j.core.config.Property;
import org.apache.logging.log4j.core.impl.MutableLogEvent;
@@ -24,53 +21,45 @@ import org.apache.logging.log4j.core.layout.PatternLayout;
*/
public class MinervaLoggerAppender extends AbstractAppender {
+ /**
+ * Every logger must have different name. We use this counter to create new
+ * names.
+ */
+ private static int loggerCounter = 0;
/**
* List of {@link LogLevel#DEBUG} logs.
*/
private List<LogEvent> debugEvents = new ArrayList<>();
-
/**
* List of {@link LogLevel#INFO} logs.
*/
private List<LogEvent> infoEvents = new ArrayList<>();
-
/**
* List of {@link LogLevel#WARN} logs.
*/
private List<LogEvent> warnEvents = new ArrayList<>();
-
/**
* List of {@link LogLevel#ERROR} logs.
*/
private List<LogEvent> errorEvents = new ArrayList<>();
-
/**
* List of {@link LogLevel#FATAL} logs.
*/
private List<LogEvent> fatalEvents = new ArrayList<>();
-
/**
* List of logs with unknown log level.
*/
private List<LogEvent> 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;
- /**
- * Every logger must have different name. We use this counter to create new
- * names.
- */
- private static int loggerCounter = 0;
-
/**
* Private constructor preventing instantiation. Appender should be created
* using factory method: {@link MinervaLoggerAppender#createAppender()}.
diff --git a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
index b5fd056b5e..5d18f1d867 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
@@ -12,41 +12,41 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*/
public final class ObjectUtils {
- /**
- * Default constructor. Prevents instatiation.
- */
- private 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 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());
- }
- }
+ /**
+ * 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 32fb0263a8..0b486d1627 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Pair.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
@@ -15,70 +15,70 @@ import java.io.Serializable;
*/
public class Pair<L, R> implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * First object.
- */
- private final L left;
+ /**
+ * First object.
+ */
+ private final L left;
- /**
- * Second object.
- */
- private final R right;
+ /**
+ * 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;
- }
+ /**
+ * 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 #left}
+ */
+ public L getLeft() {
+ return left;
+ }
- /**
- *
- * @return {@link #right}
- */
- public R getRight() {
- return right;
- }
+ /**
+ *
+ * @return {@link #right}
+ */
+ public R getRight() {
+ return right;
+ }
- @Override
- public int hashCode() {
- return left.hashCode() ^ right.hashCode();
- }
+ @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 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();
- }
+ @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 bfb7431ef6..c5a88f5298 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
@@ -1,14 +1,10 @@
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 java.awt.*;
+import java.awt.datatransfer.*;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
/**
* Class allowing access to system clipboard.
@@ -17,48 +13,48 @@ import org.apache.logging.log4j.*;
*
*/
public class SystemClipboard implements ClipboardOwner {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(SystemClipboard.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(SystemClipboard.class);
- @Override
- public void lostOwnership(Clipboard clipboard, Transferable contents) {
- }
+ @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;
+ }
- /**
- * 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;
- }
+ /**
+ * 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);
+ }
}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
index 3f0b8226e2..f0d5e24336 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.common;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.io.*;
import java.util.HashMap;
import java.util.Map;
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 35e9b2821c..3309e00cac 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -1,26 +1,12 @@
package lcsb.mapviewer.common;
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import java.io.StringWriter;
+import java.awt.*;
+import java.io.*;
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.Result;
-import javax.xml.transform.Source;
-import javax.xml.transform.Templates;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
+import javax.xml.parsers.*;
+import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
@@ -29,17 +15,12 @@ import org.apache.commons.io.IOUtils;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
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;
+import lcsb.mapviewer.common.exception.*;
/**
* Abstract class with methods which help in parsing xml using DOM.
@@ -49,16 +30,14 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
*/
final public class XmlParser {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger(XmlParser.class);
-
/**
* Base of the hex representation.
*/
private static final int HEX_BASE = 16;
-
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(XmlParser.class);
/**
* {@link DocumentBuilder} objects that will manipulate xml nodes.
*/
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 c7f3bd733c..fcd34e630b 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/BooleanComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/BooleanComparator.java
@@ -10,18 +10,18 @@ import java.util.Comparator;
*/
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);
- }
+ @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 efaf121466..a788fe958a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.common.comparator;
-import java.awt.Color;
+import java.awt.*;
import java.util.Comparator;
/**
@@ -11,19 +11,19 @@ import java.util.Comparator;
*/
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;
- }
+ @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());
- }
+ } 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 a1320b5f13..d5ee693a0f 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
@@ -12,45 +12,45 @@ import lcsb.mapviewer.common.Configuration;
*/
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);
- }
- }
+ /**
+ * 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 55c899d983..fc596aec83 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.common.comparator;
-import java.awt.Color;
+import java.awt.*;
import java.util.Comparator;
/**
@@ -11,19 +11,19 @@ import java.util.Comparator;
*/
public class EnumComparator<E extends Enum<E>> implements Comparator<E> {
- @Override
- public int compare(E arg0, E arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
+ @Override
+ public int compare(E arg0, E arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
- } else if (arg1 == null) {
- return -1;
- }
- return arg0.compareTo(arg1);
- }
+ } else if (arg1 == null) {
+ return -1;
+ }
+ return arg0.compareTo(arg1);
+ }
}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/LineComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/LineComparator.java
index 97fffceab0..f747b5bc06 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/LineComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/LineComparator.java
@@ -4,7 +4,7 @@ import java.awt.geom.Line2D;
import java.util.Comparator;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/ListComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/ListComparator.java
index 485d1025eb..1ceb3d00a0 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/ListComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/ListComparator.java
@@ -4,8 +4,7 @@ import java.util.Comparator;
import java.util.List;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-
+import org.apache.logging.log4j.Logger;
/**
* Comparator used for comparing lists of objects.
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 4283684288..7fd74e3cc3 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/PointComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/PointComparator.java
@@ -13,46 +13,46 @@ import lcsb.mapviewer.common.Configuration;
*/
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;
- }
- }
+ /**
+ * 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 61fa44f4e0..3ad0a9e05b 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
@@ -4,8 +4,7 @@ import java.util.Comparator;
import java.util.Set;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-
+import org.apache.logging.log4j.Logger;
/**
* Comparator used for comparing sets of strings.
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 900ebb7fea..737c4cde77 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
@@ -3,8 +3,7 @@ package lcsb.mapviewer.common.comparator;
import java.util.Comparator;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-
+import org.apache.logging.log4j.Logger;
/**
* Comparator used for {@link String} class. It's null safe (it allows to
@@ -14,45 +13,45 @@ import org.apache.logging.log4j.*;
*
*/
public class StringComparator implements Comparator<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.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 0d9eac4d59..64e715cff2 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java
@@ -4,7 +4,7 @@ import java.util.Comparator;
import java.util.List;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
/**
* Comparator used for list of strings.
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
index adbcd10916..39e6dcea24 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
@@ -4,8 +4,7 @@ import java.util.Comparator;
import java.util.Set;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-
+import org.apache.logging.log4j.Logger;
/**
* Comparator used for comparing sets of strings.
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 7303e6069b..cb75259e62 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
@@ -2,4 +2,3 @@
* 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 cc38a4c8f2..05cf420d4a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidArgumentException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidArgumentException.java
@@ -7,50 +7,50 @@ package lcsb.mapviewer.common.exception;
*
*/
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);
- }
+ /**
+ *
+ */
+ 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 c09f00529a..d6f5736b32 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidClassException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidClassException.java
@@ -8,31 +8,30 @@ package lcsb.mapviewer.common.exception;
*/
public class InvalidClassException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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.
+ *
+ * @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);
- }
+ /**
+ * 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 6c1405dfba..0c14d73324 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidStateException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidStateException.java
@@ -9,48 +9,48 @@ package lcsb.mapviewer.common.exception;
*/
public class InvalidStateException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- public InvalidStateException() {
- super();
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 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);
- }
+ /**
+ * 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 42194290a3..ba04b7b49a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaException.java
@@ -7,50 +7,50 @@ package lcsb.mapviewer.common.exception;
*
*/
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);
- }
+ /**
+ *
+ */
+ 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 816128136c..fe6a08252a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java
@@ -10,26 +10,26 @@ package lcsb.mapviewer.common.exception;
*/
public class NotImplementedException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- public NotImplementedException() {
- super();
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 fb2c61871f..f7cc179a8d 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
@@ -2,4 +2,3 @@
* 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 d9bc3ab0bb..52db39243a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.common.geometry;
-import java.awt.Color;
+import java.awt.*;
import java.util.HashMap;
import java.util.Map;
@@ -47,7 +47,7 @@ public class ColorParser {
* @return {@link Color} obtained from input text
*/
public Color parse(String string) {
- if (string==null || string.isEmpty()) {
+ if (string == null || string.isEmpty()) {
throw new InvalidArgumentException(
"Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
}
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 df71302607..bdcd1bcd79 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/CompositeStroke.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/CompositeStroke.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.common.geometry;
-import java.awt.Shape;
-import java.awt.Stroke;
+import java.awt.*;
/**
* This class represent {@link Stroke} that consist of two nested {@link Stroke
@@ -12,30 +11,32 @@ import java.awt.Stroke;
*
*/
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;
- }
+ /**
+ * Outside stroke.
+ */
+ private Stroke stroke1;
- @Override
- public Shape createStrokedShape(Shape shape) {
- return stroke2.createStrokedShape(stroke1.createStrokedShape(shape));
- }
+ /**
+ * 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/EllipseTransformation.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java
index e01a511c93..705f365f86 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java
@@ -4,11 +4,10 @@ import java.awt.geom.Ellipse2D;
import java.awt.geom.Point2D;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-
/**
* This class contains basic operators on ellipse used by converters.
*
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
index 232dc780a6..97ea610093 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.common.geometry;
-import java.awt.geom.Line2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
+import java.awt.geom.*;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
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 45c960554c..fc550dd531 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
@@ -80,8 +80,8 @@ public class PointTransformation {
* @return {@link Point2D} on line defined by input points
*/
public Point2D getPointOnLine(Point2D start, Point2D end, double coef) {
- double x = start.getX()+(end.getX()-start.getX())*coef;
- double y = start.getY()+(end.getY()-start.getY())*coef;
+ double x = start.getX() + (end.getX() - start.getX()) * coef;
+ double y = start.getY() + (end.getY() - start.getY()) * coef;
return new Point2D.Double(x, y);
}
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 d4bfcdc62c..5094095e61 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/TextAlignment.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/TextAlignment.java
@@ -8,18 +8,18 @@ package lcsb.mapviewer.common.geometry;
*/
public enum TextAlignment {
- /**
- * Text should be aligned to left.
- */
- LEFT,
+ /**
+ * Text should be aligned to left.
+ */
+ LEFT,
- /**
- * Text should be aligned to right.
- */
- RIGHT,
+ /**
+ * Text should be aligned to right.
+ */
+ RIGHT,
- /**
- * Text should be centered.
- */
- CENTER;
+ /**
+ * 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 333ba68b32..c156b8180b 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
@@ -9,4 +9,3 @@
* .
*/
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 fd4528e939..e02a29d4a6 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/package-info.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/package-info.java
@@ -2,4 +2,3 @@
* 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 7c6b6fa400..b09bf968af 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
@@ -10,16 +10,16 @@ import lcsb.mapviewer.common.geometry.AllGeometryTests;
@RunWith(Suite.class)
@SuiteClasses({ AllComparatorTests.class,
- AllExceptionTests.class,
- AllGeometryTests.class,
- ConfigurationTest.class,
- GlobalLoggerAppenderTest.class,
- MimeTypeTest.class,
- ObjectUtilsTest.class,
- PairTest.class,
- SystemClipboardTest.class,
- TextFileUtilsTest.class,
- XmlParserTest.class,
+ AllExceptionTests.class,
+ AllGeometryTests.class,
+ ConfigurationTest.class,
+ GlobalLoggerAppenderTest.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/ConfigurationTest.java b/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java
index 55034269a6..b09dcf34b9 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java
@@ -1,8 +1,6 @@
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.*;
import java.io.File;
import java.lang.reflect.Constructor;
@@ -10,117 +8,114 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ConfigurationTest extends CommonTestFunctions{
-
- Logger logger = LogManager.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());
- }
-
- @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;
- }
- }
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
+
+public class ConfigurationTest extends CommonTestFunctions {
+
+ Logger logger = LogManager.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());
+ }
+
+ @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/GlobalLoggerAppenderTest.java b/commons/src/test/java/lcsb/mapviewer/common/GlobalLoggerAppenderTest.java
index d96a0f6883..dbc65e319e 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/GlobalLoggerAppenderTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/GlobalLoggerAppenderTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.common;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
index 50189c2ae3..49af59112d 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
@@ -3,30 +3,28 @@ 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;
+import org.junit.*;
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());
- }
- }
+ @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 7cf9e2ff1a..55d750b9a8 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.common;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.lang.reflect.Constructor;
diff --git a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
index 33178d5e6a..eeceb237b1 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
@@ -1,70 +1,66 @@
package lcsb.mapviewer.common;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class PairTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() 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 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));
+ @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()));
- }
+ 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 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 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()));
- }
+ @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 938661d59e..2e0372a475 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.common;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
-import java.awt.Toolkit;
+import java.awt.*;
import java.awt.datatransfer.*;
import java.io.IOException;
@@ -38,13 +39,13 @@ public class SystemClipboardTest extends CommonTestFunctions {
clipboard.setContents(new Transferable() {
@Override
- public boolean isDataFlavorSupported(DataFlavor flavor) {
- return true;
+ public DataFlavor[] getTransferDataFlavors() {
+ return null;
}
@Override
- public DataFlavor[] getTransferDataFlavors() {
- return null;
+ public boolean isDataFlavorSupported(DataFlavor flavor) {
+ return true;
}
@Override
diff --git a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
index fbaed58e78..6773a4fd1f 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.common;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.List;
@@ -20,6 +20,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
public class XmlParserTest extends CommonTestFunctions {
Logger logger = LogManager.getLogger(XmlParserTest.class);
+ boolean threadSucceded;
@Before
public void setUp() throws Exception {
@@ -98,8 +99,6 @@ public class XmlParserTest extends CommonTestFunctions {
assertTrue(str.contains(xml));
}
- boolean threadSucceded;
-
@Test
public void testConcurrencyParse() throws Exception {
StringBuilder builder = new StringBuilder("<doc>");
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 d8329fcc9c..5391935129 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 +1,35 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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);
- }
+ @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 febdaff65a..8bb20493c9 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 +1,37 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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);
- }
+ @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 91243e054d..3a647d5c6f 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 +1,43 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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);
- }
+ @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 65b7ab4653..5406cfad4d 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 +1,34 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class IntegerComparatorTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() 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 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);
- }
+ @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/LineComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/LineComparatorTest.java
index d776645605..e2e2d145f5 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/LineComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/LineComparatorTest.java
@@ -6,17 +6,14 @@ import static org.junit.Assert.assertTrue;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class LineComparatorTest {
-
+
Point2D p1 = new Point2D.Double(106, 5.01);
Point2D p1close = new Point2D.Double(106, 5.11);
Point2D p2 = new Point2D.Double(106, 2.73);
Point2D p2far = new Point2D.Double(106, 202.73);
-
@Before
public void setUp() throws Exception {
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/ListComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/ListComparatorTest.java
index b7e6912654..9cd9736ba0 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/ListComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/ListComparatorTest.java
@@ -3,9 +3,8 @@ package lcsb.mapviewer.common.comparator;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Comparator;
+import java.awt.*;
+import java.util.*;
import java.util.List;
import org.junit.Test;
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 0d2097325e..49910828c9 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/PointComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/PointComparatorTest.java
@@ -5,43 +5,41 @@ 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.junit.*;
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);
- }
+ @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/SetComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/SetComparatorTest.java
index 4060b46bd6..59e01e39ea 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/SetComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/SetComparatorTest.java
@@ -1,11 +1,10 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Set;
+import java.awt.*;
+import java.util.*;
import org.junit.Test;
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 88b635ee56..665eb30672 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 +1,43 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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);
- }
+ @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 e22dbc1cb5..f636610c85 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 +1,54 @@
package lcsb.mapviewer.common.comparator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
import java.util.ArrayList;
import java.util.List;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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);
- }
+ @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 d74ca665e1..cebce07970 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java
@@ -6,56 +6,53 @@ 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;
+import org.junit.*;
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);
- }
-
+ @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 c97eba1515..cdb80a357e 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/AllExceptionTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/AllExceptionTests.java
@@ -5,8 +5,9 @@ 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 })
+@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 4f29bfe219..187b22ca08 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 +1,37 @@
package lcsb.mapviewer.common.exception;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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()));
- }
+ @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 4dcb0c5896..ee2f20b839 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidClassExceptionTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidClassExceptionTest.java
@@ -2,28 +2,26 @@ package lcsb.mapviewer.common.exception;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class InvalidClassExceptionTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testConstructor1() {
- assertNotNull(new InvalidClassException("str"));
- }
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new InvalidClassException("str"));
+ }
- @Test
- public void testConstructor2() {
- assertNotNull(new InvalidClassException("dsr", new Exception()));
- }
+ @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 4ff04ade68..4cc1abdb91 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 +1,37 @@
package lcsb.mapviewer.common.exception;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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()));
- }
+ @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 95ae7bbc05..1898b30907 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 +1,37 @@
package lcsb.mapviewer.common.exception;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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()));
- }
+ @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 17d933b020..45f0214c9a 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 +1,27 @@
package lcsb.mapviewer.common.exception;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class NotImplementedExceptionTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testConstructor1() {
- assertNotNull(new NotImplementedException());
- }
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new NotImplementedException());
+ }
- @Test
- public void testConstructor2() {
- assertNotNull(new NotImplementedException("str"));
- }
+ @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 acf62ccd69..6eabaa75d7 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
@@ -6,11 +6,11 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ ColorParserTest.class,
- CompositeStrokeTest.class,
- EllipseTransformationTest.class,
- LineTransformationTest.class,
- PointTransformationTest.class,
- TextAlignmentTest.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 bc6e7abe34..8a2580fc5a 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.common.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
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 a4251214cd..2ede377702 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 +1,24 @@
package lcsb.mapviewer.common.geometry;
-import java.awt.BasicStroke;
+import java.awt.*;
import java.awt.geom.Line2D;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class CompositeStrokeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() 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));
- }
+ @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 e73ada3547..501ca1183d 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/EllipseTransformationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/EllipseTransformationTest.java
@@ -1,83 +1,82 @@
package lcsb.mapviewer.common.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Point2D;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
import lcsb.mapviewer.common.Configuration;
public class EllipseTransformationTest {
- Logger logger = LogManager.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);
- }
+ Logger logger = LogManager.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 cf3bf6483d..b6faf2f5a8 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/LineTransformationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/LineTransformationTest.java
@@ -1,23 +1,13 @@
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 static org.junit.Assert.*;
+
+import java.awt.*;
+import java.awt.geom.*;
import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
import lcsb.mapviewer.common.Configuration;
@@ -84,9 +74,9 @@ public class LineTransformationTest {
p = lineTransformation.getIntersectionWithPathIterator(line, new PathIterator() {
@Override
- public void next() {
+ public int getWindingRule() {
// TODO Auto-generated method stub
-
+ return 0;
}
@Override
@@ -95,19 +85,19 @@ public class LineTransformationTest {
}
@Override
- public int getWindingRule() {
+ public void next() {
// TODO Auto-generated method stub
- return 0;
+
}
@Override
- public int currentSegment(double[] coords) {
+ public int currentSegment(float[] coords) {
// TODO Auto-generated method stub
return 0;
}
@Override
- public int currentSegment(float[] coords) {
+ public int currentSegment(double[] coords) {
// TODO Auto-generated method stub
return 0;
}
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 f9bb7c1b83..fdcfe8c7da 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/PointTransformationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/PointTransformationTest.java
@@ -1,14 +1,10 @@
package lcsb.mapviewer.common.geometry;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
import java.awt.geom.Point2D;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import lcsb.mapviewer.common.Configuration;
@@ -58,7 +54,7 @@ public class PointTransformationTest {
Point2D p1 = new Point2D.Double(1, 0);
Point2D p2 = new Point2D.Double(12, 38);
Point2D result = pt.getPointOnLine(p1, p2, 0);
-
+
assertEquals(p1, result);
}
@@ -68,7 +64,7 @@ public class PointTransformationTest {
Point2D p1 = new Point2D.Double(1, 0);
Point2D p2 = new Point2D.Double(12, 38);
Point2D result = pt.getPointOnLine(p1, p2, 1);
-
+
assertEquals(p2, result);
}
@@ -78,7 +74,7 @@ public class PointTransformationTest {
Point2D p1 = new Point2D.Double(1, 0);
Point2D p2 = new Point2D.Double(12, 38);
Point2D result = pt.getPointOnLine(p1, p2, 0.5);
-
+
assertEquals(new Point2D.Double(6.5, 19), result);
}
@@ -88,7 +84,7 @@ public class PointTransformationTest {
Point2D p1 = new Point2D.Double(2, 0);
Point2D p2 = new Point2D.Double(12, 20);
Point2D result = pt.getPointOnLine(p1, p2, 0.4);
-
+
assertEquals(new Point2D.Double(6, 8), result);
}
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 b14349b8ef..a7dae046f8 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/TextAlignmentTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/TextAlignmentTest.java
@@ -2,28 +2,26 @@ package lcsb.mapviewer.common.geometry;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class TextAlignmentTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (TextAlignment type : TextAlignment.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (TextAlignment type : TextAlignment.values()) {
+ assertNotNull(type);
- // for coverage tests
- TextAlignment.valueOf(type.toString());
- }
- }
+ // for coverage tests
+ TextAlignment.valueOf(type.toString());
+ }
+ }
}
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 cf70051535..bfdabc4292 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
@@ -1,25 +1,14 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-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.*;
import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@@ -40,14 +29,20 @@ public class CellDesignerElementCollection {
* Element by element identifier (it's CellDesigner identifier).
*/
private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
+ /**
+ *
+ */
+ private Map<String, String> sbmlIdByElement = new HashMap<>();
+ private Map<String, String> modificationResidueIdByHash = new HashMap<>();
+ private Set<String> usedModificationResidueIds = new HashSet<>();
/**
* Returns element by given identifier.
- *
+ *
* @param speciesId
* element identifier
* @return element by given identifier
- *
+ *
* @param <T>
* type of returned object
*/
@@ -56,15 +51,10 @@ public class CellDesignerElementCollection {
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
@@ -88,7 +78,7 @@ public class CellDesignerElementCollection {
/**
* Creates a String that identifies element as distinct SBML entity.
- *
+ *
* @param modelElement
* element that we want to identify
* @param useComplex
@@ -174,7 +164,7 @@ public class CellDesignerElementCollection {
/**
* 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,
@@ -194,7 +184,7 @@ public class CellDesignerElementCollection {
/**
* Adds cell designer structures.
- *
+ *
* @param elements
* list of objects to add
*/
@@ -206,7 +196,7 @@ public class CellDesignerElementCollection {
/**
* Adds cell designer object.
- *
+ *
* @param element
* object to add
*/
@@ -217,7 +207,7 @@ public class CellDesignerElementCollection {
/**
* Adds CellDesigner element with custom id (instead the one obtained from
* CellDesigner structure).
- *
+ *
* @param element
* element to be add
* @param id
@@ -234,7 +224,7 @@ public class CellDesignerElementCollection {
/**
* 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
@@ -247,9 +237,6 @@ public class CellDesignerElementCollection {
}
}
- private Map<String, String> modificationResidueIdByHash = new HashMap<>();
- private Set<String> usedModificationResidueIds = new HashSet<>();
-
/**
* This method computes modificationResidueId that should be used when exporting
* modification residue to CellDesigner. The identifier relies on type and
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 28bd63f9eb..37084d1bd0 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
@@ -11,19 +11,11 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
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.MimeType;
-import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.XmlParser;
+import org.w3c.dom.*;
+
+import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
+import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
@@ -33,27 +25,17 @@ import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollection
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.structure.*;
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.layout.graphics.*;
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.*;
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
@@ -251,9 +233,29 @@ public class CellDesignerXmlParser extends Converter {
return model;
}
+ @Override
+ public String model2String(Model model) throws InconsistentModelException {
+ return model2Xml(model, true);
+ }
+
+ @Override
+ public String getCommonName() {
+ return "CellDesigner SBML";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.SBML;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "xml";
+ }
+
/**
* Computes bound of the model.
- *
+ *
* @param model
* object for which computaion is done
* @return bound of the model
@@ -341,7 +343,7 @@ public class CellDesignerXmlParser extends Converter {
/**
* Parse annotation part of CellDesigner xml.
- *
+ *
* @param model
* model that is parsed (and will be updated)
* @param modelData
@@ -507,7 +509,7 @@ public class CellDesignerXmlParser extends Converter {
/**
* Parses celldesigner:listOfComplexSpeciesAliases node for annotation part of
* the CellDEsigner format.
- *
+ *
* @param model
* model that is parsed
* @param aliasNode
@@ -545,7 +547,7 @@ public class CellDesignerXmlParser extends Converter {
/**
* Parses celldesigner:listOfSpeciesAliases node for annotation part of the
* CellDesigner format.
- *
+ *
* @param model
* model that is parsed
* @param aliasNode
@@ -581,14 +583,9 @@ public class CellDesignerXmlParser extends Converter {
}
}
- @Override
- public String model2String(Model model) throws InconsistentModelException {
- return model2Xml(model, true);
- }
-
/**
* Transforms model into CellDesigner xml.
- *
+ *
* @param model
* model that should be transformed
* @return CellDesigner xml string for the model
@@ -661,7 +658,7 @@ public class CellDesignerXmlParser extends Converter {
/**
* Generates xml node that should be in annotation part of the model.
- *
+ *
* @param model
* model to transform
* @param elements
@@ -714,19 +711,4 @@ public class CellDesignerXmlParser extends Converter {
result.append("</annotation>\n");
return result.toString();
}
-
- @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 ec94fbd251..dc0038372a 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
@@ -1,15 +1,14 @@
package lcsb.mapviewer.converter.model.celldesigner;
-import java.awt.Color;
-import java.awt.Dimension;
+import java.awt.*;
import java.awt.geom.Point2D;
+import org.w3c.dom.Node;
+
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.
*
@@ -17,90 +16,90 @@ import org.w3c.dom.Node;
*
*/
public class CommonXmlParser {
- /**
- * 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(XmlParser.getNodeAttr("x", node));
- double y = Double.parseDouble(XmlParser.getNodeAttr("y", node));
- return new Point2D.Double(x, y);
+ /**
+ * 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(XmlParser.getNodeAttr("x", node));
+ double y = Double.parseDouble(XmlParser.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(XmlParser.getNodeAttr("width", node));
- double height = Double.parseDouble(XmlParser.getNodeAttr("height", node));
- Dimension result = new Dimension();
- result.setSize(width, height);
- return result;
- }
+ /**
+ * 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(XmlParser.getNodeAttr("width", node));
+ double height = Double.parseDouble(XmlParser.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(XmlParser.getNodeAttr("width", node)));
- 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(XmlParser.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 = XmlParser.getNodeAttr("color", node);
- return XmlParser.stringToColor(color);
- }
+ /**
+ * 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 = XmlParser.getNodeAttr("color", node);
+ return XmlParser.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 = XmlParser.getNode("celldesigner:innerPosition", node.getChildNodes());
- if (tmpNode != null) {
- result.setInnerPosition(getPosition(tmpNode));
- }
+ /**
+ * 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 = XmlParser.getNode("celldesigner:innerPosition", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setInnerPosition(getPosition(tmpNode));
+ }
- tmpNode = XmlParser.getNode("celldesigner:boxSize", node.getChildNodes());
- if (tmpNode != null) {
- result.setBoxSize(getDimension(tmpNode));
- }
+ tmpNode = XmlParser.getNode("celldesigner:boxSize", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setBoxSize(getDimension(tmpNode));
+ }
- tmpNode = XmlParser.getNode("celldesigner:singleLine", node.getChildNodes());
- if (tmpNode != null) {
- result.setSingleLine(getSingleLine(tmpNode));
- }
+ tmpNode = XmlParser.getNode("celldesigner:singleLine", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setSingleLine(getSingleLine(tmpNode));
+ }
- tmpNode = XmlParser.getNode("celldesigner:paint", node.getChildNodes());
- if (tmpNode != null) {
- result.setColor(getColor(tmpNode));
- }
- return result;
- }
+ tmpNode = XmlParser.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 9f854ba231..8016abea06 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
@@ -9,51 +9,51 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
*
*/
public class InvalidGroupException extends InvalidXmlSchemaException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public InvalidGroupException() {
- super();
- }
-
- /**
- * 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);
- }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public InvalidGroupException() {
+ super();
+ }
+
+ /**
+ * 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 e06a9ba21d..c37f312dd2 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
@@ -1,12 +1,12 @@
package lcsb.mapviewer.converter.model.celldesigner;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
+import java.util.*;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -14,15 +14,10 @@ import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.graphics.*;
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.layout.graphics.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
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 35c9d295ab..c70a43f7a5 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
@@ -1,9 +1,8 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -87,5 +86,5 @@ public abstract class AbstractAliasXmlParser<T extends Element> {
protected String createFontTag(T alias) {
return "<celldesigner:font size=\"" + alias.getFontSize().intValue() + "\"/>";
}
-
+
}
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 04cf980173..028d1895f6 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
@@ -1,10 +1,9 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -28,213 +27,216 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class AliasCollectionXmlParser {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.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();
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.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 c8cd11454c..9ab997e868 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
@@ -1,22 +1,17 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.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.compartment.*;
import lcsb.mapviewer.model.map.model.Model;
/**
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 cecd43d6b1..ee84daedd6 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
@@ -3,14 +3,13 @@ package lcsb.mapviewer.converter.model.celldesigner.alias;
import java.util.HashMap;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
@@ -167,51 +166,6 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
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 = XmlParser.getNodeAttr("state", node);
- if ("open".equalsIgnoreCase(state)) {
- String prefix = XmlParser.getNodeAttr("prefix", node);
- String label = XmlParser.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;
@@ -286,4 +240,49 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
sb.append("</celldesigner:complexSpeciesAlias>\n");
return sb.toString();
}
+
+ /**
+ * 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 = XmlParser.getNodeAttr("state", node);
+ if ("open".equalsIgnoreCase(state)) {
+ String prefix = XmlParser.getNodeAttr("prefix", node);
+ String label = XmlParser.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);
+ }
+ }
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index b00bd68b1d..88744fd1d0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -1,17 +1,14 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.common.XmlParser;
+import lcsb.mapviewer.common.exception.*;
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.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.*;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
@@ -159,31 +156,6 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
}
}
- /**
- * 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 = XmlParser.getNodeAttr("state", node);
- if ("open".equalsIgnoreCase(state)) {
- String prefix = XmlParser.getNodeAttr("prefix", node);
- String label = XmlParser.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);
- }
-
- }
-
@Override
public String toXml(Species species) {
Compartment ca = null;
@@ -262,4 +234,29 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
sb.append("</celldesigner:speciesAlias>\n");
return sb.toString();
}
+
+ /**
+ * 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 = XmlParser.getNodeAttr("state", node);
+ if ("open".equalsIgnoreCase(state)) {
+ String prefix = XmlParser.getNodeAttr("prefix", node);
+ String label = XmlParser.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);
+ }
+
+ }
}
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 4790cb66ee..34a3a4fb6b 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
@@ -3,4 +3,3 @@
* aliases.
*/
package lcsb.mapviewer.converter.model.celldesigner.alias;
-
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index 0eaf20fcd9..3844d7afa5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.annotation;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index 28222d70a2..152bc605dd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -1,10 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.annotation;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -14,20 +10,10 @@ import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
-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.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.comparator.*;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
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 d69c31ead7..3d155d34e8 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
@@ -2,4 +2,3 @@
* 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 cd43a8ba32..78e48e5872 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
@@ -1,12 +1,9 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -63,7 +60,7 @@ public class CompartmentCollectionXmlParser {
* @return list of compartments obtained from xml node
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
- * @throws CompartmentParserException
+ * @throws CompartmentParserException
* thrown when there is a problem with parsing a compartment
*/
public List<CellDesignerCompartment> parseXmlCompartmentCollection(Node compartmentsNode)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java
index 0a95ae8de7..1c5796a73b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.compartment;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -13,17 +14,15 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
*
*/
public class CompartmentParserException extends CellDesignerParserException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(CompartmentParserException.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Identifier of compartment that was a reason for this exception.
*/
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 61f10f6800..794d0a9fc8 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
@@ -1,11 +1,12 @@
package lcsb.mapviewer.converter.model.celldesigner.compartment;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -84,9 +85,48 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
}
}
+ @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("<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("<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(), elements.getElementId(compartment)));
+ sb.append("</annotation>\n");
+ sb.append("</compartment>\n");
+ return sb.toString();
+ }
+
/**
* Process annotation part of the xml node.
- *
+ *
* @param compartment
* object that we create
* @param xmlNode
@@ -113,7 +153,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
/**
* Process extension part of the xml node.
- *
+ *
* @param compartment
* object that we create
* @param xmlNode
@@ -136,43 +176,4 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
}
}
}
-
- @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("<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("<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(), elements.getElementId(compartment)));
- sb.append("</annotation>\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 8d5a65ecbb..6341586150 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
@@ -3,4 +3,3 @@
* compartments.
*/
package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
index c536f2f32f..c85215482a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.function;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
@@ -27,7 +28,8 @@ public class FunctionXmlParser {
throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain MathML definition (math node)");
}
String definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
- + XmlParser.nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "") + "</math>";
+ + XmlParser.nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "")
+ + "</math>";
result.setDefinition(definition);
result.setArguments(parseArgumentsFromMath(mathDefinition, functionId));
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
index 3b0eb4869f..9b8166a77d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
@@ -1,21 +1,15 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry;
-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.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
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.converter.model.celldesigner.geometry.helper.*;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -31,61 +25,50 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
*/
public abstract class AbstractCellDesignerAliasConverter<T extends Element> implements ICellDesignerAliasConverter<T> {
+ /**
+ * What is the distance between homodimer aliases when homodimer>1.
+ */
+ public static final int HOMODIMER_OFFSET = 6;
/**
* PI value.
*/
private static final double PI = Math.PI;
-
/**
* Constant determining angle of the top right corner.
*/
protected static final double RIGHT_TOP_RESIDUE_MAX_ANGLE = 0.25 * PI;
-
/**
* Constant determining angle of the top left corner.
*/
protected static final double TOP_RESIDUE_MAX_ANGLE = 0.75 * PI;
-
/**
* Constant determining angle of the bottom left corner.
*/
protected static final double LEFT_RESIDUE_MAX_ANGLE = 1.25 * PI;
-
/**
* Constant determining angle of the bottom right corner.
*/
protected static final double BOTTOM_RESIDUE_MAX_ANGLE = 1.75 * PI;
-
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(AbstractCellDesignerAliasConverter.class);
-
/**
* CellDesigner graphical helper with polygon transformation functions.
*/
private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
-
/**
* CellDesigner graphical helper with line transformation functions.
*/
private LineTransformation lineTransformation = new LineTransformation();
-
/**
* CellDesigner graphical helper with ellipse transformation functions.
*/
private CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
-
/**
* CellDesigner graphical helper with rectangle transformation functions.
*/
private CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
-
- /**
- * What is the distance between homodimer aliases when homodimer>1.
- */
- public static final int HOMODIMER_OFFSET = 6;
-
/**
* Should the converter use SBGN standard.
*/
@@ -139,10 +122,130 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
}
}
+ /**
+ * Returns coordinates on the {@link Species} border for given angle for
+ * residues.
+ *
+ * @param species
+ * object on border which the point is looked for
+ * @param angle
+ * CellDEsigner specific angle defining coordinates (;/)
+ * @return coordinates on the alias border that correspond to the angle
+ */
+ @Override
+ public Point2D getResidueCoordinates(final T species, double angle) {
+ Point2D result = null;
+ if (species.getWidth() == 0 && species.getHeight() == 0) {
+ result = species.getCenter();
+ } else {
+ double x = 0;
+ double y = 0;
+ while (angle > 2 * PI) {
+ angle -= 2 * PI;
+ }
+ while (angle < 0) {
+ angle += 2 * PI;
+ }
+ if (angle < RIGHT_TOP_RESIDUE_MAX_ANGLE) {
+ // CHECKSTYLE:OFF 0.5 is much readable than any other suggestion
+ double ratio = 0.5 + angle / (PI / 2);
+ // CHECKSTYLE:ON
+ x = species.getX() + species.getWidth();
+ y = species.getY() + species.getHeight() * (1 - ratio);
+ } else if (angle < TOP_RESIDUE_MAX_ANGLE) {
+ double ratio = (angle - RIGHT_TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY();
+ x = species.getX() + species.getWidth() * (1 - ratio);
+ } else if (angle < LEFT_RESIDUE_MAX_ANGLE) {
+ double ratio = (angle - TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY() + species.getHeight() * (ratio);
+ x = species.getX();
+ } else if (angle < BOTTOM_RESIDUE_MAX_ANGLE) {
+ double ratio = (angle - LEFT_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY() + species.getHeight();
+ x = species.getX() + species.getWidth() * ratio;
+ } else if (angle <= 2 * PI + Configuration.EPSILON) {
+ double ratio = (angle - BOTTOM_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY() + species.getHeight() * (1 - ratio);
+ x = species.getX() + species.getWidth();
+ } else {
+ throw new InvalidStateException();
+ }
+ Point2D center = species.getCenter();
+ double correctedAngle = -Math.atan2((y - center.getY()), (x - center.getX()));
+ result = getPointCoordinatesOnBorder(species, correctedAngle);
+ }
+ return result;
+
+ }
+
+ @Override
+ public Double getAngleForPoint(T element, Point2D position) {
+ double result = -1;
+ Point2D pointOnBorder = getClosestPositionOnBorder(element, position);
+
+ double epsilon = Configuration.EPSILON;
+ double distanceRight = Math.abs(pointOnBorder.getX() - element.getX() - element.getWidth());
+ double distanceTop = Math.abs(pointOnBorder.getY() - element.getY());
+ double distanceLeft = Math.abs(pointOnBorder.getX() - element.getX());
+ double distanceBottom = Math.abs(pointOnBorder.getY() - element.getY() - element.getHeight());
+
+ double minDist = Math.min(Math.min(distanceLeft, distanceRight), Math.min(distanceTop, distanceBottom));
+
+ if (distanceRight == minDist &&
+ pointOnBorder.getY() - element.getY() - element.getHeight() / 2 < epsilon) {
+ double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
+ result = (ratio - 0.5) * (PI / 2);
+ } else if (distanceTop == minDist) {
+ double ratio = 1 - (pointOnBorder.getX() - element.getX()) / element.getWidth();
+ result = ratio * (PI / 2) + RIGHT_TOP_RESIDUE_MAX_ANGLE;
+ } else if (distanceLeft == minDist) {
+ double ratio = (pointOnBorder.getY() - element.getY()) / element.getHeight();
+ result = ratio * (PI / 2) + TOP_RESIDUE_MAX_ANGLE;
+ } else if (distanceBottom == minDist) {
+ double ratio = (pointOnBorder.getX() - element.getX()) / element.getWidth();
+ result = ratio * (PI / 2) + LEFT_RESIDUE_MAX_ANGLE;
+ } else if (distanceRight == minDist &&
+ pointOnBorder.getY() - element.getY() - element.getHeight() < epsilon) {
+ double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
+ result = ratio * (PI / 2) + BOTTOM_RESIDUE_MAX_ANGLE;
+ } else {
+ result = PI / 2;
+ logger.warn("Problem with finding angle. Using default");
+ }
+
+ return result;
+ }
+
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return null;
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos) {
+ return this.getCoordinatesByPosition(element, pos, 0.0);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
+ throw new NotImplementedException("Not implemented for: " + this.getClass());
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ throw new NotImplementedException("Not implemented for: " + this.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ throw new NotImplementedException("Not implemented for: " + this.getClass());
+ }
+
/**
* This method computes coordinates that should be associated with the angle on
* the border of the alias.
- *
+ *
* @param alias
* alias to be investigated
* @param angle
@@ -171,7 +274,7 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
/**
* This method returns border of the alias as a PathIterator.
- *
+ *
* @param alias
* object for which we want to find a border
* @return border of the alias
@@ -180,7 +283,7 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
/**
* Checks if anchor is valid for the alias to find a point on the border.
- *
+ *
* @param alias
* object to be checked
* @param anchor
@@ -267,66 +370,9 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
return sbgn;
}
- /**
- * Returns coordinates on the {@link Species} border for given angle for
- * residues.
- *
- * @param species
- * object on border which the point is looked for
- * @param angle
- * CellDEsigner specific angle defining coordinates (;/)
- * @return coordinates on the alias border that correspond to the angle
- */
- @Override
- public Point2D getResidueCoordinates(final T species, double angle) {
- Point2D result = null;
- if (species.getWidth() == 0 && species.getHeight() == 0) {
- result = species.getCenter();
- } else {
- double x = 0;
- double y = 0;
- while (angle > 2 * PI) {
- angle -= 2 * PI;
- }
- while (angle < 0) {
- angle += 2 * PI;
- }
- if (angle < RIGHT_TOP_RESIDUE_MAX_ANGLE) {
- // CHECKSTYLE:OFF 0.5 is much readable than any other suggestion
- double ratio = 0.5 + angle / (PI / 2);
- // CHECKSTYLE:ON
- x = species.getX() + species.getWidth();
- y = species.getY() + species.getHeight() * (1 - ratio);
- } else if (angle < TOP_RESIDUE_MAX_ANGLE) {
- double ratio = (angle - RIGHT_TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY();
- x = species.getX() + species.getWidth() * (1 - ratio);
- } else if (angle < LEFT_RESIDUE_MAX_ANGLE) {
- double ratio = (angle - TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY() + species.getHeight() * (ratio);
- x = species.getX();
- } else if (angle < BOTTOM_RESIDUE_MAX_ANGLE) {
- double ratio = (angle - LEFT_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY() + species.getHeight();
- x = species.getX() + species.getWidth() * ratio;
- } else if (angle <= 2 * PI + Configuration.EPSILON) {
- double ratio = (angle - BOTTOM_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY() + species.getHeight() * (1 - ratio);
- x = species.getX() + species.getWidth();
- } else {
- throw new InvalidStateException();
- }
- Point2D center = species.getCenter();
- double correctedAngle = -Math.atan2((y - center.getY()), (x - center.getX()));
- result = getPointCoordinatesOnBorder(species, correctedAngle);
- }
- return result;
-
- }
-
/**
* Returns coordinates on the {@link Element} border for given angle.
- *
+ *
* @param elemnt
* {@link Element} on border which the point is looked for
* @param angle
@@ -352,44 +398,6 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
}
- @Override
- public Double getAngleForPoint(T element, Point2D position) {
- double result = -1;
- Point2D pointOnBorder = getClosestPositionOnBorder(element, position);
-
- double epsilon = Configuration.EPSILON;
- double distanceRight = Math.abs(pointOnBorder.getX() - element.getX() - element.getWidth());
- double distanceTop = Math.abs(pointOnBorder.getY() - element.getY());
- double distanceLeft = Math.abs(pointOnBorder.getX() - element.getX());
- double distanceBottom = Math.abs(pointOnBorder.getY() - element.getY() - element.getHeight());
-
- double minDist = Math.min(Math.min(distanceLeft, distanceRight), Math.min(distanceTop, distanceBottom));
-
- if (distanceRight == minDist &&
- pointOnBorder.getY() - element.getY() - element.getHeight() / 2 < epsilon) {
- double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
- result = (ratio - 0.5) * (PI / 2);
- } else if (distanceTop == minDist) {
- double ratio = 1 - (pointOnBorder.getX() - element.getX()) / element.getWidth();
- result = ratio * (PI / 2) + RIGHT_TOP_RESIDUE_MAX_ANGLE;
- } else if (distanceLeft == minDist) {
- double ratio = (pointOnBorder.getY() - element.getY()) / element.getHeight();
- result = ratio * (PI / 2) + TOP_RESIDUE_MAX_ANGLE;
- } else if (distanceBottom == minDist) {
- double ratio = (pointOnBorder.getX() - element.getX()) / element.getWidth();
- result = ratio * (PI / 2) + LEFT_RESIDUE_MAX_ANGLE;
- } else if (distanceRight == minDist &&
- pointOnBorder.getY() - element.getY() - element.getHeight() < epsilon) {
- double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
- result = ratio * (PI / 2) + BOTTOM_RESIDUE_MAX_ANGLE;
- } else {
- result = PI / 2;
- logger.warn("Problem with finding angle. Using default");
- }
-
- return result;
- }
-
private Point2D getClosestPositionOnBorder(T element, Point2D position) {
double correctedAngle = -Math.atan2((position.getY() - element.getCenterY()),
(position.getX() - element.getCenterX()));
@@ -414,29 +422,4 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
return pointOnBorder;
}
- @Override
- public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
- return null;
- }
-
- @Override
- public Point2D getCoordinatesByPosition(Element element, Double pos) {
- return this.getCoordinatesByPosition(element, pos, 0.0);
- }
-
- @Override
- public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
- throw new NotImplementedException("Not implemented for: " + this.getClass());
- }
-
- @Override
- public Double getCellDesignerSize(ModificationResidue mr) {
- throw new NotImplementedException("Not implemented for: " + this.getClass());
- }
-
- @Override
- public Double getWidthBySize(Element element, Double size) {
- throw new NotImplementedException("Not implemented for: " + this.getClass());
- }
-
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
index 613c3b51b2..a30af25d86 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
@@ -1,9 +1,6 @@
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.awt.geom.*;
import java.util.ArrayList;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -22,9 +19,15 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
*/
public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<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 sbgn
* Should the converter use sbgn standard
*/
@@ -32,12 +35,6 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
super(sbgn);
}
- /**
- * How big should be the arc in rectangle for nucleic acid feature
- * representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
@Override
public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
if (invalidAnchorPosition(alias, anchor)) {
@@ -51,6 +48,32 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
}
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return (mr.getPosition().getX() - mr.getSpecies().getX()) / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
+ double x = element.getX() + element.getWidth() * 3.0 / 4.0 * pos;
+ x = Math.max(element.getX() + width / 2, x);
+ x = Math.min(element.getX() + element.getWidth() * 3.0 / 4.0 - width / 2, x);
+ return new Point2D.Double(x, element.getY());
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ if (mr instanceof AbstractRegionModification) {
+ return ((AbstractRegionModification) mr).getWidth() / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+ throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ return size * (element.getWidth() * 3.0 / 4.0);
+ }
+
@Override
protected PathIterator getBoundPathIterator(Species alias) {
return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
@@ -58,7 +81,7 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
/**
* Returns shape of the AntisenseRna 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
@@ -85,7 +108,7 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
/**
* Returns shape of the AntisenseRna as a GeneralPath object.
- *
+ *
* @param alias
* alias for which we are looking for a border
* @return GeneralPath object defining border of the given alias
@@ -117,30 +140,4 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
return path;
}
- @Override
- public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
- return (mr.getPosition().getX() - mr.getSpecies().getX()) / (mr.getSpecies().getWidth() * 3.0 / 4.0);
- }
-
- @Override
- public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
- double x = element.getX() + element.getWidth() * 3.0 / 4.0 * pos;
- x = Math.max(element.getX() + width / 2, x);
- x = Math.min(element.getX() + element.getWidth() * 3.0 / 4.0 - width / 2, x);
- return new Point2D.Double(x, element.getY());
- }
-
- @Override
- public Double getCellDesignerSize(ModificationResidue mr) {
- if (mr instanceof AbstractRegionModification) {
- return ((AbstractRegionModification) mr).getWidth() / (mr.getSpecies().getWidth() * 3.0 / 4.0);
- }
- throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
- }
-
- @Override
- public Double getWidthBySize(Element element, Double size) {
- return size * (element.getWidth() * 3.0 / 4.0);
- }
-
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
index 6fd5c93ca8..16f9f42479 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
@@ -2,24 +2,14 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.Point2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.model.graphics.PolylineData;
-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.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.Unknown;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -43,11 +33,28 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
* Class helping with transforming objects into meaningful identifiers.
*/
private static ElementUtils eu = new ElementUtils();
+ /**
+ * Converter used for operations on the {@link Element} given in constructor.
+ */
+ @SuppressWarnings("rawtypes")
+ private ICellDesignerAliasConverter converter = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ * @param element
+ * element for which this converter will be used
+ */
+ public CellDesignerAliasConverter(Element element, boolean sbgn) {
+ converter = getConverterForAlias(element, sbgn);
+ }
/**
* Returns a converter for given {@link Element}. If converter doesn't exist
* exception is thrown.
- *
+ *
* @param element
* element for which we are looking for a converter
* @param sbgn
@@ -85,24 +92,6 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
}
}
- /**
- * Converter used for operations on the {@link Element} given in constructor.
- */
- @SuppressWarnings("rawtypes")
- private ICellDesignerAliasConverter converter = null;
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use SBGN standard
- * @param element
- * element for which this converter will be used
- */
- public CellDesignerAliasConverter(Element element, boolean sbgn) {
- converter = getConverterForAlias(element, sbgn);
- }
-
@SuppressWarnings("unchecked")
@Override
public CellDesignerAnchor getAnchorForCoordinates(Element element, Point2D point) {
@@ -123,14 +112,14 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
@SuppressWarnings("unchecked")
@Override
- public Double getAngleForPoint(Element element, Point2D position) {
- return converter.getAngleForPoint(element, position);
+ public Point2D getResidueCoordinates(Element species, double angle) {
+ return converter.getResidueCoordinates(species, angle);
}
@SuppressWarnings("unchecked")
@Override
- public Point2D getResidueCoordinates(Element species, double angle) {
- return converter.getResidueCoordinates(species, angle);
+ public Double getAngleForPoint(Element element, Point2D position) {
+ return converter.getAngleForPoint(element, position);
}
@Override
@@ -143,6 +132,11 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
return converter.getCoordinatesByPosition(element, pos);
}
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
+ return converter.getCoordinatesByPosition(element, pos, width);
+ }
+
@Override
public Double getCellDesignerSize(ModificationResidue mr) {
return converter.getCellDesignerSize(mr);
@@ -153,9 +147,4 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
return converter.getWidthBySize(element, size);
}
- @Override
- public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
- return converter.getCoordinatesByPosition(element, pos, width);
- }
-
}
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 f3de602426..6061140387 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
@@ -1,13 +1,10 @@
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.awt.geom.*;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Class that provides CellDesigner specific graphical information for
@@ -18,53 +15,54 @@ import lcsb.mapviewer.model.map.species.Complex;
*/
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;
- /**
- * How big is the triangle trimmed part of the complex.
- */
- private static final int TRIMMED_CORNER_SIZE = 5;
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected ComplexCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
- @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 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());
- }
+ @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;
- }
+ /**
+ * 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 3c3a031e06..b76fb57f5f 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
@@ -17,91 +17,91 @@ import lcsb.mapviewer.model.map.species.Species;
*/
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;
- /**
- * Part of height of the line used to cross degraded circle that goes behind
- * this circle.
- */
- private static final int DEGRADED_MARGIN = 7;
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected DegradedCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
- @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();
- }
+ @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);
- }
+ 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;
- }
+ @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;
- /**
- * 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 PathIterator getBoundPathIterator(Species alias) {
+ throw new NotImplementedException("This class doesn't have bound");
+ }
- @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;
+ /**
+ * 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;
+ }
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- throw new NotImplementedException("This class doesn't have bound");
- }
+ /**
+ * 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;
+ }
}
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 837c81674f..50ea67ccec 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
@@ -1,10 +1,7 @@
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.awt.*;
+import java.awt.geom.*;
import java.util.ArrayList;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -20,73 +17,74 @@ import lcsb.mapviewer.model.map.species.Species;
*/
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;
- /**
- * How big should be the arc in rectangle for drug representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected DrugCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- ArrayList<Point2D> list = getDrugPoints(alias);
+ @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);
- }
+ return getPolygonTransformation().getPointOnPolygonByAnchor(list, anchor);
+ }
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return getDrugShape(alias).getPathIterator(new AffineTransform());
- }
+ @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>();
+ /**
+ * 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();
+ 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;
- }
+ // 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);
- }
+ /**
+ * 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/GeneCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
index ca1c3240d1..42f1a5d048 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
@@ -1,13 +1,10 @@
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.Rectangle2D;
+import java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -25,6 +22,11 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
*/
public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Gene> {
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
/**
* Default class logger
*/
@@ -33,7 +35,7 @@ public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
/**
* Default constructor.
- *
+ *
* @param sbgn
* Should the converter use SBGN standard
*/
@@ -41,12 +43,6 @@ public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
super(sbgn);
}
- /**
- * How big should be the arc in rectangle for nucleic acid feature
- * representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
@Override
public Point2D getPointCoordinates(Gene alias, CellDesignerAnchor anchor) {
if (invalidAnchorPosition(alias, anchor)) {
@@ -56,34 +52,6 @@ public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
alias.getHeight(), anchor);
}
- /**
- * Shape representation of the gene alias.
- *
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
- */
- private Shape getGeneShape(Element alias) {
- if (!isSbgn()) {
- Shape shape;
- shape = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
- return shape;
- } else {
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
- y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- return path;
- }
- }
-
@Override
public PathIterator getBoundPathIterator(Gene alias) {
return getGeneShape(alias).getPathIterator(new AffineTransform());
@@ -120,4 +88,32 @@ public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
return size * element.getWidth();
}
+ /**
+ * Shape representation of the gene alias.
+ *
+ * @param alias
+ * alias for which we are looking for a Shape
+ * @return Shape object that represents alias
+ */
+ private Shape getGeneShape(Element alias) {
+ if (!isSbgn()) {
+ Shape shape;
+ shape = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ return shape;
+ } else {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
+ y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ return path;
+ }
+ }
+
}
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 50d1975f81..dc97aa6f44 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -43,9 +44,41 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
}
+ @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;
+
+ }
+
/**
* 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
@@ -57,7 +90,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
/**
* Returns transformed x coordinate for the ion alias.
- *
+ *
* @param alias
* object alias to to which we are looking for x coordinate
* @param diameter
@@ -71,7 +104,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
/**
* Returns diameter of the ion alias.
- *
+ *
* @param alias
* object alias to to which we are looking for diameter.
* @return diameter of the alias
@@ -83,36 +116,4 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
}
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 c09fbbb901..861323e2c5 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
@@ -1,9 +1,6 @@
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.awt.geom.*;
import java.util.ArrayList;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -19,76 +16,76 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class PhenotypeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected PhenotypeCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
+ /**
+ * 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);
- }
+ @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>();
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getPhenotypePath(alias).getPathIterator(new AffineTransform());
+ }
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
+ /**
+ * 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>();
- // 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;
- }
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- return getPhenotypePath(alias).getPathIterator(new AffineTransform());
- }
+ // 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;
+ }
- /**
- * 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;
- }
+ /**
+ * 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 858ca69689..fb8886282b 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
@@ -1,23 +1,15 @@
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.awt.*;
+import java.awt.geom.*;
import java.util.ArrayList;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.model.map.species.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -29,203 +21,207 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
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 = LogManager.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;
- }
+ /**
+ * How big should be the arc in rectangle for generic protein representation.
+ */
+ private static final int GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE = 10;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(ProteinCellDesignerAliasConverter.class);
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected ProteinCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @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 bd221e7175..3c412c80da 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
@@ -8,16 +8,15 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
*
*/
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;
+ /**
+ * 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 instantiation.
- */
- protected ReactionCellDesignerConverter() {
+ /**
+ * Default constructor that prevents instantiation.
+ */
+ protected ReactionCellDesignerConverter() {
- }
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
index 6223bf05ed..590880394c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
@@ -1,12 +1,10 @@
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.awt.geom.*;
import java.util.ArrayList;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -24,6 +22,11 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
*/
public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
/**
* Default class logger
*/
@@ -32,7 +35,7 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
/**
* Default constructor.
- *
+ *
* @param sbgn
* Should the converter use sbgn standard
*/
@@ -40,12 +43,6 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
super(sbgn);
}
- /**
- * How big should be the arc in rectangle for nucleic acid feature
- * representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
@Override
public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
if (invalidAnchorPosition(alias, anchor)) {
@@ -64,9 +61,37 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
return getRnaPath(alias).getPathIterator(new AffineTransform());
}
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return (mr.getPosition().getX() - mr.getSpecies().getX() - mr.getSpecies().getWidth() / 4.0)
+ / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double modificationWidth) {
+ double x = element.getX() + element.getWidth() / 4.0 + element.getWidth() * 3.0 / 4.0 * pos;
+ x = Math.max(element.getX() + modificationWidth / 2, x);
+ x = Math.min(element.getX() + element.getWidth() - modificationWidth / 2, x);
+
+ return new Point2D.Double(x, element.getY());
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ if (mr instanceof AbstractRegionModification) {
+ return ((AbstractRegionModification) mr).getWidth() / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+ throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ return size * (element.getWidth() * 3.0 / 4.0);
+ }
+
/**
* Returns shape of the Rna 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
@@ -92,7 +117,7 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
/**
* Returns shape of the Rna as a GeneralPath object.
- *
+ *
* @param alias
* alias for which we are looking for a border
* @return GeneralPath object defining border of the given alias
@@ -124,32 +149,4 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
return path;
}
- @Override
- public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
- return (mr.getPosition().getX() - mr.getSpecies().getX() - mr.getSpecies().getWidth() / 4.0)
- / (mr.getSpecies().getWidth() * 3.0 / 4.0);
- }
-
- @Override
- public Point2D getCoordinatesByPosition(Element element, Double pos, Double modificationWidth) {
- double x = element.getX() + element.getWidth() / 4.0 + element.getWidth() * 3.0 / 4.0 * pos;
- x = Math.max(element.getX() + modificationWidth / 2, x);
- x = Math.min(element.getX() + element.getWidth() - modificationWidth / 2, x);
-
- return new Point2D.Double(x, element.getY());
- }
-
- @Override
- public Double getCellDesignerSize(ModificationResidue mr) {
- if (mr instanceof AbstractRegionModification) {
- return ((AbstractRegionModification) mr).getWidth() / (mr.getSpecies().getWidth() * 3.0 / 4.0);
- }
- throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
- }
-
- @Override
- public Double getWidthBySize(Element element, Double size) {
- return size * (element.getWidth() * 3.0 / 4.0);
- }
-
}
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 979e7516ca..0d5eef9b9b 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
index 8dd5e721e7..a3dd0508fd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -40,11 +41,6 @@ public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAlias
alias.getHeight(), anchor);
}
- @Override
- public PathIterator getBoundPathIterator(Unknown alias) {
- throw new NotImplementedException("This class doesn't provide boundPath");
- }
-
@Override
public Point2D getAnchorPointCoordinates(Unknown alias, double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
@@ -57,6 +53,11 @@ public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAlias
}
+ @Override
+ public PathIterator getBoundPathIterator(Unknown alias) {
+ throw new NotImplementedException("This class doesn't provide boundPath");
+ }
+
@Override
public Point2D getPointCoordinatesOnBorder(Unknown unknown, final double angle) {
if (unknown.getWidth() == 0 && unknown.getHeight() == 0) {
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 374f3c09f8..84d822932b 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
@@ -2,9 +2,10 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
import java.awt.geom.Point2D;
-import lcsb.mapviewer.common.geometry.EllipseTransformation;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.*;
+import lcsb.mapviewer.common.geometry.EllipseTransformation;
/**
* This class contains basic operators on ellipse used by CellDesigner
@@ -14,35 +15,36 @@ import org.apache.logging.log4j.*;
*
*/
public class CellDesignerEllipseTransformation extends EllipseTransformation {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(CellDesignerEllipseTransformation.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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) {
+ /**
+ * 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);
- }
- }
+ 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/CellDesignerPointTransformation.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformation.java
index 3092a74500..9df531f3da 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
@@ -2,9 +2,10 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
import java.awt.geom.Point2D;
-import lcsb.mapviewer.common.geometry.PointTransformation;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.*;
+import lcsb.mapviewer.common.geometry.PointTransformation;
/**
* Class for basic point transformations.
@@ -13,78 +14,80 @@ import org.apache.logging.log4j.*;
*
*/
public class CellDesignerPointTransformation extends PointTransformation {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(CellDesignerPointTransformation.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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();
+ /**
+ * 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 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();
+ 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);
+ Point2D pointO = new Point2D.Double(x, y);
- return pointO;
- }
+ 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();
+ /**
+ * 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 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);
+ 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);
+ Point2D pointP = new Point2D.Double(x, y);
- return pointP;
- }
+ 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 8bee6c829d..4252bc66ea 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
import java.awt.geom.Point2D;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -14,97 +15,100 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*
*/
public class CellDesignerPolygonTransformation {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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);
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(CellDesignerPolygonTransformation.class.getName());
- /**
- * 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());
- }
- }
+ /**
+ * 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);
+ }
- /**
- * 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());
- }
+ /**
+ * 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());
+ }
+ }
- /**
- * 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)));
- }
- }
- }
+ /**
+ * 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 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));
- }
- }
+ /**
+ * 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 bd8b5a3b48..05cee016fc 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
import java.awt.geom.Point2D;
import java.util.ArrayList;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Class with basic operations on rectangles.
@@ -13,46 +14,46 @@ import org.apache.logging.log4j.*;
*/
public class CellDesignerRectangleTransformation {
- /**
- * Object used for transformation on the polygons.
- */
- private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(CellDesignerRectangleTransformation.class.getName());
+ /**
+ * Object used for transformation on the polygons.
+ */
+ private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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);
- }
+ /**
+ * 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/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/package-info.java
index b164954ded..bf898d1af1 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
@@ -3,4 +3,3 @@
* 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 7ac605eb0d..14b5292d68 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
@@ -3,4 +3,3 @@
* 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 89e84c422f..4a5fe50d25 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
@@ -5,4 +5,3 @@
* 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/parameter/ParameterCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java
index 8629a24939..ef8a4522d8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.parameter;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java
index 18cbbca16b..507e157ba6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.parameter;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
@@ -41,7 +42,7 @@ public class ParameterXmlParser {
result.append("units=\"" + sbmlFunction.getUnits().getUnitId() + "\" ");
}
result.append("/>");
-
+
return result.toString();
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
index 13c5b6cb0c..d3447cbb08 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
@@ -1,10 +1,9 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
@@ -12,9 +11,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
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 7920cc77f9..667adf9184 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
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 8f26b3efad..8fdfaeaf59 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
@@ -1,14 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
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 java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -16,51 +9,20 @@ 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.common.exception.*;
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.converter.model.celldesigner.geometry.helper.*;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.*;
+import lcsb.mapviewer.converter.model.celldesigner.types.*;
+import lcsb.mapviewer.model.graphics.*;
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.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.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -82,70 +44,58 @@ public class ReactionFromXml {
* Product lines in cell designer starts in the 3/5 of the center line.
*/
private static final double PRODUCT_START_RATIO = 0.6;
-
+ CellDesignerElementCollection elements;
/**
* 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<>();
-
/**
* Stores information about list of points that create line describing modifier.
*/
private Map<ReactionNode, LineProperties> linePropertiesByModifier = 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 = LogManager.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.
*
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 aeb24d7470..d94b022ec7 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
@@ -6,32 +6,7 @@ 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.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;
+import lcsb.mapviewer.model.map.reaction.type.*;
/**
* This class represent graphical information about lines/arrows that are
@@ -187,33 +162,39 @@ public enum ReactionLineData {
*/
UNKNOWN_TRANSITION(UnknownTransitionReaction.class, "UNKNOWN_TRANSITION");
+ /**
+ * 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;
/**
* {@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
@@ -225,7 +206,7 @@ public enum ReactionLineData {
}
/**
- *
+ *
* @param clazz
* {@link #reactionClass}
* @param cellDesignerString
@@ -238,7 +219,7 @@ public enum ReactionLineData {
}
/**
- *
+ *
* @param clazz
* {@link #reactionClass}
* @param cellDesignerString
@@ -254,7 +235,7 @@ public enum ReactionLineData {
}
/**
- *
+ *
* @param clazz
* {@link #reactionClass}
* @param cellDesignerString
@@ -275,6 +256,64 @@ public enum ReactionLineData {
this.cellDesignerString = cellDesignerString;
}
+ /**
+ * 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);
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Returns {@link ReactionLineData} that can be applied 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 applied 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;
+ }
+
/**
* @return the reactionClass
* @see #reactionClass
@@ -307,35 +346,6 @@ public enum ReactionLineData {
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
@@ -344,29 +354,10 @@ public enum ReactionLineData {
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
@@ -381,26 +372,4 @@ public enum ReactionLineData {
}
}
- /**
- * Returns {@link ReactionLineData} that can be applied 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 applied 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/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index f374f0fe2c..fe18a84c30 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
@@ -1,12 +1,7 @@
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.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -20,30 +15,13 @@ 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.geometry.helper.PolylineDataFactory;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.*;
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.converter.model.celldesigner.types.*;
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.AndOperator;
-import lcsb.mapviewer.model.map.reaction.AssociationOperator;
-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.reaction.type.ReducedNotation;
-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.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -531,7 +509,8 @@ public class ReactionToXml {
if (!(operator instanceof AndOperator || operator instanceof AssociationOperator
|| !operator.isReactantOperator())) {
return "BOOLEAN_LOGIC_GATE";
- } else if (operator instanceof AndOperator && operator.isReactantOperator() && reaction instanceof ReducedNotation) {
+ } else if (operator instanceof AndOperator && operator.isReactantOperator()
+ && reaction instanceof ReducedNotation) {
// check the geometry - we might need to use BOOLEAN_LOGIC_GATE if the joining
// point is not colinear with first reactant line and operator line
AbstractNode firstReactant = operator.getInputs().get(0);
@@ -703,7 +682,7 @@ public class ReactionToXml {
sb.append(getAnchorXml(alias, reactant.getLine().getBeginPoint()));
- sb.append(getConnectSchemeXmlStringForLines(new PolylineData[] {reactant.getLine()}));
+ sb.append(getConnectSchemeXmlStringForLines(new PolylineData[] { reactant.getLine() }));
sb.append(getEditPointsXmlStringForLine(new PolylineData[] { reactant.getLine() }, 0));
sb.append("<celldesigner:line ");
sb.append("width=\"" + reactant.getLine().getWidth() + "\" ");
@@ -998,16 +977,16 @@ public class ReactionToXml {
}
int centerPosition = reactant.getLine().getPoints().size() - 1;
PolylineData productLine = getLineBeforeTrimming(product);
-
+
PolylineData testLine = new PolylineData();
- testLine.addPoint(reactant.getLine().getPoints().get(reactant.getLine().getPoints().size()-2));
- testLine.addPoint(reactant.getLine().getPoints().get(reactant.getLine().getPoints().size()-1));
+ testLine.addPoint(reactant.getLine().getPoints().get(reactant.getLine().getPoints().size() - 2));
+ testLine.addPoint(reactant.getLine().getPoints().get(reactant.getLine().getPoints().size() - 1));
testLine.addPoint(productLine.getPoints().get(0));
testLine.addPoint(productLine.getPoints().get(1));
testLine = PolylineDataFactory.removeCollinearPoints(testLine);
- if (testLine.getPoints().size()>2) {
- points.add(reactant.getLine().getPoints().get(reactant.getLine().getPoints().size()-1));
- centerPosition ++;
+ if (testLine.getPoints().size() > 2) {
+ points.add(reactant.getLine().getPoints().get(reactant.getLine().getPoints().size() - 1));
+ centerPosition++;
points.add(productLine.getPoints().get(0));
}
for (int i = 1; i < productLine.getPoints().size(); i++) {
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 36ce6ae460..8b99762b00 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
@@ -19,57 +19,57 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
*/
public class ReactionXmlParser {
- /**
- * Class that allows to export data into CellDesigner xml node.
- */
- private ReactionToXml reactionToXml;
+ /**
+ * 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;
+ /**
+ * 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);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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/UnknownModifierClassException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassException.java
index 160c69da42..934aaea362 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
@@ -9,46 +9,46 @@ package lcsb.mapviewer.converter.model.celldesigner.reaction;
*/
public class UnknownModifierClassException extends ReactionParserException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Type of reaction that was a reason for this exception.
- */
- private String modificationType;
+ /**
+ * 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;
- }
+ /**
+ * 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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 3a0bc37998..bb86585488 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
@@ -3,4 +3,3 @@
* {@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/AbstractElementXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
index 4b4c18b2ff..57088e7a92 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
@@ -3,10 +3,9 @@ package lcsb.mapviewer.converter.model.celldesigner.species;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
@@ -48,21 +47,6 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
*/
private RestAnnotationParser rap = new RestAnnotationParser();
- /**
- * Method that parses CellDesigner xml node and translate it into object.
- * Returns a {@link Pair} containing CellDesigner identifier in
- * {@link Pair#getLeft()} and element in {@link Pair#getRight()}.
- *
- * @param node
- * xml node be parsed
- * @return {@link Pair} containing CellDesigner identifier in {@link Pair#getLeft()}
- * and element parsed from xml node in {@link Pair#getRight()}.
- * @throws InvalidXmlSchemaException
- * thrown when xml is invalid
- * @throws CompartmentParserException
- */
- public abstract Pair<String, T> parseXmlElement(Node node) throws InvalidXmlSchemaException, CellDesignerParserException;
-
/**
* Default constructor.
*/
@@ -124,6 +108,23 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
encodedStrings.add(new Pair<String, String>("_omega_", "ω"));
}
+ /**
+ * Method that parses CellDesigner xml node and translate it into object.
+ * Returns a {@link Pair} containing CellDesigner identifier in
+ * {@link Pair#getLeft()} and element in {@link Pair#getRight()}.
+ *
+ * @param node
+ * xml node be parsed
+ * @return {@link Pair} containing CellDesigner identifier in
+ * {@link Pair#getLeft()} and element parsed from xml node in
+ * {@link Pair#getRight()}.
+ * @throws InvalidXmlSchemaException
+ * thrown when xml is invalid
+ * @throws CompartmentParserException
+ */
+ public abstract Pair<String, T> parseXmlElement(Node node)
+ throws InvalidXmlSchemaException, CellDesignerParserException;
+
/**
* Parses CellDEsigner xml node that is given as a plain text into element.
* Returns a {@link Pair} containing CellDesigner identifier in
@@ -131,13 +132,15 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
*
* @param xmlString
* node to parse
- * @return {@link Pair} containing CellDesigner identifier in {@link Pair#getLeft()}
- * and element parsed from xml node in {@link Pair#getRight()}.
+ * @return {@link Pair} containing CellDesigner identifier in
+ * {@link Pair#getLeft()} and element parsed from xml node in
+ * {@link Pair#getRight()}.
* @throws InvalidXmlSchemaException
* thrown when xmlString is invalid
- * @throws CellDesignerParserException
+ * @throws CellDesignerParserException
*/
- public Pair<String, T> parseXmlElement(String xmlString) throws InvalidXmlSchemaException, CellDesignerParserException {
+ public Pair<String, T> parseXmlElement(String xmlString)
+ throws InvalidXmlSchemaException, CellDesignerParserException {
Document doc = XmlParser.getXmlDocumentFromString(xmlString);
NodeList root = doc.getChildNodes();
return parseXmlElement(root.item(0));
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
index 45005aeaed..3365b858a8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
@@ -1,11 +1,12 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
index 1a3fbbfc96..913c6a0ec4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
@@ -1,11 +1,12 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -85,9 +86,38 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
return new Pair<String, CellDesignerGene>(identifier, gene);
}
+ @Override
+ public String toXml(Gene gene) {
+ String attributes = "";
+ String result = "";
+ attributes += " id=\"g_" + elements.getElementId(gene) + "\"";
+ if (!gene.getName().equals("")) {
+ attributes += " name=\"" + XmlParser.escapeXml(encodeName(gene.getName())) + "\"";
+ }
+ result += "<celldesigner:gene" + attributes + ">";
+ result += "<celldesigner:notes>";
+ result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
+ RestAnnotationParser rap = new RestAnnotationParser();
+ result += rap.createAnnotationString(gene);
+ result += gene.getNotes();
+ result += "</body></html>";
+ result += "</celldesigner:notes>";
+
+ if (gene.getModificationResidues().size() > 0) {
+ result += "<celldesigner:listOfRegions>\n";
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ result += modificationResidueXmlParser.toXml(mr);
+ }
+ result += "</celldesigner:listOfRegions>\n";
+ }
+
+ result += "</celldesigner:gene>";
+ return result;
+ }
+
/**
* Parse modification for a gene.
- *
+ *
* @param residueNode
* source xml node
* @return object representing modification
@@ -118,33 +148,4 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
return residue;
}
- @Override
- public String toXml(Gene gene) {
- String attributes = "";
- String result = "";
- attributes += " id=\"g_" + elements.getElementId(gene) + "\"";
- if (!gene.getName().equals("")) {
- attributes += " name=\"" + XmlParser.escapeXml(encodeName(gene.getName())) + "\"";
- }
- result += "<celldesigner:gene" + attributes + ">";
- result += "<celldesigner:notes>";
- result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
- RestAnnotationParser rap = new RestAnnotationParser();
- result += rap.createAnnotationString(gene);
- result += gene.getNotes();
- result += "</body></html>";
- result += "</celldesigner:notes>";
-
- if (gene.getModificationResidues().size() > 0) {
- result += "<celldesigner:listOfRegions>\n";
- for (ModificationResidue mr : gene.getModificationResidues()) {
- result += modificationResidueXmlParser.toXml(mr);
- }
- result += "</celldesigner:listOfRegions>\n";
- }
-
- result += "</celldesigner:gene>";
- return result;
- }
-
}
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 26770e3b4a..0c97522c1b 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
@@ -1,25 +1,13 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import lcsb.mapviewer.converter.model.celldesigner.structure.*;
/**
* This class contains information about all species in model that are relevant
@@ -30,185 +18,185 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown
*/
public class InternalModelSpeciesData {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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/ModificationResidueXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
index 36be726939..c2322a5dbb 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
@@ -9,18 +9,8 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
-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.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.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
public class ModificationResidueXmlParser {
@@ -92,7 +82,8 @@ public class ModificationResidueXmlParser {
* because we have to merge elements when exporting to CellDesigner and this
* might introduce inconsistent identifiers.
*
- * @param region {@link ModificationResidue} for which we want to find out identifier
+ * @param region
+ * {@link ModificationResidue} for which we want to find out identifier
* @return identifier that can be used in CellDesigner
*/
private String computeModificationResidueId(ModificationResidue region) {
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 67dc601b64..8463544ddc 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
@@ -1,18 +1,11 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import lcsb.mapviewer.converter.model.celldesigner.structure.*;
+import lcsb.mapviewer.model.map.species.*;
/**
* This enum contains information about mapping between CellDesigner xml nodes
@@ -23,133 +16,131 @@ import lcsb.mapviewer.model.map.species.TruncatedProtein;
*/
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 = LogManager.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);
- }
- }
+ /**
+ * {@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");
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(ProteinMapping.class);
+ /**
+ * CellDesigner xml node type.
+ */
+ private String cellDesignerString;
+ /**
+ * Model class that should be used to represent cell designer node.
+ */
+ private Class<? extends Protein> clazz;
+ /**
+ * {@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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * 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/ProteinXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
index 4066b611b6..019ca19c7d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
@@ -3,12 +3,13 @@ package lcsb.mapviewer.converter.model.celldesigner.species;
import java.util.ArrayList;
import java.util.List;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -17,9 +18,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.field.BindingRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Class that performs parsing of the CellDesigner xml for
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
index 3520d7bae2..afc3f7e985 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
@@ -1,11 +1,12 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.annotation.RestAnnotationParser;
@@ -85,34 +86,6 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
return new Pair<String, CellDesignerRna>(identifier, rna);
}
- /**
- * Parses CellDesigner xml node for RnaRegion.
- *
- * @param residueNode
- * xml node to parse
- * @return {@link CellDesignerModificationResidue} object created from the node
- * @throws InvalidXmlSchemaException
- * thrown when input xml node doesn't follow defined schema
- */
- private CellDesignerModificationResidue getRnaRegion(Node residueNode) throws InvalidXmlSchemaException {
- CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
- residue.setIdModificationResidue(XmlParser.getNodeAttr("id", residueNode));
- residue.setSize(XmlParser.getNodeAttr("size", residueNode));
- residue.setPos(XmlParser.getNodeAttr("pos", residueNode));
- String typeString = XmlParser.getNodeAttr("type", residueNode);
- if (typeString != null) {
- residue.setModificationType(ModificationType.getByCellDesignerName(typeString));
- }
- NodeList list = residueNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
- }
- }
- return residue;
- }
-
@Override
public String toXml(Rna rna) {
String attributes = "";
@@ -142,4 +115,32 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
return result;
}
+ /**
+ * Parses CellDesigner xml node for RnaRegion.
+ *
+ * @param residueNode
+ * xml node to parse
+ * @return {@link CellDesignerModificationResidue} object created from the node
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ private CellDesignerModificationResidue getRnaRegion(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ residue.setIdModificationResidue(XmlParser.getNodeAttr("id", residueNode));
+ residue.setSize(XmlParser.getNodeAttr("size", residueNode));
+ residue.setPos(XmlParser.getNodeAttr("pos", residueNode));
+ String typeString = XmlParser.getNodeAttr("type", residueNode);
+ if (typeString != null) {
+ residue.setModificationType(ModificationType.getByCellDesignerName(typeString));
+ }
+ NodeList list = residueNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
+
}
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 731647113e..3326eb4223 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
@@ -1,11 +1,9 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
@@ -25,149 +23,149 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies
*/
public class SpeciesCollection<C extends CellDesignerSpecies<?>> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.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;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.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/SpeciesCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
index fcec0ffa91..c7647412b1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
@@ -1,10 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -18,20 +14,9 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
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.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-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.converter.model.celldesigner.structure.*;
import lcsb.mapviewer.model.map.InconsistentModelException;
-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.*;
/**
* Class used to parse CellDesigner xml nodes containing collections of
@@ -88,8 +73,9 @@ public class SpeciesCollectionXmlParser {
*/
private AbstractElementXmlParser<CellDesignerElement<?>, Element> helpParser = new AbstractElementXmlParser<CellDesignerElement<?>, Element>() {
@Override
- public String encodeName(String name) {
- return super.encodeName(name);
+ public Pair<String, CellDesignerElement<?>> parseXmlElement(Node node)
+ throws InvalidXmlSchemaException {
+ throw new NotImplementedException();
}
@Override
@@ -98,9 +84,8 @@ public class SpeciesCollectionXmlParser {
}
@Override
- public Pair<String, CellDesignerElement<?>> parseXmlElement(Node node)
- throws InvalidXmlSchemaException {
- throw new NotImplementedException();
+ public String encodeName(String name) {
+ return super.encodeName(name);
}
};
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
index c086811d0c..c16ecad2f3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
@@ -1,30 +1,8 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
import lcsb.mapviewer.common.exception.InvalidStateException;
-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;
-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.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.Unknown;
+import lcsb.mapviewer.converter.model.celldesigner.structure.*;
+import lcsb.mapviewer.model.map.species.*;
/**
* This enum contains information about mapping between CellDesigner xml nodes
@@ -121,14 +99,35 @@ public enum SpeciesMapping {
}
/**
- * Sets new cellDesignerClazz value.
- *
- * @param cellDesignerClazz2
- * new cellDesignerClazz value
+ * Returns {@link SpeciesMapping} for given CellDesigner xml node name.
+ *
+ * @param string
+ * CellDesigner xml node name
+ * @return {@link SpeciesMapping} for given CellDesigner xml node name
*/
- @SuppressWarnings("unchecked")
- private void setCellDesignerClazz(Class<?> cellDesignerClazz2) {
- cellDesignerClazz = (Class<? extends CellDesignerSpecies<?>>) cellDesignerClazz2;
+ public static SpeciesMapping getMappingByString(String string) {
+ for (SpeciesMapping mapping : SpeciesMapping.values()) {
+ if (mapping.getCellDesignerString().equalsIgnoreCase(string)) {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@link SpeciesMapping} for given {@link CellDesignerSpecies} class.
+ *
+ * @param searchClazz
+ * {@link CellDesignerSpecies} class
+ * @return {@link SpeciesMapping} for given {@link CellDesignerSpecies} class
+ */
+ public static SpeciesMapping getMappingByModelClass(Class<? extends Element> searchClazz) {
+ for (SpeciesMapping mapping : SpeciesMapping.values()) {
+ if (mapping.getModelClazz().isAssignableFrom(searchClazz)) {
+ return mapping;
+ }
+ }
+ return null;
}
/**
@@ -147,9 +146,20 @@ public enum SpeciesMapping {
return cellDesignerClazz;
}
+ /**
+ * Sets new cellDesignerClazz value.
+ *
+ * @param cellDesignerClazz2
+ * new cellDesignerClazz value
+ */
+ @SuppressWarnings("unchecked")
+ private void setCellDesignerClazz(Class<?> cellDesignerClazz2) {
+ cellDesignerClazz = (Class<? extends CellDesignerSpecies<?>>) cellDesignerClazz2;
+ }
+
/**
* Returns model class that represent the species.
- *
+ *
* @return model class that represent the species
*/
public Class<? extends Element> getModelClazz() {
@@ -159,7 +169,7 @@ public enum SpeciesMapping {
/**
* Creates instance of {@link CellDesignerSpecies} specific for this
* {@link SpeciesMapping}.
- *
+ *
* @param result
* parameter that should be passed to the constructor
* @return new instance of {@link CellDesignerSpecies} specific for this
@@ -172,36 +182,4 @@ public enum SpeciesMapping {
throw new InvalidStateException(e);
}
}
-
- /**
- * Returns {@link SpeciesMapping} for given CellDesigner xml node name.
- *
- * @param string
- * CellDesigner xml node name
- * @return {@link SpeciesMapping} for given CellDesigner xml node name
- */
- public static SpeciesMapping getMappingByString(String string) {
- for (SpeciesMapping mapping : SpeciesMapping.values()) {
- if (mapping.getCellDesignerString().equalsIgnoreCase(string)) {
- return mapping;
- }
- }
- return null;
- }
-
- /**
- * Returns {@link SpeciesMapping} for given {@link CellDesignerSpecies} class.
- *
- * @param searchClazz
- * {@link CellDesignerSpecies} class
- * @return {@link SpeciesMapping} for given {@link CellDesignerSpecies} class
- */
- public static SpeciesMapping getMappingByModelClass(Class<? extends Element> searchClazz) {
- for (SpeciesMapping mapping : SpeciesMapping.values()) {
- if (mapping.getModelClazz().isAssignableFrom(searchClazz)) {
- return mapping;
- }
- }
- return null;
- }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index 27cdf027f8..de2bdea00a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -1,37 +1,24 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.*;
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.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-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.*;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.model.ModelData;
-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;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
@@ -146,7 +133,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
if (positionToCompartment != null) {
PositionToCompartment position = PositionToCompartment.getByString(XmlParser.getNodeValue(positionToCompartment));
if (position == null) {
- throw new InvalidXmlSchemaException("Unknown position on compartment: " + XmlParser.getNodeValue(positionToCompartment));
+ throw new InvalidXmlSchemaException(
+ "Unknown position on compartment: " + XmlParser.getNodeValue(positionToCompartment));
}
species.setPositionToCompartment(position);
}
@@ -170,7 +158,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
species.setBoundaryCondition(XmlParser.getNodeAttr("boundaryCondition", spieciesNode));
species.setConstant(XmlParser.getNodeAttr("constant", spieciesNode));
- CellDesignerCompartment compartment = elements.getElementByElementId(XmlParser.getNodeAttr("compartment", spieciesNode));
+ CellDesignerCompartment compartment = elements
+ .getElementByElementId(XmlParser.getNodeAttr("compartment", spieciesNode));
if (compartment != null) {
species.setParent(compartment);
}
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 6f59a20abe..5d519a76ca 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
@@ -3,4 +3,3 @@
* {@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/CellDesignerAntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index 942d2f895b..7b4ee8990f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -3,17 +3,15 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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.AntisenseRna;
import lcsb.mapviewer.model.map.species.Species;
-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.*;
/**
* Class representing CellDesigner {@link AntisenseRna}.
@@ -62,21 +60,12 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
super();
}
- @Override
- public CellDesignerAntisenseRna copy() {
- if (this.getClass() == CellDesignerAntisenseRna.class) {
- return new CellDesignerAntisenseRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
/**
* Add antisense rna region (part of rna sequence that has some meaning) to the
* object. If the region with given id exists then the data of this region is
* copied to the one that is already in the {@link CellDesignerAntisenseRna}.
- *
- *
+ *
+ *
* @param region
* region to add
*/
@@ -102,11 +91,44 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
}
}
+ @Override
+ public CellDesignerAntisenseRna copy() {
+ if (this.getClass() == CellDesignerAntisenseRna.class) {
+ return new CellDesignerAntisenseRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public AntisenseRna createModelElement(String aliasId) {
+ AntisenseRna result = new AntisenseRna(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species species) {
+ AntisenseRna antisenseRna = (AntisenseRna) species;
+ for (CellDesignerModificationResidue region : regions) {
+ ModificationResidue mr = region.createModificationResidue(antisenseRna);
+ if (mr instanceof CodingRegion) {
+ antisenseRna.addCodingRegion((CodingRegion) mr);
+ } else if (mr instanceof ModificationSite) {
+ antisenseRna.addModificationSite((ModificationSite) mr);
+ } else if (mr instanceof ProteinBindingDomain) {
+ antisenseRna.addProteinBindingDomain((ProteinBindingDomain) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
+ }
+ }
+
/**
* Method update antisense rna region from the object in params (if the object
* with the same id already exists). If there is no object with given id then
* new object is added to antisense rna.
- *
+ *
* @param param
* - object with new data from where update should be performed
*/
@@ -137,28 +159,4 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
this.regions = regions;
}
- @Override
- public AntisenseRna createModelElement(String aliasId) {
- AntisenseRna result = new AntisenseRna(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
- @Override
- public void updateModelElementAfterLayoutAdded(Species species) {
- AntisenseRna antisenseRna = (AntisenseRna) species;
- for (CellDesignerModificationResidue region : regions) {
- ModificationResidue mr = region.createModificationResidue(antisenseRna);
- if (mr instanceof CodingRegion) {
- antisenseRna.addCodingRegion((CodingRegion) mr);
- } else if (mr instanceof ModificationSite) {
- antisenseRna.addModificationSite((ModificationSite) mr);
- } else if (mr instanceof ProteinBindingDomain) {
- antisenseRna.addProteinBindingDomain((ProteinBindingDomain) mr);
- } else {
- throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
- }
- }
- }
-
}
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 0146ba0bbd..f2cad15edd 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
@@ -13,113 +13,113 @@ import lcsb.mapviewer.model.map.species.Chemical;
*/
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);
- }
+ /**
+ *
+ */
+ 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/CellDesignerCompartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
index e33cb055d9..35116e044d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -84,6 +85,12 @@ public class CellDesignerCompartment extends CellDesignerElement<Compartment>
return 0;
}
+ @Override
+ public int hashCode() {
+ String result = compartmentId + "_" + getName();
+ return result.hashCode();
+ }
+
@Override
public boolean equals(Object param) {
if (this == param) {
@@ -97,9 +104,13 @@ public class CellDesignerCompartment extends CellDesignerElement<Compartment>
}
@Override
- public int hashCode() {
- String result = compartmentId + "_" + getName();
- return result.hashCode();
+ public String getElementId() {
+ return compartmentId;
+ }
+
+ @Override
+ public void setElementId(String id) {
+ this.compartmentId = id;
}
@Override
@@ -111,18 +122,18 @@ public class CellDesignerCompartment extends CellDesignerElement<Compartment>
}
@Override
- public String getElementId() {
- return compartmentId;
- }
-
- @Override
- public void setElementId(String id) {
- this.compartmentId = id;
+ public Compartment createModelElement(String aliasId) {
+ Compartment result = new Compartment(aliasId);
+ super.setModelObjectFields(result);
+ if (elements.size() > 0) {
+ throw new NotImplementedException();
+ }
+ return result;
}
/**
* Adds element.
- *
+ *
* @param element
* element to add
*/
@@ -132,21 +143,11 @@ public class CellDesignerCompartment extends CellDesignerElement<Compartment>
}
/**
- *
+ *
* @return {@link #elements}
*/
public Set<CellDesignerElement<?>> getElements() {
return elements;
}
- @Override
- public Compartment createModelElement(String aliasId) {
- Compartment result = new Compartment(aliasId);
- super.setModelObjectFields(result);
- if (elements.size() > 0) {
- throw new NotImplementedException();
- }
- return result;
- }
-
}
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 0de3bc46d8..2a815be82a 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -17,154 +18,155 @@ import lcsb.mapviewer.model.map.species.Complex;
*/
public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.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;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.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());
+ }
+ }
+
+ @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;
+ }
+
+ /**
+ * 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;
+ }
}
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 1bde95f6c9..ee9c982679 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
@@ -11,41 +11,41 @@ import lcsb.mapviewer.model.map.species.Degraded;
*/
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;
- }
+ /**
+ *
+ */
+ 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 290938153d..d51e63aa64 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
@@ -11,41 +11,41 @@ import lcsb.mapviewer.model.map.species.Drug;
*/
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;
- }
+ /**
+ *
+ */
+ 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/CellDesignerElement.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
index 2174a5c872..eaa0c94a79 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
@@ -1,13 +1,10 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -146,9 +143,17 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
*/
public abstract String getElementId();
+ /**
+ * Sets element identifier.
+ *
+ * @param elementId
+ * element identifier
+ */
+ public abstract void setElementId(String elementId);
+
/**
* Adds {@link MiriamData} to the element.
- *
+ *
* @param md
* object to be added
*/
@@ -162,21 +167,6 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
}
- /**
- * Sets notes about the object.
- *
- * @param notes
- * new notes
- */
- public void setNotes(String notes) {
- if (notes != null) {
- if (notes.contains("</html>")) {
- throw new InvalidArgumentException("Notes cannot contain html tags...");
- }
- }
- this.notes = notes;
- }
-
/**
* Makes a copy of the element.
*
@@ -211,9 +201,24 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
return notes;
}
+ /**
+ * Sets notes about the object.
+ *
+ * @param notes
+ * new notes
+ */
+ public void setNotes(String notes) {
+ if (notes != null) {
+ if (notes.contains("</html>")) {
+ throw new InvalidArgumentException("Notes cannot contain html tags...");
+ }
+ }
+ this.notes = notes;
+ }
+
/**
* Returns the symbol of the element.
- *
+ *
* @return the symbol of the element
*/
public String getSymbol() {
@@ -222,7 +227,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Sets symbol of the element.
- *
+ *
* @param symbol
* new symbol
*/
@@ -249,9 +254,9 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Returns the name of the object.
- *
+ *
* @return name of the object
- *
+ *
*/
public String getName() {
return name;
@@ -268,7 +273,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Get list of synonyms.
- *
+ *
* @return list of synonyms
*/
public List<String> getSynonyms() {
@@ -277,7 +282,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Sets list of synonyms to the element.
- *
+ *
* @param synonyms
* new list
*/
@@ -338,7 +343,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Returns list of {@link MiriamData annotations} for the object.
- *
+ *
* @return list of {@link MiriamData annotations} for the object
*/
public Set<MiriamData> getMiriamData() {
@@ -347,7 +352,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Returns the abbreviation.
- *
+ *
* @return the abbreviation
*/
public String getAbbreviation() {
@@ -356,7 +361,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Sets abbreviation.
- *
+ *
* @param abbreviation
* new abbreviation
*/
@@ -366,7 +371,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Returns the formula.
- *
+ *
* @return the formula
*/
public String getFormula() {
@@ -375,7 +380,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Sets formula.
- *
+ *
* @param formula
* new formula
*/
@@ -385,7 +390,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Adds synonym.
- *
+ *
* @param synonym
* synonym to add
*/
@@ -395,7 +400,7 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
/**
* Adds former symbol.
- *
+ *
* @param formerSymbol
* former symbol to add
*/
@@ -403,14 +408,6 @@ public abstract class CellDesignerElement<T extends Element> implements Serializ
this.formerSymbols.add(formerSymbol);
}
- /**
- * Sets element identifier.
- *
- * @param elementId
- * element identifier
- */
- public abstract void setElementId(String elementId);
-
/**
* Creates model object from this CellDesigner structure.
*
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 8981dc8488..1b98b75310 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
@@ -3,18 +3,15 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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.Gene;
import lcsb.mapviewer.model.map.species.Species;
-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.RegulatoryRegion;
-import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Class representing CellDesigner {@link Gene}.
@@ -23,17 +20,15 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
*
*/
public class CellDesignerGene extends CellDesignerSpecies<Gene> {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(CellDesignerGene.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* List of modifications for the Gene.
*/
@@ -55,6 +50,22 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
}
}
+ /**
+ * 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());
+ }
+ }
+
@Override
public void update(CellDesignerSpecies<?> species) {
super.update(species);
@@ -67,25 +78,35 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
}
}
- /**
- * Default constructor.
- */
- public CellDesignerGene() {
- super();
+ @Override
+ public Gene createModelElement(String aliasId) {
+ Gene result = new Gene(aliasId);
+ super.setModelObjectFields(result);
+ return result;
}
@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());
+ public void updateModelElementAfterLayoutAdded(Species species) {
+ Gene gene = (Gene) species;
+ for (CellDesignerModificationResidue region : modificationResidues) {
+ ModificationResidue mr = region.createModificationResidue(gene);
+ if (mr instanceof CodingRegion) {
+ gene.addCodingRegion((CodingRegion) mr);
+ } else if (mr instanceof ModificationSite) {
+ gene.addModificationSite((ModificationSite) mr);
+ } else if (mr instanceof RegulatoryRegion) {
+ gene.addRegulatoryRegion((RegulatoryRegion) mr);
+ } else if (mr instanceof TranscriptionSite) {
+ gene.addTranscriptionSite((TranscriptionSite) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
}
}
/**
* Adds modification to the gene.
- *
+ *
* @param modificationResidue
* modification to add
*/
@@ -117,30 +138,4 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
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 species) {
- Gene gene = (Gene) species;
- for (CellDesignerModificationResidue region : modificationResidues) {
- ModificationResidue mr = region.createModificationResidue(gene);
- if (mr instanceof CodingRegion) {
- gene.addCodingRegion((CodingRegion) mr);
- } else if (mr instanceof ModificationSite) {
- gene.addModificationSite((ModificationSite) mr);
- } else if (mr instanceof RegulatoryRegion) {
- gene.addRegulatoryRegion((RegulatoryRegion) mr);
- } else if (mr instanceof TranscriptionSite) {
- gene.addTranscriptionSite((TranscriptionSite) mr);
- } else {
- throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
- }
- }
- }
}
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 52b1d1c780..dcc83900fa 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -13,17 +14,16 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
*/
public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProtein> {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private transient Logger logger = LogManager.getLogger(CellDesignerGenericProtein.class);
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Default constructor.
*/
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 bd9cc31b09..d824925d92 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
@@ -11,42 +11,42 @@ import lcsb.mapviewer.model.map.species.IonChannelProtein;
*/
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;
- }
+ /**
+ *
+ */
+ 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 6611cc4c50..cc81c685f3 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
@@ -11,42 +11,41 @@ import lcsb.mapviewer.model.map.species.Phenotype;
*/
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;
- }
+ /**
+ *
+ */
+ 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/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index 70ca0ed345..70e447b371 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -3,16 +3,15 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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.Protein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.BindingRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Class representing CellDesigner {@link Protein} object.
@@ -62,6 +61,22 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
}
}
+ /**
+ * Default constructor.
+ */
+ public CellDesignerProtein() {
+ super();
+ }
+
+ @Override
+ public CellDesignerProtein<T> copy() {
+ if (this.getClass().equals(CellDesignerProtein.class)) {
+ return new CellDesignerProtein<T>(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
@Override
public void update(CellDesignerSpecies<?> species) {
super.update(species);
@@ -76,25 +91,30 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
}
}
- /**
- * Default constructor.
- */
- public CellDesignerProtein() {
- super();
+ @Override
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
+ result.setStructuralState(structuralState);
}
@Override
- public CellDesignerProtein<T> copy() {
- if (this.getClass().equals(CellDesignerProtein.class)) {
- return new CellDesignerProtein<T>(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ public void updateModelElementAfterLayoutAdded(Species species) {
+ Protein protein = (Protein) species;
+ for (CellDesignerModificationResidue region : modificationResidues) {
+ ModificationResidue mr = region.createModificationResidue(protein);
+ if (mr instanceof Residue) {
+ protein.addResidue((Residue) mr);
+ } else if (mr instanceof BindingRegion) {
+ protein.addBindingRegion((BindingRegion) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
}
}
/**
* Adds modification to the protein.
- *
+ *
* @param modificationResidue
* modification to add
*/
@@ -147,25 +167,4 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
this.modificationResidues = modificationResidues;
}
- @Override
- protected void setModelObjectFields(T result) {
- super.setModelObjectFields(result);
- result.setStructuralState(structuralState);
- }
-
- @Override
- public void updateModelElementAfterLayoutAdded(Species species) {
- Protein protein= (Protein) species;
- for (CellDesignerModificationResidue region : modificationResidues) {
- ModificationResidue mr = region.createModificationResidue(protein);
- if (mr instanceof Residue) {
- protein.addResidue((Residue) mr);
- } else if (mr instanceof BindingRegion) {
- protein.addBindingRegion((BindingRegion) mr);
- } else {
- throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
- }
- }
- }
-
}
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 6779848bf1..c7720c90dd 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
@@ -11,42 +11,42 @@ import lcsb.mapviewer.model.map.species.ReceptorProtein;
*/
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;
- }
+ /**
+ *
+ */
+ 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/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index 42ae597ea7..94063368e0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -3,17 +3,15 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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.Rna;
import lcsb.mapviewer.model.map.species.Species;
-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.*;
/**
* Class representing CellDesigner {@link Rna}.
@@ -83,9 +81,33 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
}
}
+ @Override
+ public Rna createModelElement(String aliasId) {
+ Rna result = new Rna(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species species) {
+ Rna rna = (Rna) species;
+ for (CellDesignerModificationResidue region : regions) {
+ ModificationResidue mr = region.createModificationResidue(rna);
+ if (mr instanceof CodingRegion) {
+ rna.addCodingRegion((CodingRegion) mr);
+ } else if (mr instanceof ModificationSite) {
+ rna.addModificationSite((ModificationSite) mr);
+ } else if (mr instanceof ProteinBindingDomain) {
+ rna.addProteinBindingDomain((ProteinBindingDomain) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
+ }
+ }
+
/**
* Updates region in the rna. If region doesn't exist then it is added.
- *
+ *
* @param param
* region that with the data to update
*/
@@ -102,7 +124,7 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
/**
* Adds region. If the region with given id exists then the data of this region
* is copied to the one that is already in the {@link CellDesignerRna}.
- *
+ *
* @param rnaRegion
* region to add
*/
@@ -136,28 +158,4 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
this.regions = regions;
}
- @Override
- public Rna createModelElement(String aliasId) {
- Rna result = new Rna(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
- @Override
- public void updateModelElementAfterLayoutAdded(Species species) {
- Rna rna = (Rna) species;
- for (CellDesignerModificationResidue region : regions) {
- ModificationResidue mr = region.createModificationResidue(rna);
- if (mr instanceof CodingRegion) {
- rna.addCodingRegion((CodingRegion) mr);
- } else if (mr instanceof ModificationSite) {
- rna.addModificationSite((ModificationSite) mr);
- } else if (mr instanceof ProteinBindingDomain) {
- rna.addProteinBindingDomain((ProteinBindingDomain) mr);
- } else {
- throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
- }
- }
- }
-
}
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 04e722dfe6..03497615f2 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
@@ -13,47 +14,47 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
*/
public class CellDesignerSimpleMolecule extends CellDesignerChemical<SimpleMolecule> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 4835b7a64f..2f162057b6 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -75,20 +76,9 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
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
*/
@@ -117,7 +107,7 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
/**
* Default constructor with species identifier as a parameter.
- *
+ *
* @param id
* species identifier
*/
@@ -127,23 +117,9 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
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
*/
@@ -244,80 +220,9 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
}
}
- /**
- * 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
*/
@@ -345,6 +250,49 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
}
}
+ @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;
+ }
+
+ @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);
+ if (result.getInitialAmount() == null && result.getInitialConcentration() == null) {
+ result.setInitialConcentration(0.0);
+ }
+ if (onlySubstanceUnits != null) {
+ result.setOnlySubstanceUnits(onlySubstanceUnits);
+ }
+ if (constant != null) {
+ result.setConstant(constant);
+ }
+ if (boundaryCondition != null) {
+ result.setBoundaryCondition(boundaryCondition);
+ }
+ result.setSubstanceUnits(substanceUnits);
+ result.setHomodimer(homodimer);
+ result.setPositionToCompartment(positionToCompartment);
+ result.setHypothetical(hypothetical);
+ }
+
/**
* @return the initialAmount
* @see #initialAmount
@@ -353,6 +301,27 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
return initialAmount;
}
+ /**
+ * 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;
+ }
+
+ }
+
/**
* @param initialAmount
* the initialAmount to set
@@ -370,6 +339,26 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
return charge;
}
+ /**
+ * 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;
+ }
+
+ }
+
/**
* @param charge
* the charge to set
@@ -387,6 +376,17 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
return onlySubstanceUnits;
}
+ /**
+ * 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);
+ }
+
/**
* @param onlySubstanceUnits
* the onlySubstanceUnits to set
@@ -404,6 +404,25 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
return initialConcentration;
}
+ /**
+ * 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;
+ }
+ }
+
/**
* @param initialConcentration
* the initialConcentration to set
@@ -421,6 +440,17 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
return hypothetical;
}
+ /**
+ * 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");
+ }
+
/**
* @param hypothetical
* the hypothetical to set
@@ -472,35 +502,6 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
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);
- if (result.getInitialAmount()==null && result.getInitialConcentration()==null) {
- result.setInitialConcentration(0.0);
- }
- if (onlySubstanceUnits != null) {
- result.setOnlySubstanceUnits(onlySubstanceUnits);
- }
- if (constant != null) {
- result.setConstant(constant);
- }
- if (boundaryCondition != null) {
- result.setBoundaryCondition(boundaryCondition);
- }
- result.setSubstanceUnits(substanceUnits);
- result.setHomodimer(homodimer);
- result.setPositionToCompartment(positionToCompartment);
- result.setHypothetical(hypothetical);
- }
-
public void setSubstanceUnits(SbmlUnitType substanceUnits) {
this.substanceUnits = substanceUnits;
}
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 aec05429b1..22dae6e805 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
@@ -11,43 +11,43 @@ import lcsb.mapviewer.model.map.species.TruncatedProtein;
*/
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;
- }
+ /**
+ *
+ */
+ 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 c6d0326199..2047fb2147 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
@@ -10,41 +10,41 @@ import lcsb.mapviewer.model.map.species.Unknown;
*
*/
public class CellDesignerUnknown extends CellDesignerSpecies<Unknown> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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() {
- }
+ /**
+ * 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 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;
- }
+ @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/CellDesignerModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index b131818c5f..afcd75d2bf 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -2,7 +2,8 @@ package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.io.Serializable;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -10,15 +11,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.map.species.Element;
-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.ModificationState;
-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.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* This class represent modification residue in a Species.
@@ -222,43 +215,6 @@ public class CellDesignerModificationResidue implements Serializable {
}
}
- /**
- * Sets {@link #angle} .
- *
- * @param text
- * angle in text format
- */
- public void setAngle(String text) {
- try {
- if (text != null && !text.equals("")) {
- angle = Double.parseDouble(text);
- } else {
- angle = null;
- }
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
-
- }
-
- /**
- * Sets {@link #size}.
- *
- * @param text
- * size in text format.
- */
- public void setSize(String text) {
- try {
- if (text != null && !text.equals("")) {
- size = Double.parseDouble(text);
- } else {
- size = null;
- }
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid size: " + text, e);
- }
- }
-
/**
* @return the id
* @see #idModificationResidue
@@ -335,6 +291,25 @@ public class CellDesignerModificationResidue implements Serializable {
return angle;
}
+ /**
+ * Sets {@link #angle} .
+ *
+ * @param text
+ * angle in text format
+ */
+ public void setAngle(String text) {
+ try {
+ if (text != null && !text.equals("")) {
+ angle = Double.parseDouble(text);
+ } else {
+ angle = null;
+ }
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+
+ }
+
/**
* @param angle
* the angle to set
@@ -352,6 +327,24 @@ public class CellDesignerModificationResidue implements Serializable {
return size;
}
+ /**
+ * Sets {@link #size}.
+ *
+ * @param text
+ * size in text format.
+ */
+ public void setSize(String text) {
+ try {
+ if (text != null && !text.equals("")) {
+ size = Double.parseDouble(text);
+ } else {
+ size = null;
+ }
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid size: " + text, e);
+ }
+ }
+
/**
* @param size
* the size to set
@@ -506,9 +499,17 @@ public class CellDesignerModificationResidue implements Serializable {
this.modificationType = modificationType;
}
+ /**
+ * @return the pos
+ * @see #pos
+ */
+ public Double getPos() {
+ return pos;
+ }
+
/**
* Sets position from the string.
- *
+ *
* @param text
* position to parse and set
* @see #pos
@@ -521,14 +522,6 @@ public class CellDesignerModificationResidue implements Serializable {
}
}
- /**
- * @return the pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
/**
* @param pos
* the pos to set
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 dcdab0a36f..21bb054225 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.util.HashMap;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* CellDEsigner structure used for storing some line information.
@@ -13,100 +14,100 @@ import org.apache.logging.log4j.*;
*/
public class ConnectScheme {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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>();
+ }
+
+ /**
+ * @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 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));
+ }
+
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ *
+ * @param directions
+ * the directions to set
+ * @see #directions
+ */
+ public void setLineDirections(Map<String, String> directions) {
+ lineDirections = directions;
+ }
}
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 f60dc0441d..dd45ccc521 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-import java.awt.Color;
+import java.awt.*;
import lcsb.mapviewer.model.graphics.PolylineData;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
index db5a5e258b..ac4058e4ae 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
@@ -18,10 +18,6 @@ public enum ModificationType {
this.cellDesignerName = cellDesignerName;
}
- public String getCellDesignerName() {
- return cellDesignerName;
- }
-
public static ModificationType getByCellDesignerName(String name) {
for (ModificationType type : ModificationType.values()) {
if (type.getCellDesignerName() != null && type.getCellDesignerName().equals(name)) {
@@ -30,4 +26,8 @@ public enum ModificationType {
}
throw new InvalidArgumentException("Unknown CellDesigner name: " + name);
}
+
+ public String getCellDesignerName() {
+ return cellDesignerName;
+ }
}
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 26dfe344ca..60c0db6f6f 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
@@ -8,26 +8,26 @@ package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
*/
public class SingleLine {
- /**
- * Width of the line.
- */
- private Double width;
+ /**
+ * Width of the line.
+ */
+ private Double width;
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return 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;
- }
+ /**
+ * @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/SpeciesState.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
index 1c20b73fad..dbd505bdc0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
@@ -3,15 +3,11 @@ package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-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.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
@@ -43,22 +39,6 @@ public class SpeciesState {
*/
private List<CellDesignerModificationResidue> modifications = new ArrayList<>();
- /**
- * Adds modification to the state.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue modification : modifications) {
- if (modification.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
- modification.update(modificationResidue);
- return;
- }
- }
- modifications.add(modificationResidue);
- }
-
/**
* Default constructor.
*/
@@ -67,7 +47,7 @@ public class SpeciesState {
/**
* Creates species state description from species element.
- *
+ *
* @param species
* object for which description is created
*/
@@ -104,16 +84,19 @@ public class SpeciesState {
}
/**
- *
- * @param homodimer
- * new {@link #homodimer} value to set (in string format)
+ * Adds modification to the state.
+ *
+ * @param modificationResidue
+ * modification to add
*/
- public void setHomodimer(String homodimer) {
- try {
- this.homodimer = Integer.parseInt(homodimer);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid homodir value: " + homodimer);
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue modification : modifications) {
+ if (modification.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
+ modification.update(modificationResidue);
+ return;
+ }
}
+ modifications.add(modificationResidue);
}
/**
@@ -124,6 +107,19 @@ public class SpeciesState {
return homodimer;
}
+ /**
+ *
+ * @param homodimer
+ * new {@link #homodimer} value to set (in string format)
+ */
+ public void setHomodimer(String homodimer) {
+ try {
+ this.homodimer = Integer.parseInt(homodimer);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid homodir value: " + homodimer);
+ }
+ }
+
/**
* @param homodimer
* the homodimer to set
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 dd0a00f02f..176e8aa21f 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
@@ -1,7 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-import java.awt.Color;
-import java.awt.Dimension;
+import java.awt.*;
import java.awt.geom.Point2D;
/**
@@ -11,84 +10,84 @@ import java.awt.geom.Point2D;
*
*/
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;
- }
+ /**
+ * No idea what this parameter describes.
+ */
+ private Point2D innerPosition;
- /**
- * @param innerPosition
- * the innerPosition to set
- */
- public void setInnerPosition(Point2D innerPosition) {
- this.innerPosition = innerPosition;
- }
+ /**
+ * Size of the element.
+ */
+ private Dimension boxSize;
- /**
- * @return the boxSize
- */
- public Dimension getBoxSize() {
- return boxSize;
- }
+ /**
+ * Width of the line.
+ */
+ private SingleLine singleLine;
- /**
- * @param boxSize
- * the boxSize to set
- */
- public void setBoxSize(Dimension boxSize) {
- this.boxSize = boxSize;
- }
+ /**
+ * Color of the element.
+ */
+ private Color color;
- /**
- * @return the singleLine
- */
- public SingleLine getSingleLine() {
- return singleLine;
- }
+ /**
+ * @return the innerPosition
+ */
+ public Point2D getInnerPosition() {
+ return innerPosition;
+ }
- /**
- * @param singleLine
- * the singleLine to set
- */
- public void setSingleLine(SingleLine singleLine) {
- this.singleLine = singleLine;
- }
+ /**
+ * @param innerPosition
+ * the innerPosition to set
+ */
+ public void setInnerPosition(Point2D innerPosition) {
+ this.innerPosition = innerPosition;
+ }
- /**
- * @return the color
- */
- public Color getColor() {
- return color;
- }
+ /**
+ * @return the boxSize
+ */
+ public Dimension getBoxSize() {
+ return boxSize;
+ }
- /**
- * @param color
- * the color to set
- */
- public void setColor(Color color) {
- this.color = color;
- }
+ /**
+ * @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/types/ModifierType.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
index 3a907fea11..db7e340685 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
@@ -1,16 +1,8 @@
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.graphics.*;
+import lcsb.mapviewer.model.map.modifier.*;
import lcsb.mapviewer.model.map.reaction.Modifier;
/**
@@ -21,182 +13,184 @@ import lcsb.mapviewer.model.map.reaction.Modifier;
*
*/
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;
- }
+
+ /**
+ * 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 4e6d2650ea..d2bd4390d2 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
@@ -3,17 +3,15 @@ package lcsb.mapviewer.converter.model.celldesigner.types;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.reaction.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -26,281 +24,282 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class ModifierTypeUtils {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(ModifierTypeUtils.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 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;
- }
+ /**
+ * 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);
- }
- }
+ /**
+ * 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 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());
- }
+ /**
+ * 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();
+ Reaction reaction = modifier.getReaction();
+ PolylineData line = modifier.getLine();
- String result = getTragteLineIndex(modType, reaction, line);
- return result;
- }
+ 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());
+ /**
+ * 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());
- }
+ if (modType == null) {
+ throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
+ }
- Reaction reaction = modifier.getReaction();
- PolylineData line = modifier.getLine();
+ Reaction reaction = modifier.getReaction();
+ PolylineData line = modifier.getLine();
- String result = getTragteLineIndex(modType, reaction, line);
- return result;
- }
- }
+ 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 identifies TargetLine index for modifier line
- */
- private String getTragteLineIndex(ModifierType modType, Reaction reaction, PolylineData originalLine) {
- PolylineData line = new PolylineData(originalLine);
- line.trimEnd(-modType.getTrimLength());
+ /**
+ * 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 identifies 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;
- }
+ 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
- * reaction 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) {
- int countLines = reaction.getLine().getPoints().size()-1;
- Line2D centerLine = reaction.getLine().getLines().get(countLines/2);
- 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);
+ /**
+ * 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
+ * reaction 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) {
+ int countLines = reaction.getLine().getPoints().size() - 1;
+ Line2D centerLine = reaction.getLine().getLines().get(countLines / 2);
+ 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);
- }
+ 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;
- }
+ } 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);
- }
+ /**
+ * 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 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());
- }
+ /**
+ * 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());
- }
+ /**
+ * 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 7f6d880876..5c0ad3dab2 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
@@ -1,10 +1,6 @@
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;
+import lcsb.mapviewer.model.map.reaction.*;
/**
* This enum defines how different types of CellDesigner operators should be
@@ -15,80 +11,80 @@ import lcsb.mapviewer.model.map.reaction.UnknownOperator;
*/
public enum OperatorType {
- /**
- * Boolean and operator.
- */
- AND_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_AND", AndOperator.class),
+ /**
+ * 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 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 or operator.
+ */
+ OR_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_OR", OrOperator.class),
- /**
- * Boolean unknown operator.
- */
- UNKNOWN_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_UNKNOWN", UnknownOperator.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;
+ /**
+ * 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;
- }
+ /**
+ * 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;
- }
+ /**
+ * 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;
+ }
- /**
- * @return the clazz
- * @see #clazz
- */
- public Class<? extends NodeOperator> getClazz() {
- return clazz;
- }
+ /**
+ * @return the stringName
+ * @see #stringName
+ */
+ public String getStringName() {
+ return stringName;
+ }
- /**
- * 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;
- }
+ /**
+ * @return the clazz
+ * @see #clazz
+ */
+ public Class<? extends NodeOperator> getClazz() {
+ return clazz;
+ }
}
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 64198f2339..4cc93d5b92 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -15,78 +16,78 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
*/
public class OperatorTypeUtils {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(OperatorTypeUtils.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 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;
- }
+ /**
+ * 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;
- }
+ /**
+ * 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;
- }
+ /**
+ * 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 c61e202f20..3f916f3e82 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
@@ -3,4 +3,3 @@
* used in our model.
*/
package lcsb.mapviewer.converter.model.celldesigner.types;
-
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java
index 953a422ca2..7703997ab8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java
@@ -24,7 +24,7 @@ public class UnitCollectionXmlParser {
public String toXml(Set<SbmlUnit> units) {
StringBuilder builder = new StringBuilder();
builder.append("<listOfUnitDefinitions>\n");
- for (SbmlUnit unit: units) {
+ for (SbmlUnit unit : units) {
builder.append(unitParser.toXml(unit));
}
builder.append("</listOfUnitDefinitions>\n");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java
index fa9a1d9ac7..724e0b2386 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java
@@ -3,14 +3,13 @@ package lcsb.mapviewer.converter.model.celldesigner.unit;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-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.kinetics.*;
public class UnitXmlParser {
/**
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 9e1b17f23e..790087f132 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
@@ -2,39 +2,22 @@ package lcsb.mapviewer.converter.model.celldesigner;
import static org.junit.Assert.assertEquals;
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-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.io.*;
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.parsers.*;
+import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.junit.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.w3c.dom.*;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
@@ -48,14 +31,11 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
public abstract class CellDesignerTestFunctions {
- private Logger logger = LogManager.getLogger(CellDesignerTestFunctions.class);
-
protected static double EPSILON = Configuration.EPSILON;
-
- private MinervaLoggerAppender appender;
-
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
+ private Logger logger = LogManager.getLogger(CellDesignerTestFunctions.class);
+ private MinervaLoggerAppender appender;
@Before
public final void _setUp() throws Exception {
@@ -246,7 +226,6 @@ public abstract class CellDesignerTestFunctions {
assertEquals(0, comparator.compare(model, model2));
}
-
protected Model serializeModel(Model model)
throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
@@ -261,5 +240,4 @@ public abstract class CellDesignerTestFunctions {
return model2;
}
-
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index b2c402159d..0716583693 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -1,13 +1,14 @@
package lcsb.mapviewer.converter.model.celldesigner;
import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.*;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.*;
+import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
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 2b3f5b5628..c630d756dd 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
@@ -1,21 +1,15 @@
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 static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.io.ByteArrayInputStream;
-import java.util.ArrayList;
-import java.util.HashSet;
+import java.util.*;
import java.util.List;
-import java.util.Set;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
@@ -24,18 +18,9 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
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.ModelComparator;
-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.Protein;
-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.model.map.model.*;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class ComplexParserTests extends CellDesignerTestFunctions {
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 af15a37f2c..c393d0440d 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
@@ -2,26 +2,24 @@ package lcsb.mapviewer.converter.model.celldesigner;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class InvalidGroupExceptionTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() 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()));
- }
+ @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 efd8836919..9f9baf61dd 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
@@ -2,7 +2,7 @@ package lcsb.mapviewer.converter.model.celldesigner;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.util.Collection;
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 77be63a349..c140cc05c0 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SbmlValidationTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SbmlValidationTests.java
index 015835c412..8fdaaf5f94 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SbmlValidationTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SbmlValidationTests.java
@@ -5,9 +5,7 @@ import static org.junit.Assert.assertEquals;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
import org.apache.http.HttpEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
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 0e90824423..4da792bc5a 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
@@ -5,9 +5,9 @@ import org.junit.runners.Suite;
@RunWith(Suite.class)
@Suite.SuiteClasses({ AliasCollectionXmlParserTest.class,
- ComplexAliasXmlParserTest.class,
- CompartmentAliasXmlParserTest.class,
- SpeciesAliasXmlParserTest.class,
+ ComplexAliasXmlParserTest.class,
+ CompartmentAliasXmlParserTest.class,
+ SpeciesAliasXmlParserTest.class,
})
public class AllAliasTests {
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 3d233cffe1..aca802ebdd 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.junit.*;
@@ -14,8 +15,8 @@ import lcsb.mapviewer.model.map.species.Complex;
public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
Model model;
- private ComplexAliasXmlParser parser;
CellDesignerElementCollection elements;
+ private ComplexAliasXmlParser parser;
@Before
public void setUp() throws Exception {
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 3e983e66b9..20662bf304 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.util.ArrayList;
import java.util.List;
@@ -24,13 +24,12 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = LogManager.getLogger(SpeciesAliasXmlParser.class);
Model model;
+ CellDesignerElementCollection elements;
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 {
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 1d4244c0d4..31d2fb394d 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
@@ -2,31 +2,28 @@ 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;
+import org.junit.*;
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());
- }
- }
+ @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 b8476cc09e..ab8f482825 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
@@ -6,8 +6,8 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CompartmentCollectionXmlParserTest.class,
- CompartmentParserTests.class,
- CompartmentXmlParserTest.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 ed2af3a9f2..1907d1bb66 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 c251c2c564..f36ef35e55 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParserTest.java
index 618f799af2..b972d36396 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParserTest.java
@@ -4,7 +4,8 @@ import static org.junit.Assert.assertEquals;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.comparator.SetComparator;
@@ -19,7 +20,8 @@ public class FunctionCollectionXmlParserTest extends CellDesignerTestFunctions {
public void testToXml() throws Exception {
FunctionCollectionXmlParser parser = new FunctionCollectionXmlParser();
Set<SbmlFunction> functions = parser
- .parseXmlFunctionCollection(super.getXmlDocumentFromFile("testFiles/function/function_list.xml").getFirstChild());
+ .parseXmlFunctionCollection(
+ super.getXmlDocumentFromFile("testFiles/function/function_list.xml").getFirstChild());
String xml = parser.toXml(functions);
Set<SbmlFunction> functions2 = parser.parseXmlFunctionCollection(super.getNodeFromXmlString(xml));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
index a06fcc19c3..631326e015 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
@@ -1,12 +1,11 @@
package lcsb.mapviewer.converter.model.celldesigner.function;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
import java.io.IOException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
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 97e3e031bd..01466f3a29 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
@@ -2,20 +2,16 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import static org.junit.Assert.assertEquals;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
-
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-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;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.*;
+import lcsb.mapviewer.model.map.species.*;
public class AbstractCellDesignerAliasConverterTest extends CellDesignerTestFunctions {
Logger logger = LogManager.getLogger(AbstractCellDesignerAliasConverterTest.class);
@@ -30,11 +26,11 @@ public class AbstractCellDesignerAliasConverterTest extends CellDesignerTestFunc
@Test
public void testGetAnchorPointCoordinatesForInvalidImplementation() {
- Protein alias = new GenericProtein("id");
- alias.setWidth(1);
- alias.setHeight(1);
- converter.getAnchorPointCoordinates(alias, 0);
- assertEquals(1, getWarnings().size());
+ Protein alias = new GenericProtein("id");
+ alias.setWidth(1);
+ alias.setHeight(1);
+ converter.getAnchorPointCoordinates(alias, 0);
+ assertEquals(1, getWarnings().size());
}
@Test
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 09f80e2522..9dd9555a46 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;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.AllHelperTests;
+
@RunWith(Suite.class)
@SuiteClasses({ AbstractCellDesignerAliasConverterTest.class,
- AllHelperTests.class,
- AntisenseRnaCellDesignerAliasConverterTest.class,
- CellDesignerAliasConverterTest.class,
- ComplexConverterTest.class,
- DegradedCellDesignerAliasConverterTest.class,
- GeneCellDesignerAliasConverterTest.class,
- IonCellDesignerAliasConverterTest.class,
- ProteinConverterTest.class,
- ProteinCellDesignerAliasConverterTest.class,
- ReactionCellDesignerConverterTest.class,
- RnaCellDesignerAliasConverterTest.class,
- SimpleMoleculeCellDesignerAliasConverterTest.class,
- UnknownCellDesignerAliasConverterTest.class,
+ AllHelperTests.class,
+ AntisenseRnaCellDesignerAliasConverterTest.class,
+ CellDesignerAliasConverterTest.class,
+ ComplexConverterTest.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 a12653e3a1..2f5634b2d5 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
@@ -5,10 +5,7 @@ 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 org.junit.*;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.model.map.model.Model;
@@ -18,42 +15,42 @@ 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);
- }
+ @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/ComplexConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexConverterTest.java
index 5cadff0013..a7e10d2352 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexConverterTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
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 a91f48f823..060317c4f1 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
@@ -5,10 +5,7 @@ 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 org.junit.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Degraded;
@@ -16,42 +13,42 @@ 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"));
- }
- }
+ 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/GeneCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
index e4dfc70012..52a3079aea 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
@@ -6,7 +6,8 @@ import static org.junit.Assert.assertNotNull;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.model.map.model.Model;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
index c7cbcccba4..15fd4f9d77 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
@@ -5,10 +5,7 @@ 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 org.junit.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Ion;
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 c50ba1f308..1fefc5cd18 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
index fc6f42a034..c8774ca65f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
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 08dbb62a49..ff5601803e 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 +1,27 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ReactionCellDesignerConverterTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testConstructor() {
- ReactionCellDesignerConverter onverter = new ReactionCellDesignerConverter();
- assertNotNull(onverter);
- }
+ @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 e6f8670cc3..9ba53f5cd1 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
@@ -5,10 +5,7 @@ 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 org.junit.*;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.model.map.model.Model;
@@ -18,42 +15,42 @@ 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);
- }
+ @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/SimpleMoleculeCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
index 7fb94dd1f6..634f2ab333 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.awt.geom.Point2D;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
index 0307655070..102748f343 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
@@ -5,10 +5,7 @@ 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 org.junit.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Unknown;
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 364015e077..f883b0ad41 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
@@ -6,12 +6,12 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CellDesignerAnchorTest.class,
- CellDesignerEllipseTransformationTest.class,
- CellDesignerLineTransformationTest.class,
- CellDesignerPointTransformationTest.class,
- CellDesignerPolygonTransformationTest.class,
- CellDesignerRectangleTransformationTest.class,
- PolylineDataFactoryTest.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 d390e8afd6..fee260db95 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
@@ -2,30 +2,27 @@ 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;
+import org.junit.*;
public class CellDesignerAnchorTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testGetters() {
- for (CellDesignerAnchor value : CellDesignerAnchor.values()) {
- assertNotNull(value.getName());
- }
- }
+ @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 d72af04eab..1656978ee5 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
@@ -4,142 +4,140 @@ import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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);
- }
+ 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/CellDesignerPointTransformationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformationTest.java
index c8a1c21eac..78cdb13c41 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
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 a34cb8711a..a1c3b366e7 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
@@ -4,33 +4,30 @@ 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 org.junit.*;
import lcsb.mapviewer.common.Configuration;
public class CellDesignerRectangleTransformationTest {
- CellDesignerRectangleTransformation transformation = new CellDesignerRectangleTransformation();
+ CellDesignerRectangleTransformation transformation = new CellDesignerRectangleTransformation();
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() 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);
- }
+ @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/reaction/KineticsXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java
index 4a4c0c5eba..05ce513fec 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java
@@ -1,9 +1,6 @@
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.assertTrue;
+import static org.junit.Assert.*;
import java.io.IOException;
import java.util.HashMap;
@@ -17,9 +14,7 @@ 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.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Element;
@@ -110,18 +105,18 @@ public class KineticsXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testToXmlDefinition() throws Exception {
- Model model = super.getModelForFile("testFiles/reactions/kinetics.xml");
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
- for (Element element : model.getElements()) {
- elements.getElementId(element);
- }
- SbmlKinetics kinetics = model.getReactionByReactionId("re1").getKinetics();
-
- KineticsXmlParser parser = new KineticsXmlParser(model);
- String xml = parser.toXml(model.getReactionByReactionId("re1").getKinetics(), elements);
-
- assertNotNull(xml);
- assertTrue(xml.indexOf(elements.getElementId(kinetics.getElements().iterator().next())) >= 0);
+ Model model = super.getModelForFile("testFiles/reactions/kinetics.xml");
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ for (Element element : model.getElements()) {
+ elements.getElementId(element);
+ }
+ SbmlKinetics kinetics = model.getReactionByReactionId("re1").getKinetics();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ String xml = parser.toXml(model.getReactionByReactionId("re1").getKinetics(), elements);
+
+ assertNotNull(xml);
+ assertTrue(xml.indexOf(elements.getElementId(kinetics.getElements().iterator().next())) >= 0);
}
@Test
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java
index 01869c993a..37df0180a5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.io.FileInputStream;
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 95f92dda20..e6df431bc1 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
@@ -6,10 +6,9 @@ import static org.junit.Assert.assertNotNull;
import java.awt.geom.Line2D;
import java.util.List;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
import org.w3c.dom.Node;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -21,169 +20,169 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
- Logger logger = LogManager.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;
- }
+ Logger logger = LogManager.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/ReactionLineDataTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
index 08b6429d49..77f8e187e9 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.junit.*;
import org.mockito.Mockito;
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 ac6b375532..725fc1166e 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
@@ -2,41 +2,38 @@ 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 org.junit.*;
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());
- }
+ @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 893fccc418..a9d175d32f 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
@@ -2,10 +2,11 @@ package lcsb.mapviewer.converter.model.celldesigner.reaction;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.util.*;
+import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -25,9 +26,9 @@ import lcsb.mapviewer.model.map.species.*;
public class ReactionParserTests extends CellDesignerTestFunctions {
- private Logger logger = LogManager.getLogger(ReactionParserTests.class.getName());
ReactionXmlParser parser;
CellDesignerElementCollection elements;
+ private Logger logger = LogManager.getLogger(ReactionParserTests.class.getName());
@Before
public void setUp() throws Exception {
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 88d28638b1..8e037cae3b 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 +1,29 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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());
- }
+ @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/AntisenseRnaXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
index 4d9bc17924..5b23ce5c84 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.io.StringReader;
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 9385be4dfb..336f829172 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.when;
import java.util.ArrayList;
import java.util.List;
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 0de7742276..46bdaefefd 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.junit.*;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java
index a3b2f730ff..e73008f4bb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.awt.geom.Point2D;
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 2a6eba764b..43b397c4af 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.lang.reflect.Field;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
index b85fd90d02..c3ce2f8215 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.io.StringReader;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
index dfe1e00006..b3f2dd07b8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.lang.reflect.Field;
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 f6dbdcfc63..1919807087 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
@@ -27,11 +27,7 @@ import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.*;
public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(SpeciesSbmlParserTest.class.getName());
-
SpeciesSbmlParser parser;
-
String testGeneFile = "testFiles/xmlNodeTestExamples/sbml_gene.xml";
String testDegradedFile = "testFiles/xmlNodeTestExamples/sbml_degraded.xml";
String testDrugFile = "testFiles/xmlNodeTestExamples/sbml_drug.xml";
@@ -41,10 +37,10 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
String testRnaFile = "testFiles/xmlNodeTestExamples/sbml_rna.xml";
String testSimpleMoleculeFile = "testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml";
String testUnknownFile = "testFiles/xmlNodeTestExamples/sbml_unknown.xml";
-
CellDesignerElementCollection elements;
-
int idCounter = 0;
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(SpeciesSbmlParserTest.class.getName());
@Before
public void setUp() throws Exception {
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 e9194757a1..2dc8cbe13f 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
@@ -8,30 +8,30 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.AllFieldsTes
@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,
+ 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 aef53547d4..2aacce4623 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
@@ -2,39 +2,36 @@ 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;
+import org.junit.*;
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());
- }
+ @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/ComplexSpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
index 2add8eea61..bd7362244a 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.HashSet;
import java.util.Set;
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 5b5ba309a6..382ecbd0a1 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
@@ -5,41 +5,38 @@ 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 org.junit.*;
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());
- }
+ @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 4c3af94067..dbb8476084 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 1a2f20201d..12c297184e 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
index 266c2bdf3a..54d6368195 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 73e83739e7..56c53a16ea 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 9a9e856d67..b091b75a18 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
index ec56e6bf4c..a9ffc54b2b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 ad1c9dcc49..fd2a97d2b7 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 +1,31 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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());
- }
+ @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/PhenotypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
index 298b1523ad..cf4e64a306 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 f4736e225a..85e800dccf 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 17d0cb16d5..2c7a993afb 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 35c0176da9..e58b9ba42a 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
index 6f49cb2230..b8c7717001 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
import java.util.ArrayList;
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 ed7f2d903c..3ba57e8f19 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 0f898b7e36..f5eb8f021a 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 ae6f2152a3..d3279e5b77 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 +1,33 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.*;
+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 org.junit.*;
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());
- }
+ @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/CellDesignerModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidueTest.java
index 41d152d0db..da30520b11 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
@@ -2,29 +2,26 @@ 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;
+import org.junit.*;
public class CellDesignerModificationResidueTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void test() {
- CellDesignerModificationResidue region = new CellDesignerModificationResidue();
- assertNotNull(region.toString());
- }
+ @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 d76440b14f..6d4d31cff0 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
@@ -6,9 +6,9 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ ModifierTypeTest.class,
- ModifierTypeUtilsTest.class,
- OperatorTypeTest.class,
- OperatorTypeUtilsTest.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 b10acf49c6..2fd0635f90 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
@@ -2,30 +2,27 @@ 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;
+import org.junit.*;
public class ModifierTypeTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void test() {
- for (ModifierType type : ModifierType.values()) {
- assertNotNull(ModifierType.valueOf(type.toString()));
- }
- }
+ @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 7a87b70661..b23ea7333b 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import java.awt.geom.Point2D;
import java.lang.reflect.Field;
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 51c5880ba5..2da98c2cef 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 +1,28 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class OperatorTypeTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void test() {
- for (OperatorType type : OperatorType.values()) {
- assertNotNull(OperatorType.valueOf(type.toString()));
- }
- }
+ @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 fefc4b51cb..b4f84190bd 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNull;
import java.lang.reflect.Field;
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 0cfeba5677..95ed20c123 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
+import java.io.*;
import javax.xml.bind.JAXBException;
@@ -14,10 +12,7 @@ import org.sbgn.bindings.Sbgn;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.model.map.model.Model;
public class SbgnmlXmlConverter extends Converter {
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 3e5e337ef5..c3cc9949f4 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -1,30 +1,17 @@
package lcsb.mapviewer.converter.model.sbgnml;
import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.sbgn.ArcClazz;
-import org.sbgn.GlyphClazz;
-import org.sbgn.Language;
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Arc.End;
-import org.sbgn.bindings.Arc.Next;
-import org.sbgn.bindings.Arc.Start;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Label;
+import org.sbgn.*;
+import org.sbgn.bindings.*;
import org.sbgn.bindings.Map;
-import org.sbgn.bindings.Port;
-import org.sbgn.bindings.Sbgn;
+import org.sbgn.bindings.Arc.*;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -33,45 +20,10 @@ import lcsb.mapviewer.model.graphics.ArrowType;
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.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.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.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.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.NegativeInfluenceReaction;
-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.UnknownTransitionReaction;
-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.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.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.modifier.*;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -84,66 +36,55 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class SbgnmlXmlExporter {
- /**
- * Helps in providing human readable identifiers of elements for logging.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.getLogger(SbgnmlXmlExporter.class.getName());
-
- /**
- * Counter of the arcs parsed so far, used in generating arc's id.
- */
- private int arcCounter;
-
- /**
- * Set of all the operators parsed so far, used in generating operator's id.
- */
- private Set<NodeOperator> parsedOperators;
-
- /**
- * Map of operator IDs used when parsing arcs targeting an operator.
- */
- private java.util.Map<NodeOperator, String> operatorIds;
-
- /**
- * Map of all glyphs and ports generated so far with id as key.
- */
- private java.util.Map<String, Object> sourceTargetMap;
-
/**
* Side margin for units of information.
*/
private static final double UNIT_OF_INFORMATION_MARGIN = 10.0;
-
/**
* Height of generated units of information.
*/
private static final double UNIT_OF_INFORMATION_HEIGHT = 12.0;
-
/**
* Height and width of generated operators.
*/
private static final double OPERATOR_SIZE = 40.0;
-
/**
* Distance between operator circle and port point.
*/
private static final double OPERATOR_PORT_DISTANCE = 20.0;
-
/**
* Distance between process glyph and port point.
*/
private static final double PROCESS_PORT_DISTANCE = 10.0;
-
/**
* Length of random alphabetic string added in the begining of ID, if it is a
* number. SBGN-ML doesn't accept numbers as ID.
*/
private static final int ID_RANDOM_STRING_LENGTH = 5;
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(SbgnmlXmlExporter.class.getName());
+ /**
+ * Counter of the arcs parsed so far, used in generating arc's id.
+ */
+ private int arcCounter;
+ /**
+ * Set of all the operators parsed so far, used in generating operator's id.
+ */
+ private Set<NodeOperator> parsedOperators;
+ /**
+ * Map of operator IDs used when parsing arcs targeting an operator.
+ */
+ private java.util.Map<NodeOperator, String> operatorIds;
+ /**
+ * Map of all glyphs and ports generated so far with id as key.
+ */
+ private java.util.Map<String, Object> sourceTargetMap;
/**
* Transforms model into SBGN-ML xml.
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index c2d769e636..59866a2253 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
@@ -9,18 +9,9 @@ import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.sbgn.ArcClazz;
-import org.sbgn.GlyphClazz;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Arc.End;
-import org.sbgn.bindings.Arc.Next;
-import org.sbgn.bindings.Arc.Start;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Map;
-import org.sbgn.bindings.Port;
-import org.sbgn.bindings.Sbgn;
+import org.sbgn.*;
+import org.sbgn.bindings.*;
+import org.sbgn.bindings.Arc.*;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -33,48 +24,16 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesigner
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
-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.graphics.*;
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.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.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-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.type.KnownTransitionOmittedReaction;
-import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
-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.UnknownTransitionReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-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.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.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.modifier.*;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* This class is a parser for SBGN-ML files.
@@ -84,44 +43,37 @@ import lcsb.mapviewer.model.map.species.field.Residue;
*/
public class SbgnmlXmlParser {
+ /**
+ * Default margin for container name.
+ */
+ private static final double CONTAINER_NAME_MARGIN = 5.0;
+ /**
+ * 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 color for parsed compartments.
+ */
+ private static final Color COMPARTMENT_COLOR = new Color(0.5f, 0.5f, 1.0f);
+ private final PointTransformation pt = new PointTransformation();
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(SbgnmlXmlParser.class.getName());
-
/**
* List of all processes to be parsed.
*/
private List<Process> processes = new ArrayList<Process>();
-
/**
* List of all logic operator glyphs parsed so far.
*/
private List<Glyph> logicOperators = new ArrayList<Glyph>();
-
/**
* List of all logic arcs parsed so far.
*/
private List<Arc> logicArcs = new ArrayList<Arc>();
- /**
- * Default margin for container name.
- */
- private static final double CONTAINER_NAME_MARGIN = 5.0;
-
- /**
- * 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 color for parsed compartments.
- */
- private static final Color COMPARTMENT_COLOR = new Color(0.5f, 0.5f, 1.0f);
-
- private final PointTransformation pt = new PointTransformation();
-
/**
* Method used to create a model from SBGN-ML 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 a2833a7d9d..59cfb45c53 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 +1,5 @@
/**
- * 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 1a12c70805..4c19a4ec03 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
@@ -4,9 +4,7 @@ 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 org.sbgn.bindings.*;
import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -18,220 +16,226 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
*/
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;
- }
+ /**
+ * 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 b463f7a41a..1e3ff62dee 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 +1,5 @@
/**
- * 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 1c40a8d7eb..aba2c53f65 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
@@ -6,11 +6,11 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CellDesigner2SbgnmlConversionTest.class,
- CellDesignerToSbgnTest.class,
- DbSerializationTest.class,
- SbgnmlXmlExporterTest.class,
- SbgnmlXmlParserTest.class,
- SbgnmlXmlParserTest2.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/CellDesignerToSbgnTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
index 57144608ea..54da7290fb 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.io.File;
import java.io.FileInputStream;
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
index ba4c23cd12..7f6000f2a5 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
@@ -6,18 +6,14 @@ import java.io.File;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.annotation.Transactional;
-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.*;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.map.ModelDao;
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
index c0d037d571..0e3dd16e2c 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.awt.Desktop;
+import java.awt.*;
import java.io.File;
import java.nio.file.Files;
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
index ea82c2e93f..6df4e8cd5a 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.io.*;
import java.nio.file.*;
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 0bfed2214f..ad1836ccba 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
@@ -1,15 +1,12 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
+import java.awt.*;
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.*;
import java.util.List;
-import java.util.Map;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -18,25 +15,17 @@ 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.LayerLineConverter;
-import lcsb.mapviewer.converter.graphics.layer.LayerOvalConverter;
-import lcsb.mapviewer.converter.graphics.layer.LayerRectConverter;
-import lcsb.mapviewer.converter.graphics.layer.LayerTextConverter;
+import lcsb.mapviewer.converter.graphics.layer.*;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.Drawable;
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.layout.graphics.LayerOval;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.layout.graphics.*;
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.model.map.species.*;
/**
* This class is responsible for creation of the image from the model. It's an
@@ -77,1042 +66,1032 @@ import lcsb.mapviewer.model.map.species.Species;
*/
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 efficient (and safe) solution would be to include text
* Description as parts of the object border
*/
private static final int SINGLE_FRAME_MARGIN = 100;
-
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(AbstractImageGenerator.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();
/**
* 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;
+ /**
+ * 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;
+ /**
+ * Flag indicating {@link #draw()} method was executed.
+ */
+ private boolean drawn = false;
/**
- * This class contains a list of params that are used for drawing.
- *
- * @author Piotr Gawron
+ * 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 appropriate image
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ *
+ */
+ protected AbstractImageGenerator(final Params params) {
+ this.params = params;
+ }
+
+ /**
+ * Don't allow to create default public constructors with empty list of
+ * parameters.
+ */
+ protected AbstractImageGenerator() {
+ super();
+ }
+
+ /**
+ * 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);
+
+ /**
+ * Draw a model into {@link #getGraphics()} object.
*
+ * @throws DrawingException
+ * thrown when there is a problem with drawing
*/
- public static class Params {
+ protected void draw() throws DrawingException {
+ if (isDrawn()) {
+ logger.warn("Model was already drawn. Skipping");
+ return;
+ }
+ this.level = params.getLevel();
+ this.scale = params.getScale();
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(Params.class);
+ colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
- /**
- * Scale at which we want to visualize the map. The default value is 1.0 (no
- * magnification).
- */
- private double scale = 1;
+ // 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());
- /**
- * x coordinate from which we start to draw a map. This is absolute value on the
- * map (scale doesn't influence it).
- */
+ // turn on anti-aliasing
+ graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
- private double x = 0;
+ graphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
- /**
- * 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;
+ graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
- /**
- * 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;
+ // set scale
+ graphics.scale(1 / scale, 1 / scale);
- /**
- * 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;
+ // move the upper left corner to coordinates
+ graphics.translate(-params.getX(), -params.getY());
- /**
- * Model to be visualized.
- */
- private Model model = null;
+ 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);
+ }
- /**
- * Should we draw white background.
- */
- private boolean background = true;
+ // Get the SBGN display format option from the model
+ this.sbgnFormat = params.isSbgn();
- /**
- * 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;
+ List<Drawable> bioEntities = new ArrayList<>();
+ bioEntities.addAll(params.getModel().getBioEntities());
+ for (Layer layer : params.getModel().getLayers()) {
+ if (layer.isVisible()) {
+ bioEntities.addAll(layer.getDrawables());
+ }
+ }
+ bioEntities.sort(BioEntity.Z_INDEX_COMPARATOR);
- /**
- * Should the visualization include hierarchical view or not.
- */
- private boolean nested = false;
+ // draw all elements
+ for (Drawable element : bioEntities) {
+ if (element instanceof Species) {
+ drawSpecies((Species) element);
+ } else if (element instanceof Reaction) {
+ drawReaction((Reaction) element);
+ } else if (element instanceof Compartment) {
+ drawCompartment((Compartment) element);
+ } else if (element instanceof LayerText) {
+ drawText((LayerText) element);
+ } else if (element instanceof LayerOval) {
+ drawOval((LayerOval) element);
+ } else if (element instanceof LayerRect) {
+ drawRect((LayerRect) element);
+ } else if (element instanceof PolylineData) {
+ drawLine((PolylineData) element);
+ } else {
+ throw new DrawingException("Unknown class type: " + element);
+ }
+ }
+ closeImageObject();
+ setDrawn(true);
+ }
- /**
- * Should sbgn standard be used.
- */
- private boolean sbgn = false;
+ private void drawText(LayerText element) {
+ new LayerTextConverter().draw(element, graphics);
+ }
- /**
- * 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<>();
+ private void drawRect(LayerRect element) {
+ new LayerRectConverter().draw(element, graphics);
+ }
- /**
- * Color that should be used for drawing overlays with minimum value.
- */
- private Color minColor = Color.BLACK;
+ private void drawOval(LayerOval element) {
+ new LayerOvalConverter().draw(element, graphics);
+ }
- /**
- * Color that should be used for drawing overlays with maximum value.
- */
- private Color maxColor = Color.BLACK;
+ private void drawLine(PolylineData element) {
+ new LayerLineConverter().draw(element, graphics);
+ }
- private Color simpleColor = Color.BLACK;
+ /**
+ * Method called after drawing. It should close drawing canvas properly.
+ */
+ protected abstract void closeImageObject();
- /**
- * @param scale
- * scale to set
- * @return object with all parameters
- * @see #scale
- */
- public Params scale(final double scale) {
- this.scale = scale;
- return this;
- }
+ /**
+ * 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);
- /**
- * @param scale
- * scale to set
- * @return object with all parameters
- * @see #scale
- */
- public Params scale(final int scale) {
- this.scale = scale;
- return this;
+ if (params.nested) {
+ compartmentParams.scale(Math.max(scale, 1));
}
- /**
- *
- * @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;
- }
+ converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
- /**
- * @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;
+ if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
+ if (!compartment.containsIdenticalSpecies()) {
+ if (!(compartment instanceof PathwayCompartment)) {
+ converter.drawText(compartment, graphics, compartmentParams);
+ }
+ }
}
+ }
- /**
- * @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;
+ /**
+ * 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;
}
- /**
- * @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;
+ 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;
+ }
+ }
+ }
}
- /**
- * @param width
- * width to set
- * @return object with all parameters
- * @see #width
- */
- public Params width(final double width) {
- this.width = width;
- return this;
+ // 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));
- /**
- * @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;
+ /**
+ * 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));
+ }
- /**
- * @param height
- * height to set
- * @return object with all parameters
- * @see #height
- */
- public Params height(final int height) {
- this.height = (double) height;
- return this;
+ /**
+ * 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;
+ }
- /**
- *
- * @param background
- * background flag to set
- * @return object with all parameters
- * @see #background
- */
- public Params background(final boolean background) {
- this.background = background;
- return this;
- }
+ /**
+ * 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);
+ }
- /**
- *
- * @param nested
- * nested flag to set
- * @return object with all parameters
- * @see #nested
- */
- public Params nested(final boolean nested) {
- this.nested = nested;
- return this;
- }
+ /**
+ * @return the graphics
+ */
+ protected Graphics2D getGraphics() {
+ return graphics;
+ }
- /**
- *
- * @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 graphics
+ * the graphics to set
+ */
+ protected void setGraphics(Graphics2D graphics) {
+ this.graphics = graphics;
+ }
- /**
- *
- * @param level
- * level to set
- * @return object with all parameters
- * @see #level
- */
- public Params level(final int level) {
- this.level = level;
- return this;
+/**
+ * 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);
+ }
/**
- *
- * @return scale value
- * @see #scale
- */
- public double getScale() {
- return scale;
- }
+ * 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;;
- /**
- *
- * @return x coordinate value
- * @see #x
- */
- public double getX() {
- return x;
+ /**
+ * 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();
}
+ saveToOutputStreamImplementation(os);
+ }
- /**
- *
- * @return y coordinate value
- * @see #y
- */
- public double getY() {
- return y;
+ /**
+ * 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;
+ }
+
+ /**
+ * This class contains a list of params that are used for drawing.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class Params {
/**
- *
- * @return width value
- * @see #width
+ * Default class logger.
*/
- public double getWidth() {
- return width;
- }
+ private final Logger logger = LogManager.getLogger(Params.class);
/**
- *
- * @return height value
- * @see #height
+ * Scale at which we want to visualize the map. The default value is 1.0 (no
+ * magnification).
*/
- public double getHeight() {
- return height;
- }
+ private double scale = 1;
/**
- *
- * @return model object
- * @see #model
+ * x coordinate from which we start to draw a map. This is absolute value on the
+ * map (scale doesn't influence it).
*/
- public Model getModel() {
- return model;
- }
+
+ private double x = 0;
/**
- *
- * @return background value
- * @see #background
+ * y coordinate from which we start to draw a map. This is absolute value on the
+ * map (scale doesn't influence it).
*/
- public boolean isBackground() {
- return background;
- }
+ private double y = 0;
/**
- *
- * @return nested value
- * @see #nested
+ * 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.
*/
- public boolean isNested() {
- return nested;
- }
+ private Double width = null;
/**
- * @return the level
- * @see #level
+ * 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.
*/
- public int getLevel() {
- return level;
- }
+ private Double height = null;
/**
- * Sets {@link #level} parameter from {@link String}.
- *
- * @param zoomLevel
- * new {@link #level} value
- * @return object with all parameters
+ * Model to be visualized.
*/
- public Params level(String zoomLevel) {
- if (zoomLevel == null) {
- logger.warn("Parameter equals to null...");
- } else {
- this.level = Integer.valueOf(zoomLevel);
- }
- return this;
- }
+ private Model model = null;
- @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;
- }
+ /**
+ * Should we draw white background.
+ */
+ private boolean background = true;
/**
- * 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
+ * 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.
*/
- public void addVisibleLayout(Map<Object, ColorSchema> map) {
- visibleLayouts.add(map);
- }
+ private int level = Integer.MAX_VALUE;
/**
- * @return the visibleLayouts
- * @see #visibleLayouts
+ * Should the visualization include hierarchical view or not.
*/
- public List<Map<Object, ColorSchema>> getVisibleLayouts() {
- return visibleLayouts;
+ 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;
}
/**
- * 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
+ * @param scale
+ * scale to set
+ * @return object with all parameters
+ * @see #scale
*/
- public List<ColorSchema> getVisibleLayoutsForElement(Object object) {
- List<ColorSchema> result = new ArrayList<>();
- for (Map<Object, ColorSchema> map : visibleLayouts) {
- result.add(map.get(object));
- }
- return result;
+ public Params scale(final int scale) {
+ this.scale = scale;
+ return this;
}
/**
- * 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
+ *
+ * @param x
+ * x coordinate to be set
+ * @return object with all parameters
+ * @see #x
*/
- public Color getMaxColor() {
- return maxColor;
+ public Params x(final double x) {
+ this.x = x;
+ return this;
}
- public Color getSimpleColor() {
- return simpleColor;
+ /**
+ * @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;
}
/**
- * 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
+ * @param y
+ * y coordinate to be set
+ * @return object with all parameters
+ * @see #y
*/
- public Color getMinColor() {
- return minColor;
+ public Params y(final double y) {
+ this.y = y;
+ return this;
}
/**
- * @param minColor
- * minColor to set
+ * @param y
+ * y coordinate to be set
* @return object with all parameters
- * @see #minColor
+ * @see #y
*/
- public Params minColor(Color minColor) {
- this.minColor = minColor;
+ public Params y(final int y) {
+ this.y = y;
return this;
}
/**
- * @param maxColor
- * maxColor to set
+ * @param width
+ * width to set
* @return object with all parameters
- * @see #maxColor
+ * @see #width
*/
- public Params maxColor(Color maxColor) {
- this.maxColor = maxColor;
+ public Params width(final double width) {
+ this.width = width;
return this;
}
/**
- * @param simpleColor
- * simpleColor to set
+ * @param width
+ * width to set
* @return object with all parameters
- * @see #simpleColor
+ * @see #width
*/
- public Params simpleColor(Color simpleColor) {
- this.simpleColor = simpleColor;
+ public Params width(final int width) {
+ this.width = (double) width;
return this;
}
/**
- * @return the sbgn
- * @see #sbgn
+ *
+ * @param height
+ * height to set
+ * @return object with all parameters
+ * @see #height
*/
- public boolean isSbgn() {
- return sbgn;
+ public Params height(final double height) {
+ this.height = height;
+ return this;
}
/**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
+ * @param height
+ * height to set
* @return object with all parameters
+ * @see #height
*/
- public Params sbgn(boolean sbgn) {
- this.sbgn = sbgn;
+ public Params height(final int height) {
+ this.height = (double) height;
return this;
}
- public Params colorExtractor(ColorExtractor colorExtractor) {
- return minColor(colorExtractor.getMinColor()).maxColor(colorExtractor.getMaxColor())
- .simpleColor(colorExtractor.getSimpleColor());
+ /**
+ *
+ * @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;
+ }
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger(AbstractImageGenerator.class);
+ /**
+ *
+ * @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;
+ }
- /**
- * Graphics object which allows to draw objects.
- */
- private Graphics2D graphics;
+ /**
+ *
+ * @param level
+ * level to set
+ * @return object with all parameters
+ * @see #level
+ */
+ public Params level(final int level) {
+ this.level = level;
+ return this;
+ }
- /**
- * SBGN display format.
- */
- private boolean sbgnFormat = false;
+ /**
+ *
+ * @return scale value
+ * @see #scale
+ */
+ public double getScale() {
+ return scale;
+ }
- /**
- * List of params used for drawing.
- */
- private Params params;
+ /**
+ *
+ * @return x coordinate value
+ * @see #x
+ */
+ public double getX() {
+ return x;
+ }
- /**
- * 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 appropriate 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;
+ /**
+ *
+ * @return y coordinate value
+ * @see #y
+ */
+ public double getY() {
+ return y;
}
- this.level = params.getLevel();
- this.scale = params.getScale();
- colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
+ /**
+ *
+ * @return width value
+ * @see #width
+ */
+ public double getWidth() {
+ return width;
+ }
- // 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());
+ /**
+ *
+ * @return height value
+ * @see #height
+ */
+ public double getHeight() {
+ return height;
+ }
- // turn on anti-aliasing
- graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ /**
+ *
+ * @return model object
+ * @see #model
+ */
+ public Model getModel() {
+ return model;
+ }
- graphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+ /**
+ *
+ * @return background value
+ * @see #background
+ */
+ public boolean isBackground() {
+ return background;
+ }
- graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+ /**
+ *
+ * @return nested value
+ * @see #nested
+ */
+ public boolean isNested() {
+ return nested;
+ }
- // set scale
- graphics.scale(1 / scale, 1 / scale);
+ /**
+ * @return the level
+ * @see #level
+ */
+ public int getLevel() {
+ return level;
+ }
- // move the upper left corner to coordinates
- graphics.translate(-params.getX(), -params.getY());
+ /**
+ * 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;
+ }
- 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);
+ @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;
}
- // Get the SBGN display format option from the model
- this.sbgnFormat = params.isSbgn();
+ /**
+ * 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);
+ }
- List<Drawable> bioEntities = new ArrayList<>();
- bioEntities.addAll(params.getModel().getBioEntities());
- for (Layer layer : params.getModel().getLayers()) {
- if (layer.isVisible()) {
- bioEntities.addAll(layer.getDrawables());
- }
+ /**
+ * @return the visibleLayouts
+ * @see #visibleLayouts
+ */
+ public List<Map<Object, ColorSchema>> getVisibleLayouts() {
+ return visibleLayouts;
}
- bioEntities.sort(BioEntity.Z_INDEX_COMPARATOR);
- // draw all elements
- for (Drawable element : bioEntities) {
- if (element instanceof Species) {
- drawSpecies((Species) element);
- } else if (element instanceof Reaction) {
- drawReaction((Reaction) element);
- } else if (element instanceof Compartment) {
- drawCompartment((Compartment) element);
- } else if (element instanceof LayerText) {
- drawText((LayerText) element);
- } else if (element instanceof LayerOval) {
- drawOval((LayerOval) element);
- } else if (element instanceof LayerRect) {
- drawRect((LayerRect) element);
- } else if (element instanceof PolylineData) {
- drawLine((PolylineData) element);
- } else {
- throw new DrawingException("Unknown class type: " + element);
+ /**
+ * 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;
}
- closeImageObject();
- setDrawn(true);
- }
- private void drawText(LayerText element) {
- new LayerTextConverter().draw(element, graphics);
- }
+ /**
+ * 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;
+ }
- private void drawRect(LayerRect element) {
- new LayerRectConverter().draw(element, graphics);
- }
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
- private void drawOval(LayerOval element) {
- new LayerOvalConverter().draw(element, graphics);
- }
+ /**
+ * 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;
+ }
- private void drawLine(PolylineData element) {
- new LayerLineConverter().draw(element, graphics);
- }
+ /**
+ * @param minColor
+ * minColor to set
+ * @return object with all parameters
+ * @see #minColor
+ */
+ public Params minColor(Color minColor) {
+ this.minColor = minColor;
+ return this;
+ }
- /**
- * Method called after drawing. It should close drawing canvas properly.
- */
- protected abstract void closeImageObject();
+ /**
+ * @param maxColor
+ * maxColor to set
+ * @return object with all parameters
+ * @see #maxColor
+ */
+ public Params maxColor(Color maxColor) {
+ this.maxColor = maxColor;
+ return this;
+ }
- /**
- * 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));
- }
-
- converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
-
- if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
- 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));
-
- }
-
- /**
- * 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();
+ /**
+ * @param simpleColor
+ * simpleColor to set
+ * @return object with all parameters
+ * @see #simpleColor
+ */
+ public Params simpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ return this;
}
- 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();
+ /**
+ * @return the sbgn
+ * @see #sbgn
+ */
+ public boolean isSbgn() {
+ return sbgn;
}
- saveToOutputStreamImplementation(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();
+ /**
+ * @param sbgn
+ * the sbgn to set
+ * @see #sbgn
+ * @return object with all parameters
+ */
+ public Params sbgn(boolean sbgn) {
+ this.sbgn = sbgn;
+ return this;
}
- 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();
+ public Params colorExtractor(ColorExtractor colorExtractor) {
+ return minColor(colorExtractor.getMinColor()).maxColor(colorExtractor.getMaxColor())
+ .simpleColor(colorExtractor.getSimpleColor());
}
- 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 5e09864ab1..a791fe3f3d 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
@@ -8,111 +8,111 @@ package lcsb.mapviewer.converter.graphics;
*/
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;
+ /**
+ * 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;
+ /**
+ * 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;
+ /**
+ * Should the map be displayed in SBGN format.
+ */
+ private boolean sbgnFormat = false;
- /**
- * Does the visualization include nesting/hierarchy.
- */
- private boolean nested = 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 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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 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;
- }
+ /**
+ * @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 scale
+ * @see #scale
+ */
+ public double getScale() {
+ return scale;
+ }
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
- /**
- * @return the nested
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
+ /**
+ * @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;
- }
+ @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 bf1d439e69..a92ed96b7a 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
@@ -8,31 +8,31 @@ package lcsb.mapviewer.converter.graphics;
*/
public class DrawingException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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
+ * @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);
- }
+ /**
+ * 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 1380ea0939..c0cecc00c7 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
@@ -1,12 +1,13 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Color;
+import java.awt.*;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.Pair;
@@ -24,155 +25,156 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
*
*/
public class ImageGenerators {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(ImageGenerators.class);
- /**
- * List of {@link AbstractImageGenerator} classes available in the system.
- */
- private List<Pair<String, Class<? extends AbstractImageGenerator>>> availableGenerators;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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;
+ /**
+ * 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()));
- }
+ /**
+ * 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);
- }
- }
+ } 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;
- }
+ /**
+ * 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
+ * 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);
+ /**
+ * 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
+ * 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);
- }
+ /**
+ * 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 e5c57e4b79..1fbff3b27e 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
@@ -1,11 +1,8 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
+import java.io.*;
import javax.imageio.ImageIO;
@@ -20,65 +17,66 @@ import lcsb.mapviewer.common.MimeType;
*/
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);
- }
+ /**
+ * 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
+ protected void closeImageObject() {
+ }
- @Override
- public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
- ImageIO.write(getBi(), "JPG", os);
- }
+ @Override
+ public void saveToFileImplementation(String fileName) throws IOException {
+ FileOutputStream fos = new FileOutputStream(new File(fileName));
+ saveToOutputStreamImplementation(fos);
+ fos.close();
+ }
- @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 saveToOutputStreamImplementation(OutputStream os) throws IOException {
+ ImageIO.write(getBi(), "JPG", os);
+ }
- @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 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 String getFormatName() {
- return "JPG image";
- }
+ @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 MimeType getMimeType() {
- return MimeType.JPG;
- }
+ @Override
+ public String getFormatName() {
+ return "JPG image";
+ }
- @Override
- public String getFileExtension() {
- return "jpg";
- }
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.JPG;
+ }
- @Override
- protected void closeImageObject() {
- }
+ @Override
+ public String getFileExtension() {
+ return "jpg";
+ }
}
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 5a288dec28..a761e69120 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
@@ -4,7 +4,8 @@ import java.io.File;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -22,6 +23,176 @@ import lcsb.mapviewer.model.map.model.Model;
*/
public class MapGenerator {
+ /**
+ * 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;
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(MapGenerator.class.getName());
+
+ /**
+ * 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 when there are some problems with removing files
+ */
+ public void removeLayout(final Layout dbLayout, String homeDir) throws IOException {
+ for (DataOverlayImageLayer imageLayer : dbLayout.getDataOverlayImageLayers()) {
+ String directory = imageLayer.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 + ")");
+ }
+ }
+ }
+
/**
* Parameter class with information for generating set of images:
* <ul>
@@ -33,37 +204,37 @@ public class MapGenerator {
* <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
@@ -230,176 +401,4 @@ public class MapGenerator {
}
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.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 when there are some problems with removing files
- */
- public void removeLayout(final Layout dbLayout, String homeDir) throws IOException {
- for (DataOverlayImageLayer imageLayer: dbLayout.getDataOverlayImageLayers()) {
- String directory = imageLayer.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 + ")");
- }
- }
- }
-
}
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 bae85e5d45..c12642bec7 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.converter.graphics;
import java.awt.image.BufferedImage;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Extension of the image generator class that use standard awt implementation
@@ -12,54 +13,54 @@ import org.apache.logging.log4j.*;
*
*/
public abstract class NormalImageGenerator extends AbstractImageGenerator {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(NormalImageGenerator.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(NormalImageGenerator.class);
- /**
- * Buffered image structure used for image generating.
- */
- private BufferedImage bi;
+ /**
+ * 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);
- }
+ /**
+ * 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());
- }
+ @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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/PdfFontMapper.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfFontMapper.java
index 0f1b991e9a..544f7a7574 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfFontMapper.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfFontMapper.java
@@ -1,9 +1,10 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Font;
+import java.awt.*;
import java.io.IOException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import com.itextpdf.awt.DefaultFontMapper;
import com.itextpdf.text.DocumentException;
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 fac7551c2a..575afeb5c6 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
@@ -1,15 +1,11 @@
package lcsb.mapviewer.converter.graphics;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
+import java.io.*;
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.*;
import com.itextpdf.text.pdf.PdfContentByte;
import com.itextpdf.text.pdf.PdfWriter;
@@ -36,6 +32,21 @@ public class PdfImageGenerator extends AbstractImageGenerator {
*/
private Document pdfDocument;
+ /**
+ * 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 createImageObject(final double width, final double height) {
try {
@@ -53,6 +64,12 @@ public class PdfImageGenerator extends AbstractImageGenerator {
}
+ @Override
+ protected void closeImageObject() {
+ getGraphics().dispose();
+ pdfDocument.close();
+ }
+
@Override
public void saveToFileImplementation(final String fileName) throws IOException {
FileOutputStream fos = new FileOutputStream(fileName);
@@ -60,27 +77,6 @@ public class PdfImageGenerator extends AbstractImageGenerator {
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);
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 2c92508fcd..732fba87c8 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
@@ -1,15 +1,13 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
+import java.io.*;
import javax.imageio.ImageIO;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.MimeType;
@@ -22,71 +20,72 @@ import lcsb.mapviewer.common.MimeType;
*/
public class PngImageGenerator extends NormalImageGenerator {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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";
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 3ab694582f..def8beed96 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
@@ -1,15 +1,10 @@
package lcsb.mapviewer.converter.graphics;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
+import java.io.*;
import org.apache.batik.dom.GenericDOMImplementation;
import org.apache.batik.svggen.SVGGraphics2D;
-import org.w3c.dom.DOMImplementation;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -22,84 +17,86 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
public class SvgImageGenerator extends AbstractImageGenerator {
-
+
/**
* Root dom element. We need it to be able to provide viewBox.
*/
private Element root;
- @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.
- SVGGraphics2D graphics =new SVGGraphics2D(document);
- root = graphics.getRoot();
- root.setAttributeNS(null, "viewBox", "0 0 "+(int)width+" "+(int)height);
- setGraphics(graphics);
-
- }
-
- @Override
- public void saveToFileImplementation(final String fileName) throws IOException {
- saveToOutputStreamImplementation(new FileOutputStream(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 {
- //for some reason if you remove this line either viewbox is not define or content is not there
- ((SVGGraphics2D) getGraphics()).getRoot(root);
- ((SVGGraphics2D) getGraphics()).stream(root, 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";
- }
+ /**
+ * 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 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.
+ SVGGraphics2D graphics = new SVGGraphics2D(document);
+ root = graphics.getRoot();
+ root.setAttributeNS(null, "viewBox", "0 0 " + (int) width + " " + (int) height);
+ setGraphics(graphics);
+
+ }
+
+ @Override
+ protected void closeImageObject() {
+ }
+
+ @Override
+ public void saveToFileImplementation(final String fileName) throws IOException {
+ saveToOutputStreamImplementation(new FileOutputStream(fileName));
+ }
+
+ @Override
+ public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
+ // for some reason if you remove this line either viewbox is not define or
+ // content is not there
+ ((SVGGraphics2D) getGraphics()).getRoot(root);
+ ((SVGGraphics2D) getGraphics()).stream(root, 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 558e6f9c71..81bb5195e9 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.converter.graphics.bioEntity;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -14,15 +15,8 @@ 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;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.species.*;
/**
* This interface defines what operations should be possible to convert
@@ -35,12 +29,16 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public abstract class BioEntityConverter<T extends BioEntity> {
+ /**
+ * Alpha value (0..255) used for visualizing overlay data that are normally
+ * visualized in javascript.
+ */
+ public static final int LAYOUT_ALPHA = 200;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private final Logger logger = LogManager.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
@@ -48,12 +46,6 @@ public abstract class BioEntityConverter<T extends BioEntity> {
*/
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.
*
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 e8648ce214..40f9413fa2 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
@@ -1,60 +1,24 @@
package lcsb.mapviewer.converter.graphics.bioEntity;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.element.compartment.*;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.*;
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.compartment.*;
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.model.map.species.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -66,138 +30,119 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(BioEntityConverterImpl.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(BioEntityConverterImpl.class.getName());
+ /**
+ * Converter used for conversion of the {@link Element} given in constructor.
+ */
+ @SuppressWarnings("rawtypes")
+ private BioEntityConverter elementConverter = null;
- /**
- * 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");
- }
- }
+ /**
+ * 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) {
- /**
- * Converter used for conversion of the {@link Element} given in constructor.
- */
- @SuppressWarnings("rawtypes")
- private BioEntityConverter elementConverter = null;
+ // 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);
+ }
- /**
- * 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);
- }
+ // 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());
+ }
+ }
- @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);
- }
- }
+ /**
+ * 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 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);
- }
- }
+ /**
+ * 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");
+ }
+ }
@SuppressWarnings("unchecked")
@Override
@@ -205,4 +150,26 @@ public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
elementConverter.draw(bioEntity, 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);
+ }
+ }
+
+ @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);
+ }
+ }
+
}
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 973cf072fc..440e420986 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
@@ -1,7 +1,6 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element;
-import java.awt.Graphics2D;
-import java.awt.Image;
+import java.awt.*;
import java.io.ByteArrayInputStream;
import java.io.IOException;
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 6e5b24fa09..8f67f5ba6e 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
@@ -1,15 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -27,70 +22,73 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class BottomSquareCompartmentConverter extends CompartmentConverter<BottomSquareCompartment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(BottomSquareCompartmentConverter.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * 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
- protected void drawImpl(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();
+ @Override
+ protected void drawImpl(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()));
+ // 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;
- }
+ 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);
+ // 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);
+ // 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);
- }
- }
+ // 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 99ace59a81..7efa86da7d 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.util.List;
@@ -34,156 +32,154 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public abstract class CompartmentConverter<T extends Compartment> extends ElementConverter<T> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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();
-
- /**
- * 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 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 {
- if (alias.getGlyph() != null) {
- drawGlyph(alias, graphics);
- } else {
- drawImpl(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);
- }
+ /**
+ * Alpha level for inside of the transparent compartments.
+ */
+ public static final int DEFAULT_ALPHA_LEVEL = 8;
+ /**
+ * Default alpha level for semi-transparent borders.
+ */
+ protected static final int HIGH_ALPHA_LEVEL = 127;
+ /**
+ * Default font size.
+ */
+ private static final int DEFAULT_FONT_SIZE = 10;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(CompartmentConverter.class.getName());
+ /**
+ * Default alpha level for transparent compartments.
+ */
+ private static int alphaLevel = DEFAULT_ALPHA_LEVEL;
+ /**
+ * Class used for transformation of lines.
+ */
+ private LineTransformation lineTransformation = new LineTransformation();
+ /**
+ * 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;
+ };
+
+ /**
+ * @return the alphaLevel
+ */
+ public static int getAlphaLevel() {
+ return alphaLevel;
+ }
+
+ /**
+ * @param alphaLevel
+ * the alphaLevel to set
+ */
+ public static void setAlphaLevel(int alphaLevel) {
+ CompartmentConverter.alphaLevel = alphaLevel;
+ }
+
+ /**
+ * @return the lineTransformation
+ */
+ protected LineTransformation getLineTransformation() {
+ return lineTransformation;
+ }
+
+ /**
+ * @param lineTransformation
+ * the lineTransformation to set
+ */
+ protected void setLineTransformation(LineTransformation lineTransformation) {
+ this.lineTransformation = lineTransformation;
+ }
+
+ @Override
+ public void draw(T alias, Graphics2D graphics, ConverterParams params,
+ List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
+ if (alias.getGlyph() != null) {
+ drawGlyph(alias, graphics);
+ } else {
+ drawImpl(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);
+ }
+
+ @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;
+ }
+ }
}
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 7ec656b2e1..b33f237530 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
@@ -1,13 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -16,8 +13,6 @@ import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import org.apache.logging.log4j.*;
-
/**
* Class responsible for drawing LeftSquareCompartment on the Graphics2D.
*
@@ -26,73 +21,75 @@ import org.apache.logging.log4j.*;
*/
public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSquareCompartment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(LeftSquareCompartmentConverter.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing elements
+ *
+ */
+ public LeftSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
- @Override
- protected void drawImpl(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();
+ @Override
+ protected void drawImpl(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()));
+ // 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;
- }
+ 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);
+ // 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);
- }
+ // 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);
+ // 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);
- }
- }
+ // 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 d52073e682..9732dffbf7 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
@@ -1,12 +1,7 @@
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 java.awt.*;
+import java.awt.geom.*;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -25,83 +20,85 @@ import lcsb.mapviewer.model.map.species.Species;
*/
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);
- }
+ /**
+ * 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());
- }
+ /**
+ * 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
- protected void drawImpl(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();
+ @Override
+ protected void drawImpl(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());
+ // 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;
- }
+ 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));
+ 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);
+ // 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);
+ // 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);
+ // 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);
- }
- }
- }
+ // 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 87bcb8fb02..b2741dec63 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
@@ -1,9 +1,6 @@
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.*;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
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 07cbf55467..53bf786fe9 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
@@ -1,13 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -17,8 +14,6 @@ import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.logging.log4j.*;
-
/**
* Class responsible for drawing RightSquareCompartment on the Graphics2D.
*
@@ -27,77 +22,80 @@ import org.apache.logging.log4j.*;
*/
public class RightSquareCompartmentConverter extends CompartmentConverter<RightSquareCompartment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(RightSquareCompartmentConverter.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * 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
- protected void drawImpl(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();
+ @Override
+ protected void drawImpl(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()));
+ // 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;
- }
+ 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);
+ // 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);
+ // 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);
+ // 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);
- }
+ // 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 28a135e7ac..f7b4fb6127 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
@@ -1,14 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -26,90 +22,92 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
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 = LogManager.getLogger(SquareCompartmentConverter.class.getName());
+ /**
+ * 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 = LogManager.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);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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
- protected void drawImpl(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();
+ @Override
+ protected void drawImpl(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());
+ // 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;
- }
+ 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));
+ 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);
+ // 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);
+ // 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);
+ // 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);
- }
- }
+ // 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 fb9f79783f..f24d5b112a 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
@@ -1,13 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -17,8 +14,6 @@ import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.logging.log4j.*;
-
/**
* Class responsible for drawing TopSquareCompartment on the {@link Graphics2D}.
*
@@ -27,68 +22,70 @@ import org.apache.logging.log4j.*;
*/
public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquareCompartment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(TopSquareCompartmentConverter.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * 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
- protected void drawImpl(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
+ @Override
+ protected void drawImpl(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()));
+ 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;
- }
+ 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);
+ // 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);
- }
+ 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);
- }
- }
+ // 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 cda3756654..157e0c61eb 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}.
+ * 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/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index df69b75fdd..1acd6b1f19 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -1,14 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
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 7d1ec5191d..5f523dfa78 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
@@ -1,15 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -163,9 +158,14 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
}
}
+ @Override
+ public PathIterator getBoundPathIterator(final Complex complex) {
+ return getAliasPath(complex).getPathIterator(new AffineTransform());
+ }
+
/**
* Returns the border of {@link Complex}.
- *
+ *
* @param complex
* exact object for which we want to get a border
* @return border of the {@link Complex}
@@ -183,9 +183,4 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
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 3d0c456e88..888cd469a5 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
@@ -1,15 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -26,110 +21,110 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
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 = LogManager.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
- protected void drawImpl(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");
- }
+ /**
+ * 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 = LogManager.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
+ protected void drawImpl(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 b737c0071d..3d59e03818 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
@@ -1,16 +1,11 @@
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.awt.*;
+import java.awt.geom.*;
import java.util.ArrayList;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -27,96 +22,98 @@ import lcsb.mapviewer.model.map.species.Species;
*/
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 = LogManager.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
- protected void drawImpl(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());
- }
+ /**
+ * 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 = LogManager.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
+ protected void drawImpl(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/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
index 434fd029f5..f14871e30a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
@@ -1,14 +1,11 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.Stroke;
+import java.awt.*;
import java.awt.geom.AffineTransform;
import java.awt.geom.PathIterator;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
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 c8b7b82220..ffe8c75cfd 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
@@ -1,13 +1,11 @@
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.*;
import java.awt.geom.Ellipse2D;
import java.awt.geom.PathIterator;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
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 9523b1052e..a2ed8af2c6 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
@@ -1,14 +1,10 @@
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -23,64 +19,64 @@ import lcsb.mapviewer.model.map.species.Phenotype;
*
*/
public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(PhenotypeConverter.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing elements
+ *
+ */
+ public PhenotypeConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
- @Override
- protected void drawImpl(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getPhenotypePath(phenotype);
+ @Override
+ protected void drawImpl(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);
- }
+ 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;
- }
+ /**
+ * 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());
- }
+ @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/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
index 740c279f09..5f223086fb 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
@@ -1,31 +1,18 @@
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.Area;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
+import java.awt.*;
+import java.awt.geom.*;
import java.util.ArrayList;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-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.Species;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index 0d1976a6bd..0182f77db3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
@@ -7,15 +7,11 @@
*/
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 java.awt.*;
+import java.awt.geom.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
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 c62e51d3af..e5b42d58b5 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
@@ -1,12 +1,7 @@
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 java.awt.*;
+import java.awt.geom.*;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -23,110 +18,112 @@ import lcsb.mapviewer.model.map.species.Species;
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
- protected void drawImpl(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());
- }
+ /**
+ * 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
+ protected void drawImpl(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/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
index 3f1ef8a8e6..a72c5318ea 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
@@ -1,13 +1,11 @@
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.*;
import java.awt.geom.Ellipse2D;
import java.awt.geom.PathIterator;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -42,7 +40,8 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
}
@Override
- protected void drawImpl(final SimpleMolecule simpleMolecule, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final SimpleMolecule simpleMolecule, final Graphics2D graphics,
+ final ConverterParams params) {
int homodir;
if (params.isSbgnFormat()) {
// If the SBGN display mode is set, multimer is shown as two stacked
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 393a369d95..eec1afd1cb 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -1,15 +1,7 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
+import java.awt.*;
+import java.awt.geom.*;
import java.util.List;
import org.apache.logging.log4j.LogManager;
@@ -22,22 +14,11 @@ 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.ArrowTransformation;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.graphics.*;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
-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.ModificationState;
-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.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* This class defines basics used for drawing {@link Species} (node in the graph
@@ -50,93 +31,76 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
*/
public abstract class SpeciesConverter<T extends Species> extends ElementConverter<T> {
+ /**
+ * Length of the arrow for transcription site visualization.
+ */
+ public static final int TRANSCRIPTION_SITE_ARROW_LENGTH = 8;
+ /**
+ * Angle of the arrow for transcription site visualization.
+ */
+ public static final double TRANSCRIPTION_SITE_ARROW_ANGLE = 3 * Math.PI / 4;
+ /**
+ * What is the distance between homodimer aliases when homodimer>1.
+ */
+ public static final int HOMODIMER_OFFSET = 6;
/**
* Default font size for the modifier description.
*/
protected static final int DEFAULT_SPECIES_MODIFIER_FONT_SIZE = 10;
-
/**
* Default diameter of the modification residues.
*/
protected static final int DEFAULT_MODIFICATION_DIAMETER = 15;
-
/**
* How far from the original shape should the activity border be drawn.
*/
protected static final int ACTIVITY_BORDER_DISTANCE = 5;
-
/**
* Default species font size.
*/
protected static final int DEFAULT_SPECIES_FONT_SIZE = 12;
-
/**
* Height of the ellipse that contain structural state description.
*/
private static final int STRUCTURAL_STATE_HEIGHT = 20;
-
/**
* Height of the rectangle that contains unit of information.
*/
private static final int UNIT_OF_INFORMATION_HEIGHT = 20;
-
/**
* Size of the margin in the structural state description.
*/
private static final int TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC = 40;
-
/**
* Size of the margin in the unit of information description.
*/
private static final int TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC = 20;
-
/**
* Minimum width of the structural state ellipse.
*/
private static final int MIN_STRUCTURAL_STATE_WIDTH = 60;
-
/**
* Minimum width of the unit of information rectangle.
*/
private static final int MIN_UNIT_OF_INFORMATION_WIDTH = 40;
-
- /**
- * Length of the arrow for transcription site visualization.
- */
- public static final int TRANSCRIPTION_SITE_ARROW_LENGTH = 8;
-
- /**
- * Angle of the arrow for transcription site visualization.
- */
- public static final double TRANSCRIPTION_SITE_ARROW_ANGLE = 3 * Math.PI / 4;
-
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(SpeciesConverter.class.getName());
-
/**
* Graphical helper object with line transformation functions.
*/
private LineTransformation lineTransformation = new LineTransformation();
private ArrowTransformation arrowTransformation = new ArrowTransformation();
-
/**
* Default font used to draw structural state of the species.
*/
private Font structuralFont = null;
-
/**
* Default font used to draw unit of information of the species.
*/
private Font unitOfInformationFont = null;
-
- /**
- * What is the distance between homodimer aliases when homodimer>1.
- */
- public static final int HOMODIMER_OFFSET = 6;
-
/**
* Object that helps to convert {@link ColorSchema} values into colors.
*/
@@ -203,29 +167,9 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
return name;
}
- @Override
- public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
- String text = getText(species);
- Font oldFont = graphics.getFont();
- Font font = getFont(species, params);
- graphics.setColor(Color.BLACK);
- graphics.setFont(font);
-
- Point2D point = species.getCenter();
- if (species instanceof Complex) {
- if (((Complex) species).getElements().size() > 0) {
- if (isTransparent(species, params)) {
- point.setLocation(point.getX(), species.getY() + species.getHeight() - graphics.getFontMetrics().getAscent());
- }
- }
- }
- drawText(point, text, graphics, true, true);
- graphics.setFont(oldFont);
- }
-
/**
* Return width of the text.
- *
+ *
* @param text
* width of this text will be computed
* @param graphics
@@ -251,7 +195,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Returns text height.
- *
+ *
* @param text
* height of this text will be computed
* @param graphics
@@ -276,7 +220,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
* This method draws a string on graphics using current font. The coordinates of
* the text is given as a point. Both parameters centered described if text
* should be automatically centered horizontally and vertically.
- *
+ *
* @param point
* where the text should be drawn
* @param text
@@ -311,7 +255,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Returns line style used for drawing alias border.
- *
+ *
* @param species
* {@link Species} to be drawn
* @return style of the line used to draw {@link Species}
@@ -334,7 +278,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Returns border of the {@link Species} as {@link PathIterator}.
- *
+ *
* @param species
* {@link Species} for which we are looking for a border
* @return {@link PathIterator} object defining given {@link Species}
@@ -389,7 +333,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Draws structural state description of the alias (ellipse in the top part of
* the alias).
- *
+ *
* @param text
* state description text
* @param species
@@ -434,7 +378,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Draws unit of information for the {@link Species} (rectangle in the top part
* of the alias).
- *
+ *
* @param text
* unit of information text
* @param species
@@ -505,6 +449,26 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
graphics.setColor(oldColor);
}
+ @Override
+ public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
+ String text = getText(species);
+ Font oldFont = graphics.getFont();
+ Font font = getFont(species, params);
+ graphics.setColor(Color.BLACK);
+ graphics.setFont(font);
+
+ Point2D point = species.getCenter();
+ if (species instanceof Complex) {
+ if (((Complex) species).getElements().size() > 0) {
+ if (isTransparent(species, params)) {
+ point.setLocation(point.getX(), species.getY() + species.getHeight() - graphics.getFontMetrics().getAscent());
+ }
+ }
+ }
+ drawText(point, text, graphics, true, true);
+ graphics.setFont(oldFont);
+ }
+
/**
* This method draws modification of the alias. If drawEmptyModification is set
* to false then modification is not drawn if empty. If drawDescription is set
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
index 1bd3793542..0dd8e7577f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
@@ -1,13 +1,11 @@
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.*;
import java.awt.geom.Ellipse2D;
import java.awt.geom.PathIterator;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
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 7ef5183bd3..e5785c8222 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
@@ -1,13 +1,7 @@
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.awt.*;
+import java.awt.geom.*;
import java.util.ArrayList;
import java.util.List;
@@ -22,17 +16,10 @@ 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.graphics.*;
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.*;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
/**
@@ -43,50 +30,44 @@ import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
*/
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();
-
+ /**
+ * When drawing operator this value defines radius of the joining operator
+ * circle.
+ */
+ private static final int DEFAULT_OPERATOR_RADIUS = 6;
/**
* 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 = LogManager.getLogger(ReactionConverter.class.getName());
+ static {
+ DEFAULT_COLOR_SCHEMA.setColor(Color.BLACK);
+ DEFAULT_COLOR_SCHEMA.setLineWidth(DEFAULT_COLOR_SCHEMA_LINE_WIDTH);
+ }
+
/**
* Font used for drawing reaction description on the map.
*/
@@ -140,19 +121,21 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
Point2D startPoint = line.getPoints().get(line.getPoints().size() / 2 - 1);
Point2D endPoint = line.getPoints().get(line.getPoints().size() / 2);
if (startPoint.distance(endPoint) > RECT_SIZE) {
- Point2D rectStartPoint = pointTransformation.getPointOnLine(startPoint, endPoint, 0.5 - RECT_SIZE/(2*startPoint.distance(endPoint)));
- Point2D rectEndPoint = pointTransformation.getPointOnLine(startPoint, endPoint, 0.5 + RECT_SIZE/(2*startPoint.distance(endPoint)));
+ Point2D rectStartPoint = pointTransformation.getPointOnLine(startPoint, endPoint,
+ 0.5 - RECT_SIZE / (2 * startPoint.distance(endPoint)));
+ Point2D rectEndPoint = pointTransformation.getPointOnLine(startPoint, endPoint,
+ 0.5 + RECT_SIZE / (2 * startPoint.distance(endPoint)));
PolylineData preRectangleLine = new PolylineData();
preRectangleLine.addPoint(startPoint);
preRectangleLine.addPoint(rectStartPoint);
-
+
PolylineData postRectangleLine = new PolylineData();
postRectangleLine.addPoint(rectEndPoint);
postRectangleLine.addPoint(endPoint);
-
+
arrowTransformation.drawLine(preRectangleLine, graphics);
arrowTransformation.drawLine(postRectangleLine, graphics);
-
+
startPoint = rectStartPoint;
endPoint = rectEndPoint;
}
@@ -299,9 +282,13 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
}
+ @Override
+ public void drawText(Reaction bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+ }
+
/**
* Modify reaction with data from {@link ColorSchema}.
- *
+ *
* @param reaction
* reaction to modify
* @param colorSchema
@@ -326,7 +313,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
/**
* Draw modifier on the graphics2d.
- *
+ *
* @param graphics
* where we want to draw the object
* @param modifier
@@ -339,7 +326,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
/**
* Draw operator on the graphics2d.
- *
+ *
* @param graphics
* where we want to draw the object
* @param operator
@@ -386,7 +373,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
/**
* Draw product on the graphics2D.
- *
+ *
* @param graphics
* where we want to draw the object
* @param product
@@ -398,7 +385,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
/**
* Draw reactant on the graphics2D.
- *
+ *
* @param graphics
* where the reactant should be drawn
* @param reactant
@@ -409,7 +396,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @return {@link #descFont}
*/
protected Font getDescFont() {
@@ -417,7 +404,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @param descFont
* new {@link #descFont} value
*/
@@ -426,7 +413,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @return {@link #lineTransformation}
*/
protected LineTransformation getLineTransformation() {
@@ -434,7 +421,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @param lineTransformation
* new {@link #lineTransformation}
*/
@@ -443,7 +430,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @return {@link #arrowTransformation}
*/
protected ArrowTransformation getArrowTransformation() {
@@ -451,7 +438,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @param arrowTransformation
* new {@link #arrowTransformation}
*/
@@ -460,7 +447,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @return {@link #pointTransformation}
*/
protected PointTransformation getPointTransformation() {
@@ -468,7 +455,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
/**
- *
+ *
* @param pointTransformation
* new {@link #pointTransformation}
*/
@@ -476,8 +463,4 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
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 679fb7d63c..185e64decf 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
@@ -4,4 +4,3 @@
* {@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 e7af708f14..4c52c29168 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
@@ -1,23 +1,16 @@
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.awt.*;
+import java.awt.geom.*;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
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 lcsb.mapviewer.model.graphics.*;
/**
* Class containing basic function for drawing arrows.
@@ -301,9 +294,9 @@ public class ArrowTransformation {
/**
* This method creates a General Path that describes triangle end of an arrow.
- * The parameters determine position of segment line (line), the length of
- * arrow end (len) and angle of an arrow. The open field determines if triangle
- * should be closed or not.
+ * The parameters determine position of segment 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
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 07d1aac5b1..d49999491e 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
@@ -1,14 +1,14 @@
package lcsb.mapviewer.converter.graphics.geometry;
-import java.awt.Font;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.List;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.*;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
/**
* This is utility class that helps to find optimal font to fit text into
@@ -18,230 +18,232 @@ import org.apache.logging.log4j.*;
*
*/
public final class FontFinder {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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);
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 e9618b89bb..4b97186c13 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
@@ -9,18 +9,18 @@ package lcsb.mapviewer.converter.graphics.geometry;
*/
public class RectangleTooSmallException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor with text message.
- *
- * @param message
- * string message for this exception
- */
- public RectangleTooSmallException(String message) {
- super(message);
- }
+ /**
+ * 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 4ca2ad7a80..2f5d349063 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
@@ -3,4 +3,3 @@
*
*/
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 aafbe66929..fbba074aa8 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
@@ -1,14 +1,12 @@
package lcsb.mapviewer.converter.graphics.layer;
-import java.awt.Graphics2D;
+import java.awt.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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 lcsb.mapviewer.model.map.layout.graphics.*;
/**
* This class allows to draw layer on Graphics2D.
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerLineConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerLineConverter.java
index 5ec1818d22..c89d1d9876 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerLineConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerLineConverter.java
@@ -1,9 +1,9 @@
package lcsb.mapviewer.converter.graphics.layer;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
import lcsb.mapviewer.model.graphics.PolylineData;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerOvalConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerOvalConverter.java
index 3ab35e7117..2cfc3360a9 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerOvalConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerOvalConverter.java
@@ -1,10 +1,10 @@
package lcsb.mapviewer.converter.graphics.layer;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Ellipse2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerRectConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerRectConverter.java
index 5f8a26d202..757a9e0906 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerRectConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerRectConverter.java
@@ -1,10 +1,10 @@
package lcsb.mapviewer.converter.graphics.layer;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Rectangle2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerTextConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerTextConverter.java
index 1f7d1958c5..66908cb1c9 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerTextConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerTextConverter.java
@@ -1,10 +1,10 @@
package lcsb.mapviewer.converter.graphics.layer;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Rectangle2D;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -16,17 +16,15 @@ import lcsb.mapviewer.model.map.layout.graphics.LayerText;
*/
public class LayerTextConverter {
+ /**
+ * Color used for text frames.
+ */
+ private static final Color FRAME_COLOR = Color.LIGHT_GRAY;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(LayerTextConverter.class.getName());
-
- /**
- * Color used for text frames.
- */
- private static final Color FRAME_COLOR = Color.LIGHT_GRAY;
-
/**
* Should the border around text be visible.
*/
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 62859860b8..2def339c01 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
@@ -3,4 +3,3 @@
* 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 405d155a7b..a159255963 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
@@ -8,9 +8,9 @@
* AbstractImageGenerator} is recommended. There are two implementation of this
* class:
* <ul>
- * <li> {@link lcsb.mapviewer.converter.graphics.NormalImageGenerator
+ * <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
+ * <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
@@ -24,4 +24,3 @@
*
*/
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 e2961fbbf5..d4ec37f45d 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
@@ -1,14 +1,10 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -24,459 +20,456 @@ import lcsb.mapviewer.model.map.species.Element;
*/
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 = LogManager.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;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(PlaceFinder.class.getName());
+ /**
+ * 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();
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+ }
}
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 8968ad062e..678984743c 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
@@ -3,4 +3,3 @@
* among many overlapping rectangles.
*/
package lcsb.mapviewer.converter.graphics.placefinder;
-
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java
index 18164cfa01..2ea7cfcd77 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java
@@ -4,13 +4,11 @@ import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
-import java.awt.Graphics2D;
+import java.awt.*;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
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 3d6271639f..d526090d6f 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
@@ -10,16 +10,16 @@ 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,
- SvgImageGeneratorTest.class
+ AbstractImageGeneratorTest.class,
+ AllBioEntityTests.class,
+ AllGeometryTests.class,
+ AllPlaceFinderTest.class,
+ ConverterTest.class,
+ ImageGeneratorsTest.class,
+ MapGeneratorTest.class,
+ NormalImageGeneratorTest.class,
+ PdfImageGeneratorTest.class,
+ SvgImageGeneratorTest.class
})
public class AllGraphicsTests {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java
index 7631445290..5cbfae2e29 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.graphics;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.awt.*;
import java.awt.geom.Point2D;
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 70ab35b83a..c86497984e 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
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 691dce81bf..472f5be2d3 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
import java.io.File;
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 00307235fc..61e529e794 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfFontMapperTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfFontMapperTest.java
index ce988d264e..af04bd96ed 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfFontMapperTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfFontMapperTest.java
@@ -3,7 +3,7 @@ package lcsb.mapviewer.converter.graphics;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
-import java.awt.Font;
+import java.awt.*;
import org.junit.Test;
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 5d1a0f1d0b..6ca76d4d91 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
@@ -1,11 +1,12 @@
package lcsb.mapviewer.converter.graphics;
-import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.io.File;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java
index 1557f4b872..d6ad4e15a0 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java
@@ -4,9 +4,7 @@ import static org.junit.Assert.assertTrue;
import java.io.ByteArrayOutputStream;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -24,14 +22,14 @@ public class SvgImageGeneratorTest extends GraphicsTestFunctions {
@Test
public void testSaveToFile() throws Exception {
- Model model = createCompartmentModel();
+ Model model = createCompartmentModel();
- SvgImageGenerator sig = new SvgImageGenerator(new AbstractImageGenerator.Params().model(model));
+ SvgImageGenerator sig = new SvgImageGenerator(new AbstractImageGenerator.Params().model(model));
- ByteArrayOutputStream output = new ByteArrayOutputStream();
- sig.saveToOutputStream(output);
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ sig.saveToOutputStream(output);
- assertTrue(output.toString().contains("viewBox"));
+ assertTrue(output.toString().contains("viewBox"));
}
private Model createCompartmentModel() {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
index 84b9cdc5c0..69bf1f7d0e 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
@@ -1,14 +1,10 @@
package lcsb.mapviewer.converter.graphics.bioEntity;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.anyInt;
-import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Image;
+import java.awt.*;
import java.awt.geom.GeneralPath;
import java.awt.geom.Point2D;
import java.awt.image.BufferedImage;
@@ -16,10 +12,7 @@ import java.awt.image.ImageObserver;
import java.io.File;
import java.nio.file.Files;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.commands.ColorExtractor;
@@ -29,10 +22,7 @@ import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.modifier.Catalysis;
-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.model.map.reaction.*;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class BioEntityConverterImplTest extends GraphicsTestFunctions {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java
index 7b04cd3b36..5f0c137114 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.image.BufferedImage;
import org.junit.Test;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java
index 1e97a005a4..acd62dd972 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java
@@ -1,9 +1,9 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.image.BufferedImage;
import org.apache.logging.log4j.LogManager;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index f8cc62d449..051b9670fe 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -1,8 +1,10 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
import java.awt.*;
import java.awt.geom.Point2D;
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 aedacee988..237da54fe4 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
@@ -1,28 +1,20 @@
package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
import static org.junit.Assert.assertTrue;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.anyDouble;
-import static org.mockito.ArgumentMatchers.anyInt;
-import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.awt.image.BufferedImage;
-import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.*;
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.junit.*;
import org.mockito.InOrder;
import org.mockito.Mockito;
@@ -34,13 +26,7 @@ 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.reaction.*;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
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 ed479adf11..e3c0ad0918 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
@@ -1,9 +1,8 @@
package lcsb.mapviewer.converter.graphics.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
-import java.awt.Graphics2D;
+import java.awt.*;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.image.BufferedImage;
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 4e2b9ac0d4..3b069c197f 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.graphics.geometry;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.*;
import java.awt.geom.Rectangle2D;
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 d06da1242e..ca7a275e2b 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
@@ -7,7 +7,8 @@ import java.awt.geom.Rectangle2D;
import java.io.IOException;
import java.util.Arrays;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -17,131 +18,130 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
public class AllPlaceFinderTest {
- Logger logger = LogManager.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);
- }
- }
+ final String out = "map_images/testOutput";
+ final String folder = "testFiles/placeFinderFiles/";
+ Logger logger = LogManager.getLogger(AllPlaceFinderTest.class);
+ 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/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index c834d312ae..fc092330c4 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -1,35 +1,19 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.awt.Color;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.awt.*;
+import java.util.*;
import javax.xml.stream.XMLStreamException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.SBasePlugin;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.BoundingBox;
-import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.sbml.jsbml.ext.render.ColorDefinition;
-import org.sbml.jsbml.ext.render.Ellipse;
-import org.sbml.jsbml.ext.render.LineEnding;
-import org.sbml.jsbml.ext.render.LocalRenderInformation;
-import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.*;
import org.sbml.jsbml.ext.render.Polygon;
-import org.sbml.jsbml.ext.render.RenderConstants;
-import org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin;
-import org.sbml.jsbml.ext.render.RenderGroup;
-import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
-import org.sbml.jsbml.ext.render.RenderPoint;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -44,27 +28,21 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(SbmlBioEntityExporter.class);
-
+ protected Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
+ Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
/**
* SBML Layout used when exporting map.
*/
private Layout layout;
-
/**
* Map that we are exporting.
*/
private lcsb.mapviewer.model.map.model.Model minervaModel;
-
/**
* SBML model to which we are exporting.
*/
private Model sbmlModel;
-
private Map<String, S> sbmlElementByElementId = new HashMap<>();
- Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
-
- protected Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
-
private int idCounter = 0;
private Set<SbmlExtension> sbmlExtensions = new HashSet<>();
@@ -417,12 +395,12 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
return style;
}
- public void setProvideDefaults(boolean provideDefaults) {
- this.provideDefaults = provideDefaults;
- }
-
protected boolean isProvideDefaults() {
return provideDefaults;
}
+ public void setProvideDefaults(boolean provideDefaults) {
+ this.provideDefaults = provideDefaults;
+ }
+
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index 4b6d452cf1..294eb975e2 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -1,26 +1,17 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.HashMap;
-import java.util.HashSet;
+import java.awt.*;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.ext.SBasePlugin;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
-import org.sbml.jsbml.ext.layout.TextGlyph;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.sbml.jsbml.ext.render.LocalRenderInformation;
-import org.sbml.jsbml.ext.render.LocalStyle;
-import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
+import org.sbml.jsbml.ext.render.*;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
@@ -60,10 +51,11 @@ public class SbmlBioEntityParser {
* Counter for identifiers that cannot be inferred from SBML.
*/
private int idCounter = 0;
+ private Map<String, List<TextGlyph>> textGlyphByElementId = null;
/**
* Default constructor.
- *
+ *
* @param sbmlModel
* SBML model that we are parsing
* @param minervaModel
@@ -164,7 +156,7 @@ public class SbmlBioEntityParser {
/**
* Returns {@link LocalStyle} from the layout data identified by glyph id.
- *
+ *
* @param glyph
*
* @return {@link LocalStyle} from the layout data
@@ -193,8 +185,6 @@ public class SbmlBioEntityParser {
return null;
}
- private Map<String, List<TextGlyph>> textGlyphByElementId = null;
-
/**
* Returns list of {@link TextGlyph} that describes
* {@link AbstractReferenceGlyph}.
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
index 0ce8175cd4..953741acf6 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -2,12 +2,10 @@ package lcsb.mapviewer.converter.model.sbml;
import java.util.Collection;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.BoundingBox;
-import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Point;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.render.ColorDefinition;
import org.sbml.jsbml.ext.render.LocalStyle;
@@ -27,15 +25,6 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
super(sbmlModel, minervaModel, sbmlExtensions);
}
- @Override
- protected LocalStyle createStyle(T element) {
- LocalStyle result = super.createStyle(element);
- ColorDefinition color = getColorDefinition(element.getColor());
- result.getGroup().setFill(color.getId());
- result.getGroup().setFontSize(element.getFontSize().shortValue());
-
- return result;
- }
protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph speciesGlyph) {
BoundingBox boundingBox = new BoundingBox();
@@ -46,7 +35,6 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
boundingBox.setDimensions(dimensions);
speciesGlyph.setBoundingBox(boundingBox);
-
if (isExtensionEnabled(SbmlExtension.RENDER)) {
LocalStyle style = createStyle(element);
@@ -55,4 +43,14 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
}
+ @Override
+ protected LocalStyle createStyle(T element) {
+ LocalStyle result = super.createStyle(element);
+ ColorDefinition color = getColorDefinition(element.getColor());
+ result.getGroup().setFill(color.getId());
+ result.getGroup().setFontSize(element.getFontSize().shortValue());
+
+ return result;
+ }
+
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index 0cf6bf8e43..e4fe38ff9a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -1,14 +1,11 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
+import java.awt.*;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
@@ -20,6 +17,8 @@ import lcsb.mapviewer.model.map.species.Element;
public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends SbmlBioEntityParser {
+ Map<String, Element> elementBySbmlId = new HashMap<>();
+ Map<String, String> sbmlIdByElementId = new HashMap<>();
/**
* Default class logger.
*/
@@ -43,10 +42,6 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
protected abstract ListOf<T> getSbmlElementList();
- Map<String, Element> elementBySbmlId = new HashMap<>();
-
- Map<String, String> sbmlIdByElementId = new HashMap<>();
-
public Element getAnyElementBySbmlElementId(String id) {
return elementBySbmlId.get(id);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 6aa238ac2f..c86d28e26e 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -1,21 +1,15 @@
package lcsb.mapviewer.converter.model.sbml;
import java.io.UnsupportedEncodingException;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.*;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.apache.logging.log4j.*;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBMLWriter;
-import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.*;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.render.GlobalRenderInformation;
import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
index 516e58830e..3058a3e326 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.FunctionDefinition;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
index 325afcb84d..68863c51ab 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
@@ -1,15 +1,14 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.w3c.dom.Node;
+import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
@@ -21,14 +20,16 @@ public class SbmlFunctionParser extends SbmlBioEntityParser {
super(sbmlModel, minervaModel);
}
- protected SbmlFunction parse(org.sbml.jsbml.FunctionDefinition unitDefinition, Model sbmlModel) throws InvalidInputDataExecption {
+ protected SbmlFunction parse(org.sbml.jsbml.FunctionDefinition unitDefinition, Model sbmlModel)
+ throws InvalidInputDataExecption {
try {
SbmlFunction result = new SbmlFunction(unitDefinition.getId());
result.setName(unitDefinition.getName());
Node node = XmlParser.getXmlDocumentFromString(unitDefinition.getMath().toMathML());
Node mathDefinition = XmlParser.getNode("math", node);
String definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
- + XmlParser.nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "") + "</math>";
+ + XmlParser.nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "")
+ + "</math>";
result.setDefinition(definition);
result.setArguments(parseArgumentsFromMath(mathDefinition, result.getFunctionId()));
return result;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java
index 684910f667..c42d0d9ff8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.Parameter;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java
index 836a91d667..b49323025e 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java
@@ -1,13 +1,10 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.logging.log4j.*;
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.QuantityWithUnit;
+import java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.*;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 12344d5b78..1e47dc8e3b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -121,6 +121,32 @@ public class SbmlParser extends Converter {
}
}
+ @Override
+ public String model2String(Model model) throws ConverterException {
+ try {
+ SbmlExporter sbmlExporter = new SbmlExporter();
+ sbmlExporter.setProvideDefaults(provideDefaults);
+ return sbmlExporter.toXml(model);
+ } catch (InconsistentModelException e) {
+ throw new ConverterException(e);
+ }
+ }
+
+ @Override
+ public String getCommonName() {
+ return "SBML";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.SBML;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "xml";
+ }
+
private void addComplexRelationsBasedOnCoordinates(Model model) {
for (Element element : model.getElements()) {
if (element instanceof Species) {
@@ -258,32 +284,6 @@ public class SbmlParser extends Converter {
}
}
- @Override
- public String model2String(Model model) throws ConverterException {
- try {
- SbmlExporter sbmlExporter = new SbmlExporter();
- sbmlExporter.setProvideDefaults(provideDefaults);
- return sbmlExporter.toXml(model);
- } catch (InconsistentModelException e) {
- throw new ConverterException(e);
- }
- }
-
- @Override
- public String getCommonName() {
- return "SBML";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.SBML;
- }
-
- @Override
- public String getFileExtension() {
- return "xml";
- }
-
public void setProvideDefaults(boolean b) {
this.provideDefaults = b;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
index 6fdcc5da88..d4d47b95c9 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -1,26 +1,14 @@
package lcsb.mapviewer.converter.model.sbml.compartment;
import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.BoundingBox;
-import org.sbml.jsbml.ext.layout.CompartmentGlyph;
-import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Point;
-import org.sbml.jsbml.ext.layout.TextGlyph;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.multi.MultiCompartmentPlugin;
-import org.sbml.jsbml.ext.render.Ellipse;
-import org.sbml.jsbml.ext.render.HTextAnchor;
-import org.sbml.jsbml.ext.render.LocalRenderInformation;
-import org.sbml.jsbml.ext.render.LocalStyle;
-import org.sbml.jsbml.ext.render.Rectangle;
-import org.sbml.jsbml.ext.render.RenderGroup;
-import org.sbml.jsbml.ext.render.VTextAnchor;
+import org.sbml.jsbml.ext.render.*;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
@@ -40,6 +28,23 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
super(sbmlModel, minervaModel, sbmlExtensions);
}
+ @Override
+ protected List<Compartment> getElementList() {
+ List<Compartment> result = new ArrayList<>();
+ result.addAll(getMinervaModel().getCompartments());
+ boolean defaultFound = false;
+ for (Compartment compartment : result) {
+ if (compartment.getElementId().equals("default")) {
+ defaultFound = true;
+ }
+ }
+ if (!defaultFound) {
+ Compartment defaultCompartment = new Compartment("default");
+ result.add(defaultCompartment);
+ }
+ return result;
+ }
+
@Override
public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
org.sbml.jsbml.Compartment result;
@@ -61,20 +66,21 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
}
@Override
- protected List<Compartment> getElementList() {
- List<Compartment> result = new ArrayList<>();
- result.addAll(getMinervaModel().getCompartments());
- boolean defaultFound = false;
- for (Compartment compartment : result) {
- if (compartment.getElementId().equals("default")) {
- defaultFound = true;
- }
+ public org.sbml.jsbml.Compartment getSbmlElement(Compartment element) throws InconsistentModelException {
+ String mapKey = getSbmlIdKey(element);
+ if (element == null && sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
+ org.sbml.jsbml.Compartment sbmlElement = createSbmlElement(element);
+ sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
}
- if (!defaultFound) {
- Compartment defaultCompartment = new Compartment("default");
- result.add(defaultCompartment);
+ return super.getSbmlElement(element);
+ }
+
+ @Override
+ protected String getSbmlIdKey(Compartment compartment) {
+ if (compartment == null || compartment.getElementId().equals("default")) {
+ return "default";
}
- return result;
+ return compartment.getName();
}
@Override
@@ -86,14 +92,6 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
return result;
}
- @Override
- protected String getSbmlIdKey(Compartment compartment) {
- if (compartment == null || compartment.getElementId().equals("default")) {
- return "default";
- }
- return compartment.getName();
- }
-
@Override
protected LocalStyle createStyle(Compartment element) {
LocalStyle style = super.createStyle(element);
@@ -166,14 +164,4 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
}
}
- @Override
- public org.sbml.jsbml.Compartment getSbmlElement(Compartment element) throws InconsistentModelException {
- String mapKey = getSbmlIdKey(element);
- if (element == null && sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
- org.sbml.jsbml.Compartment sbmlElement = createSbmlElement(element);
- sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
- }
- return super.getSbmlElement(element);
- }
-
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
index 13f0932d32..a15250b941 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
@@ -1,17 +1,16 @@
package lcsb.mapviewer.converter.model.sbml.compartment;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.CompartmentGlyph;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.layout.Point;
-import org.sbml.jsbml.ext.layout.TextGlyph;
import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
@@ -33,17 +32,6 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
super(sbmlModel, minervaModel);
}
- @Override
- protected Compartment parse(org.sbml.jsbml.Compartment compartment)
- throws InvalidInputDataExecption {
- if (compartment.getId().equals("default")) {
- return null;
- }
- Compartment result = new SquareCompartment(compartment.getId());
- assignBioEntityData(compartment, result);
- return result;
- }
-
@Override
protected ListOf<org.sbml.jsbml.Compartment> getSbmlElementList() {
return getSbmlModel().getListOfCompartments();
@@ -88,6 +76,14 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
return result;
}
+ @Override
+ protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
+ if (!style.getGroup().isSetFill() && style.getGroup().isSetStroke()) {
+ Color backgroundColor = getColorByColorDefinition(style.getGroup().getStroke());
+ elementWithLayout.setColor(backgroundColor);
+ }
+ }
+
@Override
protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs() {
List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
@@ -100,11 +96,14 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
}
@Override
- protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
- if (!style.getGroup().isSetFill() && style.getGroup().isSetStroke()) {
- Color backgroundColor = getColorByColorDefinition(style.getGroup().getStroke());
- elementWithLayout.setColor(backgroundColor);
+ protected Compartment parse(org.sbml.jsbml.Compartment compartment)
+ throws InvalidInputDataExecption {
+ if (compartment.getId().equals("default")) {
+ return null;
}
+ Compartment result = new SquareCompartment(compartment.getId());
+ assignBioEntityData(compartment, result);
+ return result;
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java
index 63d464554f..aa9fe4416c 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.converter.model.sbml.extension.multi;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.*;
public enum BioEntityFeature {
STRUCTURAL_STATE("Structural state", "", new Class<?>[] { Protein.class, Complex.class },
"minerva_structural_state_"),
- POSITION_TO_COMPARTMENT("Position to compartment", MultiPackageNamingUtils.NULL_REPRESENTATION, new Class<?>[] { Element.class },
+ POSITION_TO_COMPARTMENT("Position to compartment", MultiPackageNamingUtils.NULL_REPRESENTATION,
+ new Class<?>[] { Element.class },
"minerva_position_to_compartment_"),
SYNONYM("Synonym", null, new Class<?>[] { Element.class },
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
index 8dc5e8e95b..1fa4c03645 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
@@ -1,14 +1,12 @@
package lcsb.mapviewer.converter.model.sbml.extension.multi;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import lcsb.mapviewer.model.map.species.Element;
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.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Class responsible for providing identifiers of structures inside multi
@@ -18,17 +16,15 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
*
*/
public final class MultiPackageNamingUtils {
-
+
+ public static final String NULL_REPRESENTATION = "NULL";
+ private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_";
/**
* Default logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(MultiPackageNamingUtils.class);
- private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_";
-
- public static final String NULL_REPRESENTATION = "NULL";
-
/**
* Returns id of the {@link MultiSpeciesType} for a given minerva class.
*
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
index e0ebcd078a..7a18f3918b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
@@ -3,15 +3,10 @@ package lcsb.mapviewer.converter.model.sbml.reaction;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-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.modifier.*;
import lcsb.mapviewer.model.map.reaction.Modifier;
public enum SBOTermModifierType {
@@ -25,8 +20,8 @@ public enum SBOTermModifierType {
;
private static Logger logger = LogManager.getLogger(SBOTermModifierType.class);
- private List<String> sboTerms = new ArrayList<>();
Class<? extends Modifier> clazz;
+ private List<String> sboTerms = new ArrayList<>();
private SBOTermModifierType(Class<? extends Modifier> clazz, String[] inputSboTerms) {
this.clazz = clazz;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
index 8336f16ed7..f64c954cc0 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
@@ -3,35 +3,11 @@ package lcsb.mapviewer.converter.model.sbml.reaction;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.reaction.Reaction;
-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;
+import lcsb.mapviewer.model.map.reaction.type.*;
public enum SBOTermReactionType {
CATALYSIS(CatalysisReaction.class, new String[] { "SBO:0000013" }),
@@ -63,8 +39,8 @@ public enum SBOTermReactionType {
;
private static Logger logger = LogManager.getLogger(SBOTermReactionType.class);
- private List<String> sboTerms = new ArrayList<>();
Class<? extends Reaction> clazz;
+ private List<String> sboTerms = new ArrayList<>();
private SBOTermReactionType(Class<? extends Reaction> clazz, String[] inputSboTerms) {
this.clazz = clazz;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index 2139ddfb9f..4bf203532d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -1,37 +1,17 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
-import java.awt.BasicStroke;
-import java.awt.Stroke;
+import java.awt.*;
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.*;
import java.util.List;
-import java.util.Map;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.sbml.jsbml.ASTNode;
-import org.sbml.jsbml.KineticLaw;
-import org.sbml.jsbml.LocalParameter;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.SimpleSpeciesReference;
-import org.sbml.jsbml.Species;
-import org.sbml.jsbml.SpeciesReference;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.BoundingBox;
-import org.sbml.jsbml.ext.layout.Curve;
-import org.sbml.jsbml.ext.layout.CurveSegment;
-import org.sbml.jsbml.ext.layout.LineSegment;
+import org.sbml.jsbml.*;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.layout.Point;
-import org.sbml.jsbml.ext.layout.ReactionGlyph;
-import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
-import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
-import org.sbml.jsbml.ext.render.ColorDefinition;
-import org.sbml.jsbml.ext.render.LocalRenderInformation;
-import org.sbml.jsbml.ext.render.LocalStyle;
-import org.sbml.jsbml.ext.render.RenderGroup;
+import org.sbml.jsbml.ext.render.*;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
@@ -47,12 +27,8 @@ import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.modifier.Trigger;
-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.*;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -77,46 +53,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
this.compartmentExporter = compartmentExporter;
}
- @Override
- public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
- String reactionId = getReactionId(reaction);
- org.sbml.jsbml.Reaction result = super.getSbmlElementByElementId(reactionId);
- if (result != null) {
- return result;
- }
- result = getSbmlModel().createReaction(reactionId);
- result.setReversible(reaction.isReversible());
- String sboTerm = SBOTermReactionType.getTermByType(reaction.getClass());
- if (sboTerm != null) {
- result.setSBOTerm(sboTerm);
- }
- for (Product product : reaction.getProducts()) {
- Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
- SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
- speciesReference.setConstant(false);
- speciesReferenceByReactionNode.put(product, speciesReference);
- }
- for (Reactant reactant : reaction.getReactants()) {
- Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(reactant.getElement().getElementId());
- SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
- speciesReference.setConstant(false);
- speciesReferenceByReactionNode.put(reactant, speciesReference);
- }
- for (Modifier modifier : reaction.getModifiers()) {
- Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(modifier.getElement().getElementId());
- SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
- speciesReferenceByReactionNode.put(modifier, speciesReference);
- String term = SBOTermModifierType.getTermByType(modifier.getClass());
- if (term != null) {
- speciesReference.setSBOTerm(term);
- }
- }
- if (reaction.getKinetics() != null) {
- result.setKineticLaw(createKineticLaw(reaction));
- }
- return result;
- }
-
private KineticLaw createKineticLaw(Reaction reaction) throws InconsistentModelException {
SbmlKinetics kinetics = reaction.getKinetics();
KineticLaw result = new KineticLaw();
@@ -171,27 +107,53 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
@Override
- protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
- int separatorIndex = glyphId.indexOf("__");
- if (separatorIndex > 0) {
- glyphId = glyphId.substring(separatorIndex + 2);
+ protected Collection<Reaction> getElementList() {
+ return getMinervaModel().getReactions();
+ }
+
+ @Override
+ public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
+ String reactionId = getReactionId(reaction);
+ org.sbml.jsbml.Reaction result = super.getSbmlElementByElementId(reactionId);
+ if (result != null) {
+ return result;
}
- ReactionGlyph reactionGlyph;
- try {
- // handle case when input data cannot doesn't come from SBML parser and contains
- // "__" that mess up identifier uniqueness
- reactionGlyph = getLayout().createReactionGlyph(glyphId, sbmlElementId);
- } catch (IllegalArgumentException e) {
- glyphId += "_" + getNextId();
- reactionGlyph = getLayout().createReactionGlyph(glyphId, sbmlElementId);
+ result = getSbmlModel().createReaction(reactionId);
+ result.setReversible(reaction.isReversible());
+ String sboTerm = SBOTermReactionType.getTermByType(reaction.getClass());
+ if (sboTerm != null) {
+ result.setSBOTerm(sboTerm);
}
-
- return reactionGlyph;
+ for (Product product : reaction.getProducts()) {
+ Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
+ SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
+ speciesReference.setConstant(false);
+ speciesReferenceByReactionNode.put(product, speciesReference);
+ }
+ for (Reactant reactant : reaction.getReactants()) {
+ Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(reactant.getElement().getElementId());
+ SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
+ speciesReference.setConstant(false);
+ speciesReferenceByReactionNode.put(reactant, speciesReference);
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(modifier.getElement().getElementId());
+ SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
+ speciesReferenceByReactionNode.put(modifier, speciesReference);
+ String term = SBOTermModifierType.getTermByType(modifier.getClass());
+ if (term != null) {
+ speciesReference.setSBOTerm(term);
+ }
+ }
+ if (reaction.getKinetics() != null) {
+ result.setKineticLaw(createKineticLaw(reaction));
+ }
+ return result;
}
@Override
- protected Collection<Reaction> getElementList() {
- return getMinervaModel().getReactions();
+ protected String getSbmlIdKey(Reaction element) {
+ return element.getClass().getSimpleName() + "\n" + element.getElementId();
}
@Override
@@ -226,7 +188,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
reactionGlyph.getCurve().addCurveSegment(new LineSegment(curve.getCurveSegment(i)));
}
-
boolean firstProduct = true;
for (Product product : reaction.getProducts()) {
SpeciesReferenceGlyph productGlyph = createNodeGlyph(reactionGlyph, product);
@@ -283,6 +244,30 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
removeColinearPoints(reactionGlyph);
}
+ @Override
+ protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
+ int separatorIndex = glyphId.indexOf("__");
+ if (separatorIndex > 0) {
+ glyphId = glyphId.substring(separatorIndex + 2);
+ }
+ ReactionGlyph reactionGlyph;
+ try {
+ // handle case when input data cannot doesn't come from SBML parser and contains
+ // "__" that mess up identifier uniqueness
+ reactionGlyph = getLayout().createReactionGlyph(glyphId, sbmlElementId);
+ } catch (IllegalArgumentException e) {
+ glyphId += "_" + getNextId();
+ reactionGlyph = getLayout().createReactionGlyph(glyphId, sbmlElementId);
+ }
+
+ return reactionGlyph;
+ }
+
+ @Override
+ protected LocalStyle createStyle(Reaction reaction) {
+ return createStyle(reaction.getLine());
+ }
+
private void removeColinearPoints(ReactionGlyph glyph) {
PolylineData line = createLine(glyph.getCurve());
line = PolylineDataFactory.removeCollinearPoints(line);
@@ -318,11 +303,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
return style;
}
- @Override
- protected LocalStyle createStyle(Reaction reaction) {
- return createStyle(reaction.getLine());
- }
-
private List<Short> strokeToArray(Stroke stroke) {
if (stroke instanceof BasicStroke) {
BasicStroke basicStroke = (BasicStroke) stroke;
@@ -383,9 +363,4 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
return curve;
}
- @Override
- protected String getSbmlIdKey(Reaction element) {
- return element.getClass().getSimpleName() + "\n" + element.getElementId();
- }
-
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index cddeb2fdd8..a5349c461f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -1,41 +1,23 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.sbml.jsbml.KineticLaw;
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.LocalParameter;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ModifierSpeciesReference;
-import org.sbml.jsbml.SpeciesReference;
-import org.sbml.jsbml.ext.layout.BoundingBox;
-import org.sbml.jsbml.ext.layout.Curve;
-import org.sbml.jsbml.ext.layout.CurveSegment;
-import org.sbml.jsbml.ext.layout.LineSegment;
+import org.sbml.jsbml.*;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.layout.Point;
-import org.sbml.jsbml.ext.layout.ReactionGlyph;
-import org.sbml.jsbml.ext.layout.SpeciesGlyph;
-import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.render.LocalStyle;
import org.sbml.jsbml.ext.render.RenderGroup;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
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.common.exception.*;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
@@ -44,31 +26,14 @@ import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
import lcsb.mapviewer.converter.model.sbml.SbmlParameterParser;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
-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.graphics.*;
import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.*;
import lcsb.mapviewer.model.map.modifier.Trigger;
-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.InvalidReactionParticipantNumberException;
-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.*;
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.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
index 60d94fd7ff..44009c56f6 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
@@ -1,25 +1,11 @@
package lcsb.mapviewer.converter.model.sbml.species;
-import java.awt.Color;
+import java.awt.*;
import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-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.model.map.species.*;
public enum ElementColorEnum {
ANTISENSE_RNA(AntisenseRna.class, "#ff6666"),
@@ -41,11 +27,10 @@ public enum ElementColorEnum {
UNKNOWN(Unknown.class, "#cccccc"),
;
+ ColorParser colorParser = new ColorParser();
private Class<? extends Element> clazz;
private Color color;
- ColorParser colorParser = new ColorParser();
-
private ElementColorEnum(Class<? extends Element> clazz, String color) {
this.clazz = clazz;
if (color != null) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java
index 1be4927e69..7c63e65aa6 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java
@@ -3,23 +3,10 @@ package lcsb.mapviewer.converter.model.sbml.species;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-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.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.Species;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.*;
public enum SBOTermSpeciesType {
ANTISENSE_RNA(AntisenseRna.class, new String[] { "SBO:0000334" }),
@@ -39,8 +26,8 @@ public enum SBOTermSpeciesType {
;
private static Logger logger = LogManager.getLogger(SBOTermSpeciesType.class);
- private List<String> sboTerms = new ArrayList<>();
Class<? extends Species> clazz;
+ private List<String> sboTerms = new ArrayList<>();
private SBOTermSpeciesType(Class<? extends Species> clazz, String[] inputSboTerms) {
this.clazz = clazz;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index 0dd1cf3936..36598c25f6 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -1,37 +1,18 @@
package lcsb.mapviewer.converter.model.sbml.species;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
+import java.awt.*;
+import java.util.*;
import java.util.List;
-import java.util.Map;
import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.BoundingBox;
-import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.GeneralGlyph;
+import org.sbml.jsbml.ext.layout.*;
import org.sbml.jsbml.ext.layout.Point;
-import org.sbml.jsbml.ext.layout.ReferenceGlyph;
-import org.sbml.jsbml.ext.layout.TextGlyph;
-import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
-import org.sbml.jsbml.ext.multi.MultiSpeciesType;
-import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
-import org.sbml.jsbml.ext.multi.SpeciesFeature;
-import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
-import org.sbml.jsbml.ext.multi.SpeciesFeatureValue;
-import org.sbml.jsbml.ext.render.Ellipse;
-import org.sbml.jsbml.ext.render.HTextAnchor;
-import org.sbml.jsbml.ext.render.LocalRenderInformation;
-import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.multi.*;
+import org.sbml.jsbml.ext.render.*;
import org.sbml.jsbml.ext.render.Rectangle;
-import org.sbml.jsbml.ext.render.RenderGroup;
-import org.sbml.jsbml.ext.render.VTextAnchor;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
@@ -40,25 +21,8 @@ import lcsb.mapviewer.converter.model.sbml.extension.multi.BioEntityFeature;
import lcsb.mapviewer.converter.model.sbml.extension.multi.MultiPackageNamingUtils;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Chemical;
-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.AbstractRegionModification;
-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.SpeciesWithModificationResidue;
-import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
@@ -70,6 +34,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private static Logger logger = LogManager.getLogger(SbmlSpeciesExporter.class);
private SbmlCompartmentExporter compartmentExporter;
+ private int modificationResidueCounter = 0;
+ private Map<String, String> modificationResidueIds = new HashMap<>();
public SbmlSpeciesExporter(Model sbmlModel,
lcsb.mapviewer.model.map.model.Model minervaModel,
@@ -79,32 +45,6 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
this.compartmentExporter = compartmentExporter;
}
- @Override
- public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
- org.sbml.jsbml.Species result = getSbmlModel().createSpecies("species_" + (getNextId()));
- result.setSBOTerm(SBOTermSpeciesType.getTermByType(element.getClass()));
- result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
- if (element.getInitialAmount() != null) {
- result.setInitialAmount(element.getInitialAmount());
- }
- if (element.getInitialConcentration() != null) {
- result.setInitialConcentration(element.getInitialConcentration());
- }
- if (element.hasOnlySubstanceUnits() != null) {
- result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
- }
- if (element.getBoundaryCondition() != null) {
- result.setBoundaryCondition(element.getBoundaryCondition());
- }
- if (element.getConstant() != null) {
- result.setConstant(element.getConstant());
- }
- if (isExtensionEnabled(SbmlExtension.MULTI)) {
- assignMultiExtensionData(element, result);
- }
- return result;
- }
-
private void assignMultiExtensionData(Species element, org.sbml.jsbml.Species result) {
MultiSpeciesPlugin multiExtension = new MultiSpeciesPlugin(result);
MultiSpeciesType speciesType = getMultiSpeciesType(element);
@@ -380,14 +320,34 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
@Override
- protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
- AbstractReferenceGlyph speciesGlyph = getLayout().createSpeciesGlyph(glyphId, sbmlElementId);
- return speciesGlyph;
+ protected List<Species> getElementList() {
+ return getMinervaModel().getSpeciesList();
}
@Override
- protected List<Species> getElementList() {
- return getMinervaModel().getSpeciesList();
+ public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
+ org.sbml.jsbml.Species result = getSbmlModel().createSpecies("species_" + (getNextId()));
+ result.setSBOTerm(SBOTermSpeciesType.getTermByType(element.getClass()));
+ result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
+ if (element.getInitialAmount() != null) {
+ result.setInitialAmount(element.getInitialAmount());
+ }
+ if (element.getInitialConcentration() != null) {
+ result.setInitialConcentration(element.getInitialConcentration());
+ }
+ if (element.hasOnlySubstanceUnits() != null) {
+ result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
+ }
+ if (element.getBoundaryCondition() != null) {
+ result.setBoundaryCondition(element.getBoundaryCondition());
+ }
+ if (element.getConstant() != null) {
+ result.setConstant(element.getConstant());
+ }
+ if (isExtensionEnabled(SbmlExtension.MULTI)) {
+ assignMultiExtensionData(element, result);
+ }
+ return result;
}
@Override
@@ -449,6 +409,12 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return result;
}
+ @Override
+ protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
+ AbstractReferenceGlyph speciesGlyph = getLayout().createSpeciesGlyph(glyphId, sbmlElementId);
+ return speciesGlyph;
+ }
+
@Override
protected LocalStyle createStyle(Species element) {
LocalStyle style = super.createStyle(element);
@@ -486,6 +452,34 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return style;
}
+ @Override
+ protected void assignLayoutToGlyph(Species element, AbstractReferenceGlyph speciesGlyph) {
+ super.assignLayoutToGlyph(element, speciesGlyph);
+ if (isExtensionEnabled(SbmlExtension.MULTI)) {
+ if (element instanceof SpeciesWithModificationResidue) {
+ for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
+ createModificationGlyph(mr, speciesGlyph);
+ }
+ }
+ }
+ TextGlyph textGlyph = getLayout().createTextGlyph("text_" + element.getElementId(), element.getName());
+ textGlyph
+ .setBoundingBox(createBoundingBox(element.getX(), element.getY(), element.getZ() + 1, element.getWidth(),
+ element.getHeight()));
+ textGlyph.setReference(speciesGlyph.getId());
+
+ if (isExtensionEnabled(SbmlExtension.RENDER)) {
+ LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
+ LocalStyle style = new LocalStyle();
+ style.getIDList().add(textGlyph.getId());
+ style.setGroup(new RenderGroup());
+ style.getGroup().setVTextAnchor(VTextAnchor.MIDDLE);
+ style.getGroup().setTextAnchor(HTextAnchor.MIDDLE);
+ renderInformation.addLocalStyle(style);
+ }
+
+ }
+
@SuppressWarnings("unchecked")
private MultiSpeciesType createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
MultiSpeciesType speciesType = new MultiSpeciesType();
@@ -533,34 +527,6 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return result;
}
- @Override
- protected void assignLayoutToGlyph(Species element, AbstractReferenceGlyph speciesGlyph) {
- super.assignLayoutToGlyph(element, speciesGlyph);
- if (isExtensionEnabled(SbmlExtension.MULTI)) {
- if (element instanceof SpeciesWithModificationResidue) {
- for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
- createModificationGlyph(mr, speciesGlyph);
- }
- }
- }
- TextGlyph textGlyph = getLayout().createTextGlyph("text_" + element.getElementId(), element.getName());
- textGlyph
- .setBoundingBox(createBoundingBox(element.getX(), element.getY(), element.getZ() + 1, element.getWidth(),
- element.getHeight()));
- textGlyph.setReference(speciesGlyph.getId());
-
- if (isExtensionEnabled(SbmlExtension.RENDER)) {
- LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
- LocalStyle style = new LocalStyle();
- style.getIDList().add(textGlyph.getId());
- style.setGroup(new RenderGroup());
- style.getGroup().setVTextAnchor(VTextAnchor.MIDDLE);
- style.getGroup().setTextAnchor(HTextAnchor.MIDDLE);
- renderInformation.addLocalStyle(style);
- }
-
- }
-
private void createModificationGlyph(ModificationResidue mr, AbstractReferenceGlyph speciesGlyph) {
org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
@@ -610,9 +576,6 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return boundingBox;
}
- private int modificationResidueCounter = 0;
- private Map<String, String> modificationResidueIds = new HashMap<>();
-
private String getModificationResidueUniqueId(ModificationResidue mr) {
SpeciesWithModificationResidue species = (SpeciesWithModificationResidue) mr.getSpecies();
String modificationId = "mod" + species.getModificationResidues().indexOf(mr);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index 2cc9689aef..e7d30390f9 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -5,25 +5,12 @@ import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.CompartmentGlyph;
-import org.sbml.jsbml.ext.layout.GeneralGlyph;
-import org.sbml.jsbml.ext.layout.GraphicalObject;
-import org.sbml.jsbml.ext.layout.ReferenceGlyph;
-import org.sbml.jsbml.ext.layout.SpeciesGlyph;
-import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
-import org.sbml.jsbml.ext.multi.MultiSpeciesType;
-import org.sbml.jsbml.ext.multi.OutwardBindingSite;
-import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
-import org.sbml.jsbml.ext.multi.SpeciesFeature;
-import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
-import org.sbml.jsbml.ext.multi.SpeciesFeatureValue;
-import org.sbml.jsbml.ext.multi.SpeciesTypeInstance;
-import org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature;
+import org.sbml.jsbml.ext.layout.*;
+import org.sbml.jsbml.ext.multi.*;
import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.common.Pair;
@@ -33,81 +20,19 @@ import lcsb.mapviewer.converter.model.sbml.SbmlElementParser;
import lcsb.mapviewer.converter.model.sbml.extension.multi.BioEntityFeature;
import lcsb.mapviewer.converter.model.sbml.extension.multi.MultiPackageNamingUtils;
import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
-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.PositionToCompartment;
-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.SpeciesWithBindingRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithCodingRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationSite;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithProteinBindingDomain;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithRegulatoryRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithResidue;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithTranscriptionSite;
-import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
- Logger logger = LogManager.getLogger(SbmlSpeciesParser.class);
-
private static String ARTIFITIAL_SINK_ID = "sbml_artifitial_sink";
private static String ARTIFITIAL_SOURCE_ID = "sbml_artifitial_source";
+ Logger logger = LogManager.getLogger(SbmlSpeciesParser.class);
public SbmlSpeciesParser(Model model, lcsb.mapviewer.model.map.model.Model minervaModel) {
super(model, minervaModel);
}
- @SuppressWarnings("deprecation")
- @Override
- protected Species parse(org.sbml.jsbml.Species species) throws InvalidInputDataExecption {
- String sboTerm = extractSBOTermFromSpecies(species);
- Class<? extends Species> clazz = SBOTermSpeciesType.getTypeSBOTerm(sboTerm);
- try {
- Species result = clazz.getConstructor(String.class).newInstance(species.getId());
- if (!Double.isNaN(species.getInitialAmount())) {
- result.setInitialAmount(species.getInitialAmount());
- }
- if (!Double.isNaN(species.getInitialConcentration())) {
- result.setInitialConcentration(species.getInitialConcentration());
- }
- if (species.isSetHasOnlySubstanceUnits()) {
- result.setOnlySubstanceUnits(species.hasOnlySubstanceUnits());
- }
- if (species.isSetBoundaryCondition()) {
- result.setBoundaryCondition(species.getBoundaryCondition());
- }
- if (species.isSetConstant()) {
- result.setConstant(species.getConstant());
- }
- if (species.isSetCharge()) {
- result.setCharge(species.getCharge());
- }
- assignBioEntityData(species, result);
- if (getLayout() == null) {
- assignCompartment(result, species.getCompartment());
- }
- if (getMultiPlugin() != null) {
- assignMultiData(species, result);
- }
- return result;
- } catch (SecurityException | NoSuchMethodException | InstantiationException | IllegalAccessException
- | IllegalArgumentException | InvocationTargetException e) {
- throw new InvalidStateException(e);
- }
- }
-
private void assignMultiData(org.sbml.jsbml.Species sbmlSpecies, Species minervaElement) {
String warnPrefix = new ElementUtils().getElementTag(minervaElement);
MultiModelPlugin multiPlugin = getMultiPlugin();
@@ -360,28 +285,6 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
return sboTerm;
}
- @Override
- public List<Element> mergeLayout(List<? extends Element> elements)
- throws InvalidInputDataExecption {
- List<Element> result = super.mergeLayout(elements);
-
- for (Element element : result) {
- String compartmentId = null;
- if (getLayout().getSpeciesGlyph(element.getElementId()) != null) {
- compartmentId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId())
- .getSpeciesInstance()).getCompartment();
- } else {
- if (!element.getElementId().equals(ARTIFITIAL_SINK_ID)
- && !element.getElementId().equals(ARTIFITIAL_SOURCE_ID)) {
- compartmentId = getSbmlModel().getSpecies(element.getElementId()).getCompartment();
- }
- }
- assignCompartment(element, compartmentId);
- assignModificationResiduesLayout(element);
- }
- return result;
- }
-
private void assignModificationResiduesLayout(Element element) {
if (element instanceof SpeciesWithModificationResidue) {
for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
@@ -454,10 +357,23 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
@Override
- protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs() {
- List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
- for (SpeciesGlyph glyph : getLayout().getListOfSpeciesGlyphs()) {
- result.add(new Pair<String, AbstractReferenceGlyph>(glyph.getSpecies(), glyph));
+ public List<Element> mergeLayout(List<? extends Element> elements)
+ throws InvalidInputDataExecption {
+ List<Element> result = super.mergeLayout(elements);
+
+ for (Element element : result) {
+ String compartmentId = null;
+ if (getLayout().getSpeciesGlyph(element.getElementId()) != null) {
+ compartmentId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId())
+ .getSpeciesInstance()).getCompartment();
+ } else {
+ if (!element.getElementId().equals(ARTIFITIAL_SINK_ID)
+ && !element.getElementId().equals(ARTIFITIAL_SOURCE_ID)) {
+ compartmentId = getSbmlModel().getSpecies(element.getElementId()).getCompartment();
+ }
+ }
+ assignCompartment(element, compartmentId);
+ assignModificationResiduesLayout(element);
}
return result;
}
@@ -471,6 +387,54 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
}
+ @Override
+ protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs() {
+ List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
+ for (SpeciesGlyph glyph : getLayout().getListOfSpeciesGlyphs()) {
+ result.add(new Pair<String, AbstractReferenceGlyph>(glyph.getSpecies(), glyph));
+ }
+ return result;
+ }
+
+ @SuppressWarnings("deprecation")
+ @Override
+ protected Species parse(org.sbml.jsbml.Species species) throws InvalidInputDataExecption {
+ String sboTerm = extractSBOTermFromSpecies(species);
+ Class<? extends Species> clazz = SBOTermSpeciesType.getTypeSBOTerm(sboTerm);
+ try {
+ Species result = clazz.getConstructor(String.class).newInstance(species.getId());
+ if (!Double.isNaN(species.getInitialAmount())) {
+ result.setInitialAmount(species.getInitialAmount());
+ }
+ if (!Double.isNaN(species.getInitialConcentration())) {
+ result.setInitialConcentration(species.getInitialConcentration());
+ }
+ if (species.isSetHasOnlySubstanceUnits()) {
+ result.setOnlySubstanceUnits(species.hasOnlySubstanceUnits());
+ }
+ if (species.isSetBoundaryCondition()) {
+ result.setBoundaryCondition(species.getBoundaryCondition());
+ }
+ if (species.isSetConstant()) {
+ result.setConstant(species.getConstant());
+ }
+ if (species.isSetCharge()) {
+ result.setCharge(species.getCharge());
+ }
+ assignBioEntityData(species, result);
+ if (getLayout() == null) {
+ assignCompartment(result, species.getCompartment());
+ }
+ if (getMultiPlugin() != null) {
+ assignMultiData(species, result);
+ }
+ return result;
+ } catch (SecurityException | NoSuchMethodException | InstantiationException | IllegalAccessException
+ | IllegalArgumentException | InvocationTargetException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
public Species getArtifitialInput() {
Species result = getMinervaModel().getElementByElementId(ARTIFITIAL_SOURCE_ID);
if (result == null) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java
index 862d14cb43..7697a49a1b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml.units;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.Unit;
import org.sbml.jsbml.UnitDefinition;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java
index 22301f7a12..2f08458469 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java
@@ -1,13 +1,10 @@
package lcsb.mapviewer.converter.model.sbml.units;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.logging.log4j.*;
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.Unit;
+import java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.*;
import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java
index 4a75ac6ea5..aa896136fa 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java
@@ -86,6 +86,7 @@ public enum UnitMapping {
}
throw new InvalidArgumentException("Unknown sbml unit type: " + unitType);
}
+
public static SbmlUnitType kindToUnitType(Kind kind) {
for (UnitMapping mapping : UnitMapping.values()) {
if (mapping.sbmlUnitType == kind) {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
index 414011212d..f8ead7384e 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.io.*;
import java.nio.file.*;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java
index 10e04d311f..06c9f46030 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.io.IOException;
import java.nio.file.*;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java
index 015e5fe987..93dcd2667c 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.io.*;
import java.util.ArrayList;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToLayoutTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToLayoutTest.java
index 0d05998028..fb1a3ebf48 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToLayoutTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToLayoutTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.io.*;
import java.util.ArrayList;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java
index af722e4bb0..599bdc249d 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.io.*;
import java.util.*;
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 2b46babbaf..524ac55de4 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.io.*;
import java.nio.file.*;
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 4c56a69dfc..c554d42155 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.io.File;
import java.io.IOException;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
index 13afe4a261..e7a310b610 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.io.*;
import java.nio.file.*;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java
index 19c2ee4938..5a37355f88 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
import java.io.*;
@@ -26,9 +26,8 @@ import lcsb.mapviewer.model.map.species.Ion;
public class ReactionPropertiesExportToMultiTest extends SbmlTestFunctions {
static Logger logger = LogManager.getLogger(ReactionPropertiesExportToMultiTest.class.getName());
-
- private Model model;
private static String reactionId = "reactionId";
+ private Model model;
public ReactionPropertiesExportToMultiTest(String propertyName, Model model) {
this.model = model;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
index a349808eb9..feb38b8a57 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
@@ -1,10 +1,8 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
+import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.junit.Test;
import org.mockito.Mockito;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
index 0d44c40bd7..42baf131e2 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.io.ByteArrayInputStream;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 0cdda07e16..08b779a2df 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -2,12 +2,13 @@ package lcsb.mapviewer.converter.model.sbml;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
import java.lang.reflect.Modifier;
import java.util.*;
+import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
index 06f0468308..7db1fbe543 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.awt.Desktop;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.io.*;
import java.nio.file.Files;
@@ -26,23 +26,37 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class SbmlTestFunctions {
+ private static int identifierCounter = 0;
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
+ SbmlParser parser = new SbmlParser();
+ SbmlExporter exporter;
@SuppressWarnings("unused")
private Logger logger = Logger.getLogger(SbmlTestFunctions.class);
-
private MinervaLoggerAppender appender;
- private static int identifierCounter = 0;
-
- SbmlParser parser = new SbmlParser();
- SbmlExporter exporter;
-
public SbmlTestFunctions() {
exporter = new SbmlExporter();
}
+ protected static GenericProtein createProtein() {
+ GenericProtein result = new GenericProtein("sa" + (identifierCounter++));
+ result.setName("SNCA");
+ result.setX(10);
+ result.setWidth(10);
+ result.setY(10);
+ result.setHeight(10);
+ result.setZ(123);
+ return result;
+ }
+
+ protected static Compartment createCompartment() {
+ Compartment result = new Compartment("c" + (identifierCounter++));
+ result.setZ(124);
+
+ return result;
+ }
+
@Before
public final void _setUp() throws Exception {
MinervaLoggerAppender.unregisterLogEventStorage(appender);
@@ -70,24 +84,6 @@ public class SbmlTestFunctions {
}
- protected static GenericProtein createProtein() {
- GenericProtein result = new GenericProtein("sa" + (identifierCounter++));
- result.setName("SNCA");
- result.setX(10);
- result.setWidth(10);
- result.setY(10);
- result.setHeight(10);
- result.setZ(123);
- return result;
- }
-
- protected static Compartment createCompartment() {
- Compartment result = new Compartment("c" + (identifierCounter++));
- result.setZ(124);
-
- return result;
- }
-
protected Reaction createReaction(Element p1, Element p2) {
Reaction reaction = new StateTransitionReaction("r" + (identifierCounter++));
Reactant reactant = new Reactant(p1);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParserTest.java
index 7c4274409b..a44f7d3da7 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParserTest.java
@@ -5,7 +5,8 @@ import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
import java.io.FileNotFoundException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
index c0b35fb270..315d4169cb 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
@@ -21,27 +21,13 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
-import lcsb.mapviewer.converter.model.sbml.SbmlParser;
-import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.converter.model.sbml.*;
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.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.AssociationOperator;
-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.ReactionComparator;
-import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.TruncationOperator;
-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.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -55,6 +41,11 @@ public class SbmlReactionExportArrowType extends SbmlTestFunctions {
SbmlParser parser = new SbmlParser();
SbmlExporter exporter = new SbmlExporter();
+ Model modelToBeTested;
+
+ public SbmlReactionExportArrowType(String name, Model model) {
+ modelToBeTested = model;
+ }
@Parameters(name = "{index} : {0}")
public static Collection<Object[]> data() throws Exception {
@@ -160,12 +151,6 @@ public class SbmlReactionExportArrowType extends SbmlTestFunctions {
return result;
}
- Model modelToBeTested;
-
- public SbmlReactionExportArrowType(String name, Model model) {
- modelToBeTested = model;
- }
-
@Test
public void test() throws Exception {
try {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
index 278166360e..040d60e417 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
@@ -7,9 +7,7 @@ import java.util.Arrays;
import org.junit.Test;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.layout.*;
import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserExtractCurveTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserExtractCurveTest.java
index 2294c84bce..138226d0ac 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserExtractCurveTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserExtractCurveTest.java
@@ -29,6 +29,7 @@ public class SbmlReactionParserExtractCurveTest extends SbmlTestFunctions {
private int length;
private SbmlReactionParser sbmlReactionParser;
+ private Curve curve;
public SbmlReactionParserExtractCurveTest(String name, ReactionGlyph reactionGlyph, int length) {
this.glyph = reactionGlyph;
@@ -37,18 +38,6 @@ public class SbmlReactionParserExtractCurveTest extends SbmlTestFunctions {
sbmlReactionParser = new SbmlReactionParser(new Model(3, 2), null, null, null);
}
- private Curve curve;
-
- @Before
- public final void setUp() throws Exception {
- curve = new Curve(glyph.getCurve());
- }
-
- @After
- public final void tearDown() throws Exception {
- glyph.setCurve(curve);
- }
-
@Parameters(name = "{0}")
public static Collection<Object[]> data() throws IOException {
Collection<Object[]> data = new ArrayList<>();
@@ -79,6 +68,16 @@ public class SbmlReactionParserExtractCurveTest extends SbmlTestFunctions {
return result;
}
+ @Before
+ public final void setUp() throws Exception {
+ curve = new Curve(glyph.getCurve());
+ }
+
+ @After
+ public final void tearDown() throws Exception {
+ glyph.setCurve(curve);
+ }
+
@Test
public void testCenterLine() throws Exception {
Reaction reaction = createReaction(createProtein(), createProtein());
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
index 642f06ed56..190972f434 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
@@ -6,21 +6,18 @@ import static org.junit.Assert.assertFalse;
import java.util.Arrays;
import java.util.Collection;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import org.sbml.jsbml.SBMLDocument;
-import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
-import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
-import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.converter.model.sbml.*;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
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.Element;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
@@ -28,7 +25,6 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
org.sbml.jsbml.Model sbmlModel;
-
@Test
public void testOneElementWithTwoAliases() throws InconsistentModelException {
Element protein1 = createProtein();
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
index 953cd375d4..46380cbe56 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
@@ -5,7 +5,8 @@ import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.geometry.ColorParser;
@@ -13,21 +14,7 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.sbml.SbmlParser;
import lcsb.mapviewer.model.map.model.Model;
-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.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.*;
public class SbmlSpeciesParserTest {
Logger logger = LogManager.getLogger(SbmlSpeciesParserTest.class);
@@ -150,8 +137,9 @@ public class SbmlSpeciesParserTest {
public void testParseInitialAmount() throws Exception {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/initial_amount.xml"));
Species element = model.getElementByElementId("s1");
- assertEquals((Double)1.0, element.getInitialAmount());
+ assertEquals((Double) 1.0, element.getInitialAmount());
}
+
@Test
public void testParseHasOnlySubstanceUnits() throws Exception {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/has_only_substance_units.xml"));
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 2fbbc1f860..e1a45aa32e 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -1,43 +1,25 @@
package lcsb.mapviewer.converter;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
import java.lang.reflect.Modifier;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
+import java.util.*;
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.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
-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.converter.zip.*;
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.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.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
/**
* This class allows to create complex {@link Model} that contains submaps. It's
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
index fb5dc23bfb..4a37d60987 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
@@ -1,16 +1,12 @@
package lcsb.mapviewer.converter;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
+import java.io.*;
+import java.util.*;
import java.util.zip.ZipFile;
import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/Converter.java b/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
index 96c1cd7176..77bdcd8045 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
@@ -4,10 +4,11 @@ import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.UUID;
+import org.apache.commons.io.FileUtils;
+
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
-import org.apache.commons.io.FileUtils;
/**
* Interface used for reading data from file and putting it into {@link Model}
@@ -18,86 +19,93 @@ import org.apache.commons.io.FileUtils;
*/
public abstract class Converter {
- /**
- * Parse input source and transforms it into a model object.
- *
- * @param params
- * input params used for reading data
- * @return model obtained from input source
- * @throws InvalidInputDataExecption
- * thrown when input parameters are invalid
- */
- public abstract Model createModel(ConverterParams params) throws InvalidInputDataExecption, ConverterException;
+ /**
+ * Parse input source and transforms it into a model object.
+ *
+ * @param params
+ * input params used for reading data
+ * @return model obtained from input source
+ * @throws InvalidInputDataExecption
+ * thrown when input parameters are invalid
+ */
+ public abstract Model createModel(ConverterParams params) throws InvalidInputDataExecption, ConverterException;
- /**
- * Generate String representation of the model. Traditionally often XML but can be any other format as well.
- *
- * @param model The MINERVA ${@link Model} to be serialized
- * @return The translated Model
- */
- public abstract String model2String(Model model) throws InconsistentModelException, ConverterException;
+ /**
+ * Generate String representation of the model. Traditionally often XML but can
+ * be any other format as well.
+ *
+ * @param model
+ * The MINERVA ${@link Model} to be serialized
+ * @return The translated Model
+ */
+ public abstract String model2String(Model model) throws InconsistentModelException, ConverterException;
- /**
- * Returns a common name of data format used in the converter.
- *
- * @return common name of data format used in the converter
- */
- public abstract String getCommonName();
+ /**
+ * Returns a common name of data format used in the converter.
+ *
+ * @return common name of data format used in the converter
+ */
+ public abstract String getCommonName();
- /**
- * Returns {@link MimeType} of the exported data.
- *
- * @return {@link MimeType} of the exported data
- */
- public abstract MimeType getMimeType();
+ /**
+ * Returns {@link MimeType} of the exported data.
+ *
+ * @return {@link MimeType} of the exported data
+ */
+ public abstract MimeType getMimeType();
- /**
- * Returns extension of the exported file.
- *
- * @return extension of the exported file
- */
- public abstract String getFileExtension();
+ /**
+ * Returns extension of the exported file.
+ *
+ * @return extension of the exported file
+ */
+ public abstract String getFileExtension();
- /**
- * 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
- */
- public InputStream model2InputStream(Model model)
- throws InconsistentModelException, ConverterException {
- String modelString = model2String(model);
- return new ByteArrayInputStream(modelString.getBytes(StandardCharsets.UTF_8));
- }
+ /**
+ * 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
+ */
+ public InputStream model2InputStream(Model model)
+ throws InconsistentModelException, ConverterException {
+ String modelString = model2String(model);
+ return new ByteArrayInputStream(modelString.getBytes(StandardCharsets.UTF_8));
+ }
- /**
- * 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
- */
- public File model2File(Model model, String filePath)
- throws InconsistentModelException, IOException, ConverterException {
- String modelString = model2String(model);
- File file = new File(filePath);
+ /**
+ * 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
+ */
+ public File model2File(Model model, String filePath)
+ throws InconsistentModelException, IOException, ConverterException {
+ String modelString = model2String(model);
+ File file = new File(filePath);
File parentFile = file.getParentFile();
if (parentFile != null) {
parentFile.mkdirs();
}
- try (PrintWriter out = new PrintWriter(file)) {
- out.println(modelString);
- }
- return new File(filePath);
- }
+ try (PrintWriter out = new PrintWriter(file)) {
+ out.println(modelString);
+ }
+ return new File(filePath);
+ }
- public File inputStream2File(InputStream inputStream) throws IOException {
- File tempFile = File.createTempFile(UUID.randomUUID().toString(), ".tmp");
- tempFile.deleteOnExit();
- FileUtils.copyInputStreamToFile(inputStream, tempFile);
- return tempFile;
- }
+ public File inputStream2File(InputStream inputStream) throws IOException {
+ File tempFile = File.createTempFile(UUID.randomUUID().toString(), ".tmp");
+ tempFile.deleteOnExit();
+ FileUtils.copyInputStreamToFile(inputStream, tempFile);
+ return tempFile;
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ConverterException.java b/converter/src/main/java/lcsb/mapviewer/converter/ConverterException.java
index fad178973d..78605cf808 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 Converter} encounter
- * a problem.
+ * Generic exception thrown when implementation of {@link Converter} encounter a
+ * problem.
*
* @author Piotr Gawron
*
*/
public class ConverterException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor with exception message.
- *
- * @param message
- * error message
- */
- public ConverterException(String message) {
- super(message);
- }
+ /**
+ * 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 with super exception as a source.
+ *
+ * @param e
+ * super exception
+ */
+ public ConverterException(Exception e) {
+ super(e);
+ }
- /**
- * Default constructor - initializes instance variable to unknown.
- */
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
- public ConverterException() {
- super(); // call superclass constructor
- }
+ 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);
- }
+ /**
+ * 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 d774588c8b..214a3bb95a 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.converter;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
+import java.io.*;
import org.apache.xerces.xni.parser.XMLInputSource;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/GlyphParser.java b/converter/src/main/java/lcsb/mapviewer/converter/GlyphParser.java
index 79d5062a22..ae7e3d3bed 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/GlyphParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/GlyphParser.java
@@ -6,7 +6,8 @@ import java.util.zip.ZipFile;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/InvalidCoordinatesFile.java b/converter/src/main/java/lcsb/mapviewer/converter/InvalidCoordinatesFile.java
index cf6037be29..a558f73ca4 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.
+ * 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);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * parent exception (reason)
- */
- public InvalidCoordinatesFile(String message, Exception e) {
- super(message, e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidCoordinatesFile(Exception e) {
+ super(e);
+ }
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- */
- public InvalidCoordinatesFile(String message) {
- super(message);
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidCoordinatesFile(String message, Exception e) {
+ super(message, e);
+ }
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ */
+ public InvalidCoordinatesFile(String message) {
+ super(message);
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java b/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java
index 45c1a26809..cd96f56f85 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java
@@ -1,9 +1,9 @@
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
+ * 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
@@ -11,41 +11,41 @@ package lcsb.mapviewer.converter;
*/
public class InvalidOverviewFile extends InvalidInputDataExecption {
- /**
- * Default constructor.
- *
- * @param e
- * parent exception (reason)
- */
- public InvalidOverviewFile(Exception e) {
- super(e);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * parent exception (reason)
- */
- public InvalidOverviewFile(String message, Exception e) {
- super(message, e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidOverviewFile(Exception e) {
+ super(e);
+ }
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- */
- public InvalidOverviewFile(String message) {
- super(message);
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidOverviewFile(String message, Exception e) {
+ super(message, e);
+ }
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ */
+ public InvalidOverviewFile(String message) {
+ super(message);
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index 6bef70719c..4c162fed12 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -1,34 +1,24 @@
package lcsb.mapviewer.converter;
-import java.awt.Polygon;
+import java.awt.*;
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.io.*;
+import java.util.*;
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.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.*;
import lcsb.mapviewer.model.map.model.Model;
/**
@@ -328,7 +318,7 @@ public class OverviewParser {
}
String filename = columns[filenameColumn];
String polygon = columns[polygonColumn];
- String modelName = FilenameUtils.getBaseName(columns[targetFilenameColumn]);
+ String modelName = FilenameUtils.getBaseName(columns[targetFilenameColumn]);
String coord = columns[redirectionCoordinatesColumn];
String zoomLevel = columns[zoomLevelColumn];
String linkType = columns[targetTypeColumn];
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index 869980f1b9..ee388ac99a 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -1,28 +1,18 @@
package lcsb.mapviewer.converter;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.converter.zip.*;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.graphics.Glyph;
-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.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.layout.graphics.*;
+import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.map.species.Element;
public class ProjectFactory {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java b/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
index c491491e18..4bbbf82354 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
@@ -1,10 +1,9 @@
package lcsb.mapviewer.converter;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -14,9 +13,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
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.model.map.species.*;
/**
* This util class populate with z-index data if necessary.
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 96b1582d9d..4c811618c5 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
@@ -2,26 +2,16 @@ package lcsb.mapviewer.converter.annotation;
import java.text.ParseException;
import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.DOMException;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
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;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.model.Author;
/**
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 4ebbd0ce6b..9fea77d73d 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/package-info.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/package-info.java
@@ -4,4 +4,3 @@
*
*/
package lcsb.mapviewer.converter;
-
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 5c933d2fca..75cfe57902 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/InputFileType.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/InputFileType.java
@@ -8,36 +8,36 @@ package lcsb.mapviewer.converter.zip;
*
*/
public enum InputFileType {
- /**
- * Identifies file which is CellDesigner file.
- */
- CELLDESIGNER("CellDesigner (*.xml)"),
+ /**
+ * Identifies file which is CellDesigner file.
+ */
+ CELLDESIGNER("CellDesigner (*.xml)"),
- /**
- * Unknown file type.
- */
- UNKNOWN("Unknown (*.*)");
+ /**
+ * Unknown file type.
+ */
+ UNKNOWN("Unknown (*.*)");
- /**
- * Common name used for the type.
- */
- private String commonName;
+ /**
+ * Common name used for the type.
+ */
+ private String commonName;
- /**
- * Default constructor.
- *
- * @param commonName
- * {@link #commonName}
- */
- InputFileType(String commonName) {
- this.commonName = commonName;
- }
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * {@link #commonName}
+ */
+ InputFileType(String commonName) {
+ this.commonName = commonName;
+ }
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
}
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 b2569f492f..6a238e40f8 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ModelZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ModelZipEntryFile.java
@@ -13,188 +13,188 @@ import lcsb.mapviewer.model.map.model.SubmodelType;
*
*/
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);
- }
+ /**
+ *
+ */
+ 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;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * @param root
+ * the root to set
+ * @see #root
+ */
+ public void setRoot(String root) {
+ this.root = root;
+ }
+
+ /**
+ * 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 #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 5eb83c136b..94fa6e3cdf 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFile.java
@@ -11,75 +11,75 @@ import java.util.Map;
*
*/
public abstract class ZipEntryFile {
- /**
- * Name of the file in zip archive.
- */
- private String filename;
+ /**
+ * 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>();
+ /**
+ * 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.
+ */
+ public ZipEntryFile() {
+ }
- /**
- * Default constructor.
- *
- * @param filename
- * {@link #filename}
- */
- public ZipEntryFile(String filename) {
- this.filename = filename;
- }
+ /**
+ * Default constructor.
+ *
+ * @param filename
+ * {@link #filename}
+ */
+ public ZipEntryFile(String filename) {
+ this.filename = filename;
+ }
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return 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;
- }
+ /**
+ * @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);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 41d64302f6..a249cc8664 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
@@ -7,7 +7,8 @@ import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import org.apache.commons.io.FilenameUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.TextFileUtils;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -20,68 +21,59 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*/
public class ZipEntryFileFactory {
/**
- * Default class logger.
+ * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
+ * corresponding to the {@link LayoutZipEntryFile#type type}.
*/
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(ZipEntryFileFactory.class);
-
+ 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";
/**
* 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.graphics.Glyph} is stored. These
* entries should be by default transformed into {@link GlyphZipEntryFile}.
*/
private static final String GLYPHS_DIRECTORY = "glyphs/";
-
/**
* 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}.
+ * Default class logger.
*/
- public static final String LAYOUT_HEADER_PARAM_GENOME_VERSION = "GENOME_VERSION";
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.getLogger(ZipEntryFileFactory.class);
/**
* Generates instance of {@link ZipEntryFile} representing entry in the zip file
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 fdbf9c0a4c..607eff173e 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
@@ -2,4 +2,3 @@
* Package with structures describing zip file entries.
*/
package lcsb.mapviewer.converter.zip;
-
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ConverterTestFunctions.java b/converter/src/test/java/lcsb/mapviewer/converter/ConverterTestFunctions.java
index 15d26751d2..275ae8bbd5 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ConverterTestFunctions.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ConverterTestFunctions.java
@@ -1,37 +1,21 @@
package lcsb.mapviewer.converter;
-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.io.*;
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.parsers.*;
+import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.junit.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.w3c.dom.*;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
@@ -39,14 +23,11 @@ import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
public abstract class ConverterTestFunctions {
- private Logger logger = LogManager.getLogger(ConverterTestFunctions.class);
-
protected static double EPSILON = Configuration.EPSILON;
-
- private MinervaLoggerAppender appender;
-
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
+ private Logger logger = LogManager.getLogger(ConverterTestFunctions.class);
+ private MinervaLoggerAppender appender;
@Before
public final void _setUp() throws Exception {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java b/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java
index 2ac740ab6e..b89d181c9b 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java
@@ -7,14 +7,9 @@ import lcsb.mapviewer.common.MimeType;
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.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.*;
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.Phenotype;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
public class MockConverter extends Converter {
@@ -90,27 +85,27 @@ public class MockConverter extends Converter {
}
@Override
- public InputStream model2InputStream(Model model) throws InconsistentModelException, ConverterException {
+ public String getCommonName() {
return null;
}
@Override
- public File model2File(Model model, String filePath) throws InconsistentModelException {
+ public MimeType getMimeType() {
return null;
}
@Override
- public String getCommonName() {
+ public String getFileExtension() {
return null;
}
@Override
- public MimeType getMimeType() {
+ public InputStream model2InputStream(Model model) throws InconsistentModelException, ConverterException {
return null;
}
@Override
- public String getFileExtension() {
+ public File model2File(Model model, String filePath) throws InconsistentModelException {
return null;
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java
index 5b57488a49..5d6f98d24a 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.converter;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -13,9 +14,7 @@ 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.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
public class ZIndexPopulatorTest {
@@ -203,10 +202,9 @@ public class ZIndexPopulatorTest {
return result;
}
- private Reaction createReaction () {
+ private Reaction createReaction() {
Reaction result = new TransportReaction("s" + identifierCounter++);
return result;
}
-
}
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 541db6b893..e0ce5889dd 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.commands;
-import java.awt.Color;
+import java.awt.*;
import java.util.ArrayList;
import lcsb.mapviewer.model.map.model.Model;
@@ -13,34 +13,35 @@ import lcsb.mapviewer.model.map.model.Model;
*/
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();
- }
+ /**
+ * 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 e08bdca655..434e7d0f32 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.commands;
-import java.awt.Color;
+import java.awt.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -14,92 +14,94 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
*/
public class ColorExtractor {
- /**
- * Color that should be used for min values of {@link ColorSchema#value}.
- */
- private Color minColor;
+ /**
+ * 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;
+ /**
+ * Color that should be used for maxvalues of {@link ColorSchema#value}.
+ */
+ private Color maxColor;
- private Color simpleColor;
+ 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;
- }
+ /**
+ * 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());
- }
- }
+ /**
+ * 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;
- }
+ /**
+ * 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 minColor
+ * @see #minColor
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
- /**
- * @return the maxColor
- * @see #maxColor
- */
- public Color getMaxColor() {
- return maxColor;
- }
-
- public Color getSimpleColor() {
- return simpleColor;
- }
+ /**
+ * @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/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index 9cce0d6982..961ad55116 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -1,13 +1,11 @@
package lcsb.mapviewer.commands;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
+import java.awt.*;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -18,13 +16,8 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-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.map.reaction.AbstractNode;
-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.model.*;
+import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -322,10 +315,19 @@ public class ColorModelCommand extends ModelCommand {
throw new NotImplementedException();
}
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ try {
+ colorModel(getModel(), true);
+ } catch (InvalidColorSchemaException e) {
+ throw new CommandExecutionException(e);
+ }
+ }
+
/**
* Colors parameter model using coloring for this command. This method is used
* internally to color either top {@link Model} or one of it's sumbodels.
- *
+ *
* @param result
* model to color
* @param top
@@ -372,13 +374,4 @@ public class ColorModelCommand extends ModelCommand {
}
}
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- try {
- colorModel(getModel(), true);
- } catch (InvalidColorSchemaException e) {
- throw new CommandExecutionException(e);
- }
- }
-
}
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 ae9195d4b2..8fef89fbbf 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
@@ -8,48 +8,48 @@ package lcsb.mapviewer.commands;
*/
public class CommandExecutionException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- public CommandExecutionException() {
- super();
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 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);
- }
+ /**
+ * 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 3d5f910225..214b1df6f7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -1,38 +1,19 @@
package lcsb.mapviewer.commands;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
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.kinetics.*;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.Author;
-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;
+import lcsb.mapviewer.model.map.model.*;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.species.*;
/**
* Command that creates a new instance of the model with the same data.
@@ -257,12 +238,12 @@ public class CopyCommand extends NewModelCommand {
for (MiriamData md : model.getMiriamData()) {
result.addMiriamData(new MiriamData(md));
}
-
- if (model.getCreationDate()!=null) {
- result.setCreationDate((Calendar)(model.getCreationDate().clone()));
+
+ if (model.getCreationDate() != null) {
+ result.setCreationDate((Calendar) (model.getCreationDate().clone()));
}
-
- for (Calendar calendar: model.getModificationDates()) {
+
+ for (Calendar calendar : model.getModificationDates()) {
result.addModificationDate((Calendar) calendar.clone());
}
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 06f8c1c02d..09e86f7372 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -1,13 +1,11 @@
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 java.util.*;
import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -15,13 +13,9 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
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.layout.graphics.*;
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;
+import lcsb.mapviewer.model.map.species.*;
/**
* This {@link ModelCommand command} class allows to transform model into
@@ -32,16 +26,10 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
public class CreateHierarchyCommand extends ModelCommand {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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 compartment.
*/
@@ -50,7 +38,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* Top left corner y coordinate of the text associated with compartment.
*/
private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
-
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(CreateHierarchyCommand.class);
/**
* How many levels are possible.
*/
@@ -81,6 +73,11 @@ public class CreateHierarchyCommand extends ModelCommand {
throw new NotImplementedException();
}
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
@Override
protected void executeImplementation() {
if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
@@ -121,11 +118,6 @@ public class CreateHierarchyCommand extends ModelCommand {
}
}
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
-
/**
* Cleans hierarchical information from the model.
*/
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 b0d70db8e0..7b6855f0a7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/InvalidModelException.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/InvalidModelException.java
@@ -8,19 +8,19 @@ package lcsb.mapviewer.commands;
*
*/
public class InvalidModelException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 56394014f0..0f1288dd4b 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
@@ -26,205 +26,206 @@ import lcsb.mapviewer.model.map.species.Element;
*/
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());
- }
-
- }
+ /**
+ * 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;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public ModelCommand(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * 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;
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public ModelCommandStatus getStatus() {
+ return status;
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ protected void setStatus(ModelCommandStatus status) {
+ this.status = 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;
+ }
+
+ /**
+ * @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 5bcf5084fe..0be6884ea5 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommandStatus.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommandStatus.java
@@ -7,16 +7,16 @@ package lcsb.mapviewer.commands;
*
*/
public enum ModelCommandStatus {
- /**
- * {@link ModelCommand} was created.
- */
- CREATED,
- /**
- * {@link ModelCommand} was executed.
- */
- EXECUTED,
- /**
- * {@link ModelCommand} was undone.
- */
- UNDONE;
+ /**
+ * {@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 42aa36319f..9b8114b09b 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
@@ -17,60 +17,61 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class MoveCommand extends ModelCommand {
- /**
- * Delta x.
- */
- private double dx;
- /**
- * Delta y.
- */
- private double dy;
+ /**
+ * 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;
- }
+ /**
+ * 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 undoImplementation() {
+ throw new NotImplementedException();
+ }
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
- @Override
- protected void executeImplementation() {
+ @Override
+ protected void executeImplementation() {
- Model model = getModel();
+ 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);
- }
- }
- }
- }
+ 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 251149fcf3..cb65a4c741 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
@@ -1,25 +1,17 @@
package lcsb.mapviewer.commands;
import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
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.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.reaction.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
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 0c89b1852c..70f5ac14f7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java
@@ -10,43 +10,43 @@ import lcsb.mapviewer.model.map.model.Model;
*
*/
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();
+ /**
+ * Model on which command is performed.
+ */
+ private Model model;
- /**
- * Default constructor.
- *
- * @param model
- * {@link #model}
- */
- public NewModelCommand(Model model) {
- this.model = model;
- }
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public NewModelCommand(Model model) {
+ this.model = model;
+ }
- /**
- * @return the model
- * @see #model
- */
- protected Model getModel() {
- return model;
- }
+ /**
+ * Executed the operation.
+ *
+ * @return new {@link Model} object accoriding to initialization params
+ */
+ public abstract Model execute();
- /**
- * @param model
- * the model to set
- * @see #model
- */
- protected void setModel(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/SemanticZoomLevelMatcher.java b/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
index d49f59d7a0..d1fdee3c73 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
@@ -1,49 +1,49 @@
package lcsb.mapviewer.commands;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
public class SemanticZoomLevelMatcher {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(SemanticZoomLevelMatcher.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(SemanticZoomLevelMatcher.class);
- /**
- * Checks if level belongs to the range defined in
- * semanticZoomLevelVisibility.
- *
- * @param level
- * level to ve checked
- * @param semanticZoomLevelVisibility
- * range of levels to be checked
- * @return true if level is in the range
- */
- public boolean isVisible(int level, String semanticZoomLevelVisibility) {
- return matchLevel(level, semanticZoomLevelVisibility);
- }
+ /**
+ * Checks if level belongs to the range defined in semanticZoomLevelVisibility.
+ *
+ * @param level
+ * level to ve checked
+ * @param semanticZoomLevelVisibility
+ * range of levels to be checked
+ * @return true if level is in the range
+ */
+ public boolean isVisible(int level, String semanticZoomLevelVisibility) {
+ return matchLevel(level, semanticZoomLevelVisibility);
+ }
- public boolean isTransparent(int level, String semanticZoomLevelVisibility) {
- return matchLevel(level, semanticZoomLevelVisibility);
- }
+ public boolean isTransparent(int level, String semanticZoomLevelVisibility) {
+ return matchLevel(level, semanticZoomLevelVisibility);
+ }
- private boolean matchLevel(int level, String semanticZoomLevelVisibility) {
- if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
- return true;
- }
- if (semanticZoomLevelVisibility.contains("{")) {
- String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
- String[] ranges = strLevels.split(",");
- for (String string : ranges) {
- if (Integer.valueOf(string).equals(level)) {
- return true;
- }
- }
- }
- if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
- return true;
- }
- return false;
- }
+ private boolean matchLevel(int level, String semanticZoomLevelVisibility) {
+ if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
+ return true;
+ }
+ if (semanticZoomLevelVisibility.contains("{")) {
+ String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
+ String[] ranges = strLevels.split(",");
+ for (String string : ranges) {
+ if (Integer.valueOf(string).equals(level)) {
+ return true;
+ }
+ }
+ }
+ if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
+ return true;
+ }
+ return false;
+ }
}
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 99325ce1f1..b17a17ca27 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.commands;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -37,6 +38,11 @@ public class SetFixedHierarchyLevelCommand extends ModelCommand {
throw new NotImplementedException();
}
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
@Override
protected void executeImplementation() {
if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
@@ -70,9 +76,4 @@ public class SetFixedHierarchyLevelCommand extends ModelCommand {
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 de058e7b7e..4c6ea2f29c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -1,21 +1,17 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
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.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;
+import lcsb.mapviewer.model.map.species.*;
/**
* Creates a new instance of the model with data limited to region described by
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java
index b760013ef3..dd47fbf5dc 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java
@@ -5,7 +5,8 @@ import java.awt.geom.Point2D;
import java.util.Collection;
import java.util.HashSet;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.common.geometry.DoubleDimension;
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index 3d5c0ab39a..7af8cb6dff 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -26,17 +26,15 @@ import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.getLogger(ApplySimpleLayoutModelCommand.class);
-
public static final double COMPARTMENT_BORDER = 10;
private static final double BORDER_FROM_EXISTING_ELEMENTS = 10;
private static final int SPECIES_WIDTH = 90;
private static final int SPECIES_HEIGHT = 30;
private static final double COMPLEX_PADDING = 5;
-
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(ApplySimpleLayoutModelCommand.class);
private PointTransformation pt = new PointTransformation();
public ApplySimpleLayoutModelCommand(Model model, Collection<BioEntity> bioEntities, Double minX, Double minY,
@@ -56,30 +54,6 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
this(model, null);
}
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- Set<Model> models = new HashSet<>();
- models.add(this.getModel());
- models.addAll(this.getModel().getSubmodels());
- for (Model model : models) {
- Collection<BioEntity> bioEntites = new HashSet<>();
- for (BioEntity bioEntity : this.getBioEntities()) {
- if (bioEntity.getModel() == model) {
- bioEntites.add(bioEntity);
- }
- }
- if (bioEntites.size() > 0) {
- Dimension2D dimension = null;
- Point2D minPoint = null;
- if (model == this.getModel()) {
- dimension = getStartDimension();
- minPoint = getStartPoint();
- }
- createLayout(model, bioEntites, null, minPoint, dimension);
- }
- }
- }
-
private void createLayout(Model model, Collection<BioEntity> bioEntites, Compartment compartment, Point2D minPoint,
Dimension2D dimension) {
if (dimension == null) {
@@ -466,6 +440,30 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
throw new NotImplementedException();
}
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ Set<Model> models = new HashSet<>();
+ models.add(this.getModel());
+ models.addAll(this.getModel().getSubmodels());
+ for (Model model : models) {
+ Collection<BioEntity> bioEntites = new HashSet<>();
+ for (BioEntity bioEntity : this.getBioEntities()) {
+ if (bioEntity.getModel() == model) {
+ bioEntites.add(bioEntity);
+ }
+ }
+ if (bioEntites.size() > 0) {
+ Dimension2D dimension = null;
+ Point2D minPoint = null;
+ if (model == this.getModel()) {
+ dimension = getStartDimension();
+ minPoint = getStartPoint();
+ }
+ createLayout(model, bioEntites, null, minPoint, dimension);
+ }
+ }
+ }
+
protected void modifyComplexLocation(Complex complex, double centerX, double centerY) {
if (complex.getWidth() == null || complex.getHeight() == null) {
computeComplexSize(complex);
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 912c51cf99..43a01ab5dc 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
@@ -4,4 +4,3 @@
*
*/
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 7b94301d00..23b24ed986 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.commands.properties;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.model.Model;
@@ -17,58 +18,59 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class AddElementFormerSymbolsCommand extends AddElementPropertyListEntryCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
-
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 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());
+
+ }
+
+ @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());
+ }
}
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 ba6c059195..11d2bfcac8 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.commands.properties;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -18,57 +19,57 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class AddElementMiriamDataCommand extends AddElementPropertyListEntryCommand<MiriamData> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(AddElementMiriamDataCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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 {
+ @Override
+ protected void undoImplementation() {
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getMiriamData().removeAll(getNewValues());
- for (MiriamData md : getNewValues()) {
- if (getAlias().getMiriamData().contains(md)) {
- throw new CommandExecutionException("Cannot add miriam \"" + md + "\" to the list. Element already exists.");
- }
- }
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getMiriamData().addAll(getNewValues());
+ }
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
- @Override
- protected void undoImplementation() {
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getMiriamData().removeAll(getNewValues());
+ for (MiriamData md : getNewValues()) {
+ if (getAlias().getMiriamData().contains(md)) {
+ throw new CommandExecutionException("Cannot add miriam \"" + md + "\" to the list. Element already exists.");
+ }
+ }
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getMiriamData().addAll(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 921b7c72af..50a9a50b0f 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
@@ -2,9 +2,7 @@ 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.commands.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
@@ -20,72 +18,72 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand {
- /**
- * List of new values that should be added to property.
- */
- private List<T> newValues;
+ /**
+ * 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;
+ /**
+ * {@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;
- }
+ /**
+ * 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);
- }
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 ee8bd9971b..c39368de05 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.commands.properties;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.model.Model;
@@ -17,57 +18,57 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class AddElementSynonymsCommand extends AddElementPropertyListEntryCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(AddElementSynonymsCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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 {
+ @Override
+ protected void undoImplementation() {
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getSynonyms().removeAll(getNewValues());
- for (String string : getNewValues()) {
- if (getAlias().getSynonyms().contains(string)) {
- throw new CommandExecutionException("Cannot add synonym to the list: " + string + ". Element already exists.");
- }
- }
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getSynonyms().addAll(getNewValues());
+ }
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
- @Override
- protected void undoImplementation() {
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getSynonyms().removeAll(getNewValues());
+ for (String string : getNewValues()) {
+ if (getAlias().getSynonyms().contains(string)) {
+ throw new CommandExecutionException("Cannot add synonym to the list: " + string + ". Element already exists.");
+ }
+ }
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getSynonyms().addAll(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 acad51f8d5..4c8e92575f 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.commands.properties;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
* of the element connected to {@link Element}.
@@ -14,37 +15,37 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementAbbreviationCommand extends ChangeElementPropertyCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 5f42faaa87..8b3f9ec7b2 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
@@ -1,12 +1,13 @@
package lcsb.mapviewer.commands.properties;
-import java.awt.Color;
+import java.awt.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that
* {@link Element#color}.
@@ -16,34 +17,34 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementColorCommand extends ChangeElementPropertyCommand<Color> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 f128cba3af..09b3c9a505 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.commands.properties;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
* {@link Element#fontSize}.
@@ -14,38 +15,38 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementFontSizeCommand extends ChangeElementPropertyCommand<Double> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 5e82bf21d1..3e468ff3e0 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.commands.properties;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.model.Model;
@@ -15,50 +16,50 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class ChangeElementFormerSymbolCommand extends ChangeElementPropertyListEntryCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(ChangeElementFormerSymbolCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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;
- }
+ @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());
+ // 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());
+ 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());
- }
+ // 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 238ea5f95d..7529b9a5d2 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.commands.properties;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
@@ -14,38 +15,38 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class ChangeElementFormulaCommand extends ChangeElementPropertyCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 cdf2c16147..cfc3d8c42b 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.commands.properties;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes full
* name of the element connected to {@link Element}.
@@ -14,38 +15,38 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementFullNameCommand extends ChangeElementPropertyCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 6062330455..87a4e8ea5e 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.commands.properties;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -16,53 +17,53 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class ChangeElementMiriamDataCommand extends ChangeElementPropertyListEntryCommand<MiriamData> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(ChangeElementMiriamDataCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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;
- }
+ @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());
+ // 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());
+ 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());
- }
+ // 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 7a6f4d5d7f..6890836955 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.commands.properties;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
* of the element connected to {@link Element}.
@@ -14,34 +15,34 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementNameCommand extends ChangeElementPropertyCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 77a25a50bd..9ae0f8a006 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.commands.properties;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes notes
* of the element connected to {@link Element}.
@@ -14,38 +15,38 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementNotesCommand extends ChangeElementPropertyCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 6613c69e48..b3259d67df 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.commands.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
@@ -18,103 +16,103 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class ChangeElementPropertyCommand<T> extends ModelCommand {
- /**
- * New element property value.
- */
- private T newValue;
+ /**
+ * New element property value.
+ */
+ private T newValue;
- /**
- * Old element property value.
- */
- private T oldValue;
+ /**
+ * Old element property value.
+ */
+ private T oldValue;
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
+ /**
+ * {@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;
- }
+ /**
+ * 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 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);
- }
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 b842c08eca..cb1f3a8250 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
@@ -1,15 +1,12 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.commands.*;
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.
+ * entry in a property of the {@link Element Element} that is list.
*
* @param <T>
* class of property to edit
@@ -19,109 +16,109 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelCommand {
- /**
- * New element property value.
- */
- private T newValue;
+ /**
+ * New element property value.
+ */
+ private T newValue;
- /**
- * Old element property value.
- */
- private T oldValue;
+ /**
+ * Old element property value.
+ */
+ private T oldValue;
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
+ /**
+ * {@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;
- }
+ /**
+ * 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 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);
- }
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 646926e4d5..21197254af 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.commands.properties;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.logging.log4j.*;
-
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes symbol
* of the element connected to {@link Element}.
@@ -14,38 +15,38 @@ import org.apache.logging.log4j.*;
*/
public class ChangeElementSymbolCommand extends ChangeElementPropertyCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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());
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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 8c0d2705b0..dd3b797660 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.commands.properties;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.model.Model;
@@ -15,50 +16,50 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class ChangeElementSynonymCommand extends ChangeElementPropertyListEntryCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(ChangeElementSynonymCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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;
- }
+ @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());
+ // 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());
+ 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());
- }
+ // 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 13e233fd70..cde5df4197 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.commands.properties;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.model.Model;
@@ -17,57 +18,58 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class RemoveElementFormerSymbolsCommand extends RemoveElementPropertyListEntryCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(RemoveElementFormerSymbolsCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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 {
+ @Override
+ protected void undoImplementation() {
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getFormerSymbols().addAll(getValues());
- for (String string : getValues()) {
- if (!getAlias().getFormerSymbols().contains(string)) {
- throw new CommandExecutionException("Cannot remove former symbol \"" + string + "\" from the list. Element doesn't exist.");
- }
- }
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getFormerSymbols().removeAll(getValues());
+ }
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
- @Override
- protected void undoImplementation() {
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getFormerSymbols().addAll(getValues());
+ for (String string : getValues()) {
+ if (!getAlias().getFormerSymbols().contains(string)) {
+ throw new CommandExecutionException(
+ "Cannot remove former symbol \"" + string + "\" from the list. Element doesn't exist.");
+ }
+ }
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getFormerSymbols().removeAll(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 4a7bc50cf0..5a929d61c8 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.commands.properties;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -18,57 +19,58 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class RemoveElementMiriamDataCommand extends RemoveElementPropertyListEntryCommand<MiriamData> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(RemoveElementMiriamDataCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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 {
+ @Override
+ protected void undoImplementation() {
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getMiriamData().addAll(getValues());
- for (MiriamData string : getValues()) {
- if (!getAlias().getMiriamData().contains(string)) {
- throw new CommandExecutionException("Cannot remove miriam \"" + string + "\" from the list. Element doesn't exist.");
- }
- }
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getMiriamData().removeAll(getValues());
+ }
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
- @Override
- protected void undoImplementation() {
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getMiriamData().addAll(getValues());
+ for (MiriamData string : getValues()) {
+ if (!getAlias().getMiriamData().contains(string)) {
+ throw new CommandExecutionException(
+ "Cannot remove miriam \"" + string + "\" from the list. Element doesn't exist.");
+ }
+ }
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getMiriamData().removeAll(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 b61167bc40..0a2b660b3a 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
@@ -2,16 +2,13 @@ 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.commands.*;
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.
+ * entries from a property of the {@link Element Element} that is list.
*
* @param <T>
* class of property to edit
@@ -21,72 +18,72 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelCommand {
- /**
- * Rlement property values to be removed.
- */
- private List<T> values;
+ /**
+ * Rlement property values to be removed.
+ */
+ private List<T> values;
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
+ /**
+ * {@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;
- }
+ /**
+ * 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);
- }
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 318510ec51..f70347cc9f 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.commands.properties;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.model.Model;
@@ -17,57 +18,58 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public class RemoveElementSynonymsCommand extends RemoveElementPropertyListEntryCommand<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(RemoveElementSynonymsCommand.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.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);
- }
+ /**
+ * 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 {
+ @Override
+ protected void undoImplementation() {
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getSynonyms().addAll(getValues());
- for (String string : getValues()) {
- if (!getAlias().getSynonyms().contains(string)) {
- throw new CommandExecutionException("Cannot remove synonym from the list: " + string + ". Element doesn't exist.");
- }
- }
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getSynonyms().removeAll(getValues());
+ }
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
- @Override
- protected void undoImplementation() {
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
- getAlias().getSynonyms().addAll(getValues());
+ for (String string : getValues()) {
+ if (!getAlias().getSynonyms().contains(string)) {
+ throw new CommandExecutionException(
+ "Cannot remove synonym from the list: " + string + ". Element doesn't exist.");
+ }
+ }
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
+ getAlias().getSynonyms().removeAll(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 900c3f4675..3769d5ed6c 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
@@ -5,4 +5,3 @@
*
*/
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 1357d8589e..afc4a01a40 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
@@ -1,12 +1,12 @@
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;
+import lcsb.mapviewer.commands.layout.AllLayoutTests;
+import lcsb.mapviewer.commands.properties.AllPropertyCommandTests;
+
@RunWith(Suite.class)
@SuiteClasses({ AllLayoutTests.class,
AllPropertyCommandTests.class,
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 16db4493fc..b60c45de52 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -2,8 +2,9 @@ package lcsb.mapviewer.commands;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.util.*;
+import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
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 6ebfaff56f..88df2a2dda 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -3,12 +3,10 @@ package lcsb.mapviewer.commands;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Rule;
import lcsb.mapviewer.common.UnitTestFailedWatcher;
@@ -23,15 +21,12 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.GenericProtein;
public abstract class CommandTestFunctions {
+ private static Map<String, Model> models = new HashMap<String, Model>();
public double EPSILON = 1e-6;
-
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
Logger logger = LogManager.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);
@@ -79,11 +74,11 @@ public abstract class CommandTestFunctions {
String xmlString = parser.model2String(original);
InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
Model result = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-
- for (Drawable bioEntity: original.getDrawables()) {
+
+ for (Drawable bioEntity : original.getDrawables()) {
bioEntity.setZ(null);
}
- for (Drawable bioEntity: result.getDrawables()) {
+ for (Drawable bioEntity : result.getDrawables()) {
bioEntity.setZ(null);
}
return result;
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 881e2d9e3d..3bdcd703ad 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.commands;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
import java.awt.geom.Path2D;
import java.util.Arrays;
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 d0b9fc798b..0a456a10da 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
@@ -6,17 +6,17 @@ 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,
-
+ 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/ChangeElementColorCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
index 38fe93c7bb..bf3b226e50 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
@@ -2,7 +2,7 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
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 74762f248b..dfadfb32ea 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.commands.properties;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index c19fdba60e..f4d5edb4c8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -1,21 +1,15 @@
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 java.util.*;
import javax.persistence.*;
+import javax.persistence.Entity;
+import javax.persistence.OrderBy;
import org.apache.logging.log4j.core.LogEvent;
-
-import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.*;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -205,14 +199,14 @@ public class Project implements Serializable {
this.disease = disease;
}
- public void setOrganism(MiriamData organism) {
- this.organism = organism;
- }
-
public MiriamData getOrganism() {
return organism;
}
+ public void setOrganism(MiriamData organism) {
+ this.organism = organism;
+ }
+
public void addWarning(String warning) {
if (warning.trim().contains("\n")) {
throw new InvalidArgumentException("Warning must be one line of text");
@@ -264,7 +258,7 @@ public class Project implements Serializable {
public void addLoggingInfo(MinervaLoggerAppender appender) {
List<String> warnings = new ArrayList<>();
for (LogEvent event : appender.getWarnings()) {
- warnings.add(event.getMessage().getFormattedMessage().replaceAll("\n", "_NEW_LINE_"));
+ warnings.add(event.getMessage().getFormattedMessage().replaceAll("\n", "_NEW_LINE_"));
}
addWarnings(warnings);
}
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 ee01e60a6c..3e821853e9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/BigFileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/BigFileEntry.java
@@ -3,9 +3,7 @@ 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 javax.persistence.*;
import lcsb.mapviewer.common.IProgressUpdater;
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 419ec89421..5f7773b19b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/CacheQuery.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/CacheQuery.java
@@ -3,13 +3,7 @@ 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;
+import javax.persistence.*;
/**
* Object that defines cached value retrieved from external resource. The key in
@@ -136,6 +130,15 @@ public class CacheQuery implements Serializable {
this.type = type;
}
+ /**
+ *
+ * @param type2
+ * new {@link #type} value
+ */
+ public void setType(CacheType type2) {
+ this.type = type2.getId();
+ }
+
/**
* @return the expires
* @see #expires
@@ -170,13 +173,4 @@ public class CacheQuery implements Serializable {
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 8c209bfec6..f620f05083 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java
@@ -2,10 +2,7 @@ package lcsb.mapviewer.model.cache;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import javax.persistence.*;
/**
* Defines types of objects stored in the cache and interfaces used for
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 b4bebc29f0..ff3f241e93 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java
@@ -2,15 +2,7 @@ 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.*;
/**
* Database object representing file put in the system (it can be some cached
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 6d36a152d0..a36354e420 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
@@ -2,10 +2,7 @@ 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 javax.persistence.*;
import lcsb.mapviewer.model.user.User;
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 eeada7b7b0..7b7108e1ac 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
@@ -2,4 +2,3 @@
* 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 d59fee3b9f..f4db2ef1e4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
@@ -27,7 +27,7 @@ public enum ArrowType {
* />
*/
BLANK_CROSSBAR,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -37,7 +37,7 @@ public enum ArrowType {
*
*/
FULL_CROSSBAR,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -47,7 +47,7 @@ public enum ArrowType {
*
*/
DIAMOND,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -56,7 +56,7 @@ public enum ArrowType {
* />
*/
BLANK,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -66,7 +66,7 @@ public enum ArrowType {
*
*/
CROSSBAR,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -75,7 +75,7 @@ public enum ArrowType {
* /> *
*/
CIRCLE,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -84,7 +84,7 @@ public enum ArrowType {
* />
*/
OPEN,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -93,7 +93,7 @@ public enum ArrowType {
* />
*/
FULL,
-
+
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
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 63a3dfcfd1..33da4e15f6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.graphics;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 908cff784d..5040ec54a1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.model.graphics;
-import java.awt.BasicStroke;
-import java.awt.Stroke;
+import java.awt.*;
import java.util.List;
import lcsb.mapviewer.common.comparator.FloatComparator;
@@ -126,15 +125,6 @@ public enum LineType {
0.0f);
}
- /**
- * Return the {@link BasicStroke} for this line type.
- *
- * @return the {@link BasicStroke} for this line type
- */
- public Stroke getStroke() {
- return stroke;
- }
-
public static LineType getTypeByDashArray(List<Short> strokeDashArray) {
FloatComparator doubleComparator = new FloatComparator();
for (LineType type : LineType.values()) {
@@ -155,4 +145,13 @@ public enum LineType {
}
return LineType.SOLID;
}
+
+ /**
+ * 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/MapCanvasType.java b/model/src/main/java/lcsb/mapviewer/model/graphics/MapCanvasType.java
index 0c400788d7..8c84cfb17c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/MapCanvasType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/MapCanvasType.java
@@ -1,7 +1,8 @@
package lcsb.mapviewer.model.graphics;
public enum MapCanvasType {
- GOOGLE_MAPS_API("Google Maps API"), OPEN_LAYERS("OpenLayers");
+ GOOGLE_MAPS_API("Google Maps API"),
+ OPEN_LAYERS("OpenLayers");
private String commonName;
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 9f0fc47877..f25e0c205e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
@@ -1,31 +1,18 @@
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.awt.*;
+import java.awt.geom.*;
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.*;
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.OrderColumn;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.*;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.Type;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -232,9 +219,18 @@ public class PolylineData implements Serializable, Drawable {
return result;
}
+ /**
+ * 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);
+ }
+
/**
* Sets the new value of the last point in the line.
- *
+ *
* @param point
* new value of the last point in the line
*/
@@ -242,15 +238,6 @@ public class PolylineData implements Serializable, Drawable {
setPoint(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.
*
@@ -443,6 +430,15 @@ public class PolylineData implements Serializable, Drawable {
this.width = width;
}
+ /**
+ * @param string
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(String string) {
+ setWidth(Double.parseDouble(string));
+ }
+
/**
* @return the color
* @see #color
@@ -494,15 +490,6 @@ public class PolylineData implements Serializable, Drawable {
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.
*
@@ -537,12 +524,12 @@ public class PolylineData implements Serializable, Drawable {
}
@Override
- public double getSize() {
- return 0;
+ public String getElementId() {
+ return toString();
}
@Override
- public String getElementId() {
- return toString();
+ public double getSize() {
+ return 0;
}
}
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 0dd770744b..760d473337 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.graphics;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 12c79169f4..6f900188e2 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
@@ -3,4 +3,3 @@
* have to belong to the map.
*/
package lcsb.mapviewer.model.graphics;
-
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 9879bc60c5..59d6324012 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -1,9 +1,7 @@
package lcsb.mapviewer.model.map;
import java.io.Serializable;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
+import java.util.*;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.model.map.model.Model;
@@ -68,6 +66,15 @@ public interface BioEntity extends Serializable, Drawable {
*/
String getName();
+ /**
+ * Sets the name to the object.
+ *
+ * @param name
+ * name of the object
+ *
+ */
+ void setName(String name);
+
/**
* Returns notes about the object.
*
@@ -128,14 +135,6 @@ public interface BioEntity extends Serializable, Drawable {
*/
void setAbbreviation(String abbreviation);
- /**
- * Sets formula.
- *
- * @param formula
- * new formula
- */
- void setFormula(String formula);
-
/**
* Returns the formula.
*
@@ -144,13 +143,12 @@ public interface BioEntity extends Serializable, Drawable {
String getFormula();
/**
- * Sets the name to the object.
- *
- * @param name
- * name of the object
+ * Sets formula.
*
+ * @param formula
+ * new formula
*/
- void setName(String name);
+ void setFormula(String formula);
/**
* Returns database identifier of the object.
@@ -166,6 +164,13 @@ public interface BioEntity extends Serializable, Drawable {
*/
String getStringType();
+ /**
+ * Returns semantic zoom level visibility.
+ *
+ * @return semantic zoom level visibility
+ */
+ String getVisibilityLevel();
+
/**
* Sets semantic zoom level visibility.
*
@@ -182,13 +187,6 @@ public interface BioEntity extends Serializable, Drawable {
*/
void setVisibilityLevel(Integer zoomLevelVisibility);
- /**
- * Returns semantic zoom level visibility.
- *
- * @return semantic zoom level visibility
- */
- String getVisibilityLevel();
-
/**
* Returns the {@link Model} where BioEntity is located.
*
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 d19627c469..8747682ed2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
@@ -3,13 +3,7 @@ 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.*;
import org.hibernate.annotations.Type;
@@ -97,6 +91,10 @@ public class Comment implements Serializable {
* If feedback is located on the element, what is the identifier of the element.
*/
private Integer tableId;
+ /**
+ * Determines if comment should be visible on the map.
+ */
+ private boolean pinned = false;
/**
* @return the tableId
@@ -285,11 +283,6 @@ public class Comment implements Serializable {
this.deleted = deleted;
}
- /**
- * Determines if comment should be visible on the map.
- */
- private boolean pinned = false;
-
/**
* @return the pinned
* @see #pinned
@@ -316,7 +309,7 @@ public class Comment implements Serializable {
public void setModel(Model model2) {
this.model = model2.getModelData();
}
-
+
public void setModel(ModelData model2) {
this.model = model2;
}
@@ -339,20 +332,20 @@ public class Comment implements Serializable {
}
/**
- * @param submodel
- * the submodel to set
+ * @return the submodel
* @see #submodel
*/
- public void setSubmodel(Model submodel) {
- this.submodel = submodel.getModelData();
+ public Model getSubmodel() {
+ return this.submodel.getModel();
}
/**
- * @return the submodel
+ * @param submodel
+ * the submodel to set
* @see #submodel
*/
- public Model getSubmodel() {
- return this.submodel.getModel();
+ public void setSubmodel(Model submodel) {
+ this.submodel = submodel.getModelData();
}
}
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 1c5908da61..13c6aa49cd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
@@ -2,15 +2,11 @@ package lcsb.mapviewer.model.map;
import java.io.Serializable;
-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.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -25,17 +21,15 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
@XmlRootElement
public class MiriamData implements Comparable<MiriamData>, Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(MiriamData.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Unique database identifier.
*/
@@ -149,14 +143,6 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
this(mt, resource, null);
}
- /**
- *
- * @return {@link #resource}
- */
- public String getResource() {
- return resource;
- }
-
/**
* @param identifier
* string represents identifier.
@@ -172,6 +158,14 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
return identifier;
}
+ /**
+ *
+ * @return {@link #resource}
+ */
+ public String getResource() {
+ return resource;
+ }
+
/**
* Sets new {@link #resource}.
*
@@ -186,6 +180,11 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
}
}
+ @Override
+ public int hashCode() {
+ return (dataType + resource).hashCode();
+ }
+
@Override
public boolean equals(Object aThat) {
// check for self-comparison
@@ -212,8 +211,14 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
}
@Override
- public int hashCode() {
- return (dataType + resource).hashCode();
+ public String toString() {
+ String annotatorClass = annotator != null ? ":" + annotator.getName() : "";
+ if (relationType != null) {
+ return "[" + relationType.getStringRepresentation() + "] " + dataType + ":" + resource + annotatorClass;
+ } else {
+ return "[UNKNOWN] " + dataType + ":" + resource + annotatorClass;
+
+ }
}
@Override
@@ -276,7 +281,7 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
}
/**
- *
+ *
* @return {@link #annotator}
*/
public Class<?> getAnnotator() {
@@ -284,22 +289,11 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
}
/**
- *
+ *
* @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 6f365b2be9..2938dd8334 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamRelationType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamRelationType.java
@@ -89,17 +89,9 @@ public enum MiriamRelationType {
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
@@ -112,4 +104,12 @@ public enum MiriamRelationType {
}
return null;
}
+
+ /**
+ * @return the stringRepresentation
+ * @see #stringRepresentation
+ */
+ public String getStringRepresentation() {
+ return stringRepresentation;
+ }
}
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 0ae6e05571..d9c44cd820 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -9,13 +9,7 @@ import org.apache.logging.log4j.Logger;
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;
+import lcsb.mapviewer.model.map.species.*;
/**
* Type of known miriam annotation.
@@ -813,33 +807,9 @@ public enum MiriamType {
exampleIdentifier);
}
- /**
- *
- * @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
@@ -856,33 +826,9 @@ public enum MiriamType {
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
@@ -898,7 +844,7 @@ public enum MiriamType {
/**
* 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
@@ -923,7 +869,7 @@ public enum MiriamType {
/**
* Creates {@link MiriamData} from miriam uri.
- *
+ *
* @param miriamUri
* miriam uri defining {@link MiriamData}
* @return {@link MiriamData} from miriam uri
@@ -966,6 +912,54 @@ public enum MiriamType {
throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
}
+ /**
+ *
+ * @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;
+ }
+
+ /**
+ * @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;
+ }
+
public String getNamespace() {
return namespace;
}
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 72e0ee423d..f11a3ff3dc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
@@ -4,14 +4,7 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-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.*;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
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 26d2a1a282..0f5e232dbb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
@@ -2,7 +2,8 @@ package lcsb.mapviewer.model.map;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 d3daa9f373..6cad8e099f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.model.map;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
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 df31581e58..679b9dfb57 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -35,11 +36,6 @@ public class OverviewImageLinkComparator extends Comparator<OverviewImageLink> {
this.epsilon = epsilon;
}
- @Override
- protected Comparator<?> getParentComparator() {
- return new OverviewLinkComparator(epsilon);
- }
-
/**
* Default constructor.
*/
@@ -47,6 +43,11 @@ public class OverviewImageLinkComparator extends Comparator<OverviewImageLink> {
this(Configuration.EPSILON);
}
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new OverviewLinkComparator(epsilon);
+ }
+
@Override
protected int internalCompare(OverviewImageLink arg0, OverviewImageLink arg1) {
int result = 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 150de91e50..c73e2cdf41 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java
@@ -5,17 +5,7 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-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.*;
/**
* Abstract class representing link that connects {@link OverviewImage parent
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 675dde9e30..d4682f1764 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 ed236721b9..fa7e27a557 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.model.map;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.model.Model;
@@ -131,6 +128,21 @@ public class OverviewModelLink extends OverviewLink {
this.xCoord = xCoord;
}
+ /**
+ * 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();
+ }
+ }
+
/**
* @return the yCoord
* @see #yCoord
@@ -148,21 +160,6 @@ public class OverviewModelLink extends OverviewLink {
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}.
*
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 1338b8a25f..8e64c1ec92 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 d5270b88ad..dbe0faa688 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
@@ -2,13 +2,10 @@ package lcsb.mapviewer.model.map;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Element;
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 7e023dda8b..73b490dae3 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
@@ -1,23 +1,19 @@
package lcsb.mapviewer.model.map.compartment;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.util.HashSet;
import java.util.Set;
-import javax.persistence.DiscriminatorValue;
+import javax.persistence.*;
import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
-import org.apache.logging.log4j.*;
-import org.hibernate.annotations.Cascade;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.hibernate.annotations.*;
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.common.exception.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -306,14 +302,6 @@ public class Compartment extends Element {
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
@@ -390,6 +378,14 @@ public class Compartment extends Element {
return elements;
}
+ /**
+ * @param elements
+ * the elements to set
+ */
+ public void setElements(Set<Element> elements) {
+ this.elements = elements;
+ }
+
@Override
public String getStringType() {
return "Compartment";
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 7b4b97c17b..1aa57624bf 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
@@ -3,13 +3,12 @@ package lcsb.mapviewer.model.map.compartment;
import java.util.HashMap;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.comparator.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.ElementComparator;
@@ -45,10 +44,6 @@ public class CompartmentComparator extends Comparator<Compartment> {
this.epsilon = epsilon;
}
- protected Comparator<?> getParentComparator() {
- return new ElementComparator(epsilon);
- }
-
/**
* Default constructor.
*/
@@ -56,6 +51,10 @@ public class CompartmentComparator extends Comparator<Compartment> {
this(Configuration.EPSILON);
}
+ protected Comparator<?> getParentComparator() {
+ return new ElementComparator(epsilon);
+ }
+
@Override
protected int internalCompare(Compartment arg0, Compartment arg1) {
ElementComparator elementComparator = new ElementComparator(epsilon);
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 2c1fe73421..dfd70ecebd 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.compartment;
-import java.awt.Color;
+import java.awt.*;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
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 d6dd6c0614..36e73ed224 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.model.Model;
@@ -53,26 +54,10 @@ public class RightSquareCompartment extends Compartment {
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
* original compartment where the data was kept
*/
@@ -82,7 +67,7 @@ public class RightSquareCompartment extends Compartment {
/**
* Default constructor.
- *
+ *
* @param elementId
* identifier of the compartment
*/
@@ -90,6 +75,22 @@ public class RightSquareCompartment extends Compartment {
setElementId(elementId);
}
+ /**
+ * 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());
+ }
+
@Override
public RightSquareCompartment copy() {
if (this.getClass() == RightSquareCompartment.class) {
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 70116802e0..8be9199db2 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
@@ -4,20 +4,11 @@ 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.OrderColumn;
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -31,17 +22,15 @@ import lcsb.mapviewer.model.map.model.ModelData;
@XmlRootElement
public class SbmlFunction implements Serializable, SbmlArgument {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(SbmlFunction.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Unique database identifier.
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
index 877f176ac9..b2d2a4eed9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.kinetics;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.comparator.StringComparator;
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 7e3ce2c1ac..1c96fd0929 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
@@ -1,24 +1,13 @@
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 java.util.*;
+
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -34,17 +23,15 @@ import lcsb.mapviewer.model.map.species.Element;
@XmlRootElement
public class SbmlKinetics implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(SbmlKinetics.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
@Cascade({ CascadeType.ALL })
@ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name = "kinetic_law_parameters", joinColumns = {
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 e7d68acfcd..158d4dd886 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.kinetics;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.comparator.SetComparator;
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 11f1a54546..4fb498449d 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
@@ -2,14 +2,11 @@ package lcsb.mapviewer.model.map.kinetics;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Representation of a single SBML parameter
@@ -21,17 +18,15 @@ import org.apache.logging.log4j.*;
@XmlRootElement
public class SbmlParameter implements Serializable, SbmlArgument {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(SbmlParameter.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Unique database identifier.
*/
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 d9242e6c69..bb194bead6 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
@@ -4,16 +4,11 @@ import java.io.Serializable;
import java.util.HashSet;
import java.util.Set;
-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.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -29,17 +24,15 @@ import lcsb.mapviewer.model.map.model.ModelData;
@XmlRootElement
public class SbmlUnit implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(SbmlUnit.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Unique database identifier.
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
index 2144c14b64..9643289589 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
@@ -1,13 +1,14 @@
package lcsb.mapviewer.model.map.kinetics;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.comparator.SetComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
public class SbmlUnitComparator extends Comparator<SbmlUnit> {
- private static Logger logger =LogManager.getLogger(SbmlUnitComparator.class);
+ private static Logger logger = LogManager.getLogger(SbmlUnitComparator.class);
public SbmlUnitComparator() {
super(SbmlUnit.class);
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 bea7bc652a..5683a2eb9a 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
@@ -2,17 +2,11 @@ package lcsb.mapviewer.model.map.kinetics;
import java.io.Serializable;
-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.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Representation of a single SBML unit factor. For example unit for velocity is
@@ -29,17 +23,15 @@ import org.apache.logging.log4j.*;
@XmlRootElement
public class SbmlUnitTypeFactor implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(SbmlUnitTypeFactor.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Unique database identifier.
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java
index c54e7745fe..3bdb448691 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java
@@ -1,9 +1,7 @@
package lcsb.mapviewer.model.map.kinetics;
import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.EnumComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.*;
public class SbmlUnitTypeFactorComparator extends Comparator<SbmlUnitTypeFactor> {
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 c0dec6dc38..e20ad8a3d0 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
@@ -2,18 +2,18 @@ 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
+ * 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;
-
+ /**
+ *
+ */
+ 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 0c16a03410..c74488a69d 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
@@ -1,12 +1,9 @@
package lcsb.mapviewer.model.map.layout;
-import java.awt.Color;
+import java.awt.*;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
+import java.util.*;
import java.util.List;
-import java.util.Set;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/DataOverlayImageLayer.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/DataOverlayImageLayer.java
index cbba9f6cac..dd06b35e1d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/DataOverlayImageLayer.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/DataOverlayImageLayer.java
@@ -3,14 +3,10 @@ package lcsb.mapviewer.model.map.layout;
import java.io.Serializable;
import java.util.Comparator;
-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.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -24,11 +20,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
*/
@Entity
public class DataOverlayImageLayer implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
public static final Comparator<? super DataOverlayImageLayer> ID_COMPARATOR = new Comparator<DataOverlayImageLayer>() {
@Override
@@ -36,7 +27,10 @@ public class DataOverlayImageLayer implements Serializable {
return o1.getId() - o2.getId();
}
};
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
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 d2142f1c26..1b0db4fd86 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
@@ -1,14 +1,11 @@
package lcsb.mapviewer.model.map.layout;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
/**
* Class describing single gene variation.
@@ -18,17 +15,15 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
public class GeneVariation implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(GeneVariation.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Variation position in the genome.
*/
@@ -115,6 +110,16 @@ public class GeneVariation implements Serializable {
this.position = position;
}
+ /**
+ * Sets {@link #position}.
+ *
+ * @param position
+ * new position value
+ */
+ public void setPosition(int position) {
+ this.position = (long) position;
+ }
+
/**
* @return the originalDna
* @see #originalDna
@@ -185,7 +190,7 @@ public class GeneVariation implements Serializable {
/**
* Creates copy of the object.
- *
+ *
* @return copy of the object
*/
public GeneVariation copy() {
@@ -213,16 +218,6 @@ public class GeneVariation implements Serializable {
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
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 ead689d83e..192ae2684a 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
index af80343e57..54a13b49d3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
@@ -1,24 +1,12 @@
package lcsb.mapviewer.model.map.layout;
import java.io.Serializable;
-import java.util.Comparator;
-import java.util.HashSet;
-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.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-
-import org.apache.logging.log4j.*;
+import java.util.*;
+
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -35,11 +23,6 @@ import lcsb.mapviewer.model.user.User;
*/
@Entity
public class Layout implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
public static final Comparator<Layout> ID_COMPARATOR = new Comparator<Layout>() {
@Override
@@ -47,7 +30,6 @@ public class Layout implements Serializable {
return o1.getId() - o2.getId();
}
};
-
public static final Comparator<? super Layout> ORDER_COMPARATOR = new Comparator<Layout>() {
@Override
@@ -55,7 +37,10 @@ public class Layout implements Serializable {
return o1.getOrderIndex() - o2.getOrderIndex();
}
};
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
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 2f1a42efcd..d43eacbd2e 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
@@ -38,17 +38,9 @@ public enum LayoutStatus {
*/
private String commonName;
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-
/**
* Default constructor.
- *
+ *
* @param commonName
* {@link #commonName}
*/
@@ -56,4 +48,12 @@ public enum LayoutStatus {
this.commonName = commonName;
}
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return 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 ea3a0fbeae..bd99b2eee5 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
@@ -4,16 +4,7 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-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.*;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
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 c69adf638d..9f220014b5 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
@@ -2,12 +2,7 @@ package lcsb.mapviewer.model.map.layout;
import java.io.Serializable;
-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.*;
/**
* This object defines information about mapping genes to gene. This data is
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java
index 7aba408a26..181ebd848f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java
@@ -2,16 +2,10 @@ package lcsb.mapviewer.model.map.layout.graphics;
import java.io.Serializable;
-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.OneToOne;
-
-import org.apache.logging.log4j.*;
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -69,7 +63,8 @@ public class Glyph implements Serializable {
/**
* Constructor that creates copy of the element.
*
- * @param original element to be copied
+ * @param original
+ * element to be copied
*/
public Glyph(Glyph original) {
// we should reference to the same file
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 0574b9248b..e49a892911 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
@@ -1,24 +1,12 @@
package lcsb.mapviewer.model.map.layout.graphics;
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.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.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderColumn;
-
-import org.apache.logging.log4j.*;
+import java.util.*;
+
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -273,6 +261,17 @@ public class Layer implements Serializable {
this.locked = locked;
}
+ /**
+ * Sets locked param from the text input.
+ *
+ * @param param
+ * text representing true/false
+ * @see #locked
+ */
+ public void setLocked(String param) {
+ locked = param.equalsIgnoreCase("TRUE");
+ }
+
/**
* @return the visible
* @see #visible
@@ -290,6 +289,17 @@ public class Layer implements Serializable {
this.visible = visible;
}
+ /**
+ * Sets visible param from the text input.
+ *
+ * @param param
+ * text representing true/false
+ * @see #visible
+ */
+ public void setVisible(String param) {
+ visible = param.equalsIgnoreCase("TRUE");
+ }
+
/**
* @return the name
* @see #name
@@ -307,28 +317,6 @@ public class Layer implements Serializable {
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.
*
@@ -409,7 +397,8 @@ public class Layer implements Serializable {
}
public boolean isEmpty() {
- return this.getOvals().size() == 0 && this.getRectangles().size() == 0 && this.getTexts().size() == 0 && this.getLines().size()==0;
+ return this.getOvals().size() == 0 && this.getRectangles().size() == 0 && this.getTexts().size() == 0
+ && this.getLines().size() == 0;
}
public Set<Drawable> getDrawables() {
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 0c6ec1a1b2..fd61a1c447 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
@@ -1,12 +1,11 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.common.comparator.*;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
/**
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 c6378b539f..d9646a079a 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
@@ -1,14 +1,12 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.awt.Color;
+import java.awt.*;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import javax.persistence.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -93,65 +91,9 @@ public class LayerOval implements Serializable, Drawable {
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() {
@@ -204,6 +146,20 @@ public class LayerOval implements Serializable, Drawable {
return x;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param x
* the x to set
@@ -221,6 +177,20 @@ public class LayerOval implements Serializable, Drawable {
return y;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param y
* the y to set
@@ -238,6 +208,20 @@ public class LayerOval implements Serializable, Drawable {
return width;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param width
* the width to set
@@ -255,6 +239,20 @@ public class LayerOval implements Serializable, Drawable {
return height;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param height
* the height to set
@@ -275,13 +273,13 @@ public class LayerOval implements Serializable, Drawable {
}
@Override
- public double getSize() {
- return width * height;
+ public String getElementId() {
+ return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
}
@Override
- public String getElementId() {
- return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
+ public double getSize() {
+ return width * 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 28e0d8ca50..27d61e137c 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
@@ -2,9 +2,7 @@ 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.IntegerComparator;
+import lcsb.mapviewer.common.comparator.*;
/**
* Comparator of {@link LayerOval} class.
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 64c003fc34..32f3a36ed2 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
@@ -1,14 +1,12 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.awt.Color;
+import java.awt.*;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import javax.persistence.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -93,65 +91,9 @@ public class LayerRect implements Serializable, Drawable {
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() {
@@ -187,6 +129,20 @@ public class LayerRect implements Serializable, Drawable {
return x;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param x
* the x to set
@@ -204,6 +160,20 @@ public class LayerRect implements Serializable, Drawable {
return y;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param y
* the y to set
@@ -221,6 +191,20 @@ public class LayerRect implements Serializable, Drawable {
return width;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param width
* the width to set
@@ -238,6 +222,20 @@ public class LayerRect implements Serializable, Drawable {
return height;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param height
* the height to set
@@ -257,14 +255,14 @@ public class LayerRect implements Serializable, Drawable {
this.z = z;
}
- @Override
- public double getSize() {
- return width * height;
- }
-
@Override
public String getElementId() {
return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
}
-
+
+ @Override
+ public double getSize() {
+ return width * 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 90c3453f38..7ec13f41a9 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
@@ -2,9 +2,7 @@ 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.IntegerComparator;
+import lcsb.mapviewer.common.comparator.*;
/**
* Compparator of {@link LayerRect} class.
@@ -68,7 +66,6 @@ public class LayerRectComparator extends Comparator<LayerRect> {
return integerComparator.compare(arg0.getZ(), arg1.getZ());
}
-
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 72e9575eba..fc37eeeee9 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
@@ -1,17 +1,13 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.io.Serializable;
-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.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -143,80 +139,9 @@ public class LayerText implements Serializable, Drawable {
}
}
- /**
- * 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() {
@@ -252,6 +177,20 @@ public class LayerText implements Serializable, Drawable {
return x;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param x
* the x to set
@@ -269,6 +208,20 @@ public class LayerText implements Serializable, Drawable {
return y;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param y
* the y to set
@@ -286,6 +239,20 @@ public class LayerText implements Serializable, Drawable {
return width;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param width
* the width to set
@@ -303,6 +270,20 @@ public class LayerText implements Serializable, Drawable {
return height;
}
+ /**
+ * 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);
+ }
+ }
+
/**
* @param height
* the height to set
@@ -337,6 +318,21 @@ public class LayerText implements Serializable, Drawable {
return fontSize;
}
+ /**
+ * 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);
+ }
+
+ }
+
/**
* @param fontSize
* the fontSize to set
@@ -379,13 +375,13 @@ public class LayerText implements Serializable, Drawable {
}
@Override
- public double getSize() {
- return width * height;
+ public String getElementId() {
+ return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
}
@Override
- public String getElementId() {
- return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
+ public double getSize() {
+ return width * height;
}
public Glyph getGlyph() {
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 385f5679fa..e656f63c47 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
@@ -2,10 +2,7 @@ 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.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.comparator.*;
/**
* Comparator of {@link LayerText} class.
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 97326a877f..4002611446 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
@@ -3,4 +3,3 @@
* 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 2d03a51ab7..94a5b8a726 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
@@ -3,4 +3,3 @@
* of the map.
*/
package lcsb.mapviewer.model.map.layout;
-
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Author.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Author.java
index 54f5052ba6..9f0372bbb6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Author.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Author.java
@@ -2,13 +2,11 @@ package lcsb.mapviewer.model.map.model;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Class representing author object.
@@ -20,17 +18,15 @@ import org.apache.logging.log4j.*;
@XmlRootElement
public class Author implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(Author.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
/**
* Unique database identifier.
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/AuthorComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/AuthorComparator.java
index 5ea4038644..2c58a0c49f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/AuthorComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/AuthorComparator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.comparator.StringComparator;
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 2b9d98a088..455de1fe4a 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
@@ -2,9 +2,7 @@ package lcsb.mapviewer.model.map.model;
import java.io.Serializable;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Element;
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 c56a1ea9b2..567d385633 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 05bfbe7f99..2a46333d64 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -1,27 +1,16 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.*;
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.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.*;
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.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.model.map.species.*;
/**
* This interface defines functionality that the model container class should
@@ -64,46 +53,67 @@ public interface Model {
void setWidth(double width);
/**
- *
+ * Sets model width.
+ *
+ * @param text
+ * new model width
+ */
+ void setWidth(String text);
+
+ /**
+ *
+ * @param width
+ * new {@link ModelData#width}
+ */
+ void setWidth(int width);
+
+ /**
+ *
* @return model height
*/
double getHeight();
/**
* Sets model height.
- *
+ *
* @param height
* new model height
*/
void setHeight(double height);
- /**
- * Sets model width.
- *
- * @param text
- * new model width
- */
- void setWidth(String text);
-
/**
* Sets model height.
- *
+ *
* @param text
* new model height
*/
void setHeight(String text);
+ /**
+ *
+ * @param height
+ * new {@link ModelData#height}
+ */
+ void setHeight(int height);
+
/**
* Returns set of all elements.
- *
+ *
* @return set of all elements
*/
Set<Element> getElements();
+ /**
+ *
+ * @param elements
+ * new {@link ModelData#elements} collection
+ */
+ void setElements(Set<Element> elements);
+
/**
* Returns element with the given element identifier ({@link Element#elementId}
* ).
- *
+ *
* @param idElement
* element identifier
* @param <T>
@@ -114,7 +124,7 @@ public interface Model {
/**
* Adds reaction to the model.
- *
+ *
* @param reaction
* reaction to add
*/
@@ -122,7 +132,7 @@ public interface Model {
/**
* Returns set of reactions.
- *
+ *
* @return set of reaction in the model
*/
Set<Reaction> getReactions();
@@ -134,43 +144,43 @@ public interface Model {
/**
* Adds layer to the model.
- *
+ *
* @param layer
* object to add
*/
void addLayer(Layer layer);
/**
- *
+ *
* @return set of layers
*/
Set<Layer> getLayers();
/**
* Adds list of elements into model.
- *
+ *
* @param elements
* list of elements
*/
void addElements(Collection<? extends Element> elements);
+ /**
+ *
+ * @return short description of the model
+ */
+ String getNotes();
+
/**
* Sets new short description of the model.
- *
+ *
* @param notes
* new short description
*/
void setNotes(String notes);
- /**
- *
- * @return short description of the model
- */
- String getNotes();
-
/**
* Returns reaction with the id given in the parameter.
- *
+ *
* @param idReaction
* reaction identifier ({@link Reaction#idReaction})
* @return reaction with the id given in the parameter
@@ -179,7 +189,7 @@ public interface Model {
/**
* Adds set of layers to the model.
- *
+ *
* @param layers
* object to add
*/
@@ -187,7 +197,7 @@ public interface Model {
/**
* Adds {@link ElementGroup} to the model.
- *
+ *
* @param elementGroup
* object to add
*/
@@ -195,12 +205,18 @@ public interface Model {
/**
* Adds {@link BlockDiagram} to the model.
- *
+ *
* @param blockDiagram
* object to add
*/
void addBlockDiagream(BlockDiagram blockDiagram);
+ /**
+ * @return the idModel
+ * @see Model#idModel
+ */
+ String getIdModel();
+
/**
* @param idModel
* the idModel to set
@@ -209,10 +225,10 @@ public interface Model {
void setIdModel(String idModel);
/**
- * @return the idModel
- * @see Model#idModel
+ * @return the tileSize
+ * @see ModelData#tileSize
*/
- String getIdModel();
+ int getTileSize();
/**
* @param tileSize
@@ -222,10 +238,10 @@ public interface Model {
void setTileSize(int tileSize);
/**
- * @return the tileSize
- * @see ModelData#tileSize
+ * @return the zoomLevels
+ * @see ModelData#zoomLevels
*/
- int getTileSize();
+ int getZoomLevels();
/**
* @param zoomLevels
@@ -234,15 +250,9 @@ public interface Model {
*/
void setZoomLevels(int zoomLevels);
- /**
- * @return the zoomLevels
- * @see ModelData#zoomLevels
- */
- int getZoomLevels();
-
/**
* Removes reaction from model.
- *
+ *
* @param reaction
* reaction to remove
*/
@@ -250,7 +260,7 @@ public interface Model {
/**
* Removes {@link Element} from the model.
- *
+ *
* @param element
* element to remove
*/
@@ -258,28 +268,28 @@ public interface Model {
/**
* Returns collection of all {@link Species} excluding {@link Complex}.
- *
+ *
* @return collection of all {@link Species} excluding {@link Complex}.
*/
Collection<Species> getNotComplexSpeciesList();
/**
* Returns list of all {@link Species} in the model.
- *
+ *
* @return list of all {@link Species} in the model
*/
List<Species> getSpeciesList();
/**
* Returns collection of {@link Complex}.
- *
+ *
* @return collection of {@link Complex}
*/
Collection<Complex> getComplexList();
/**
* Adds reactions to model.
- *
+ *
* @param reactions2
* list of reaction to add
*/
@@ -287,7 +297,7 @@ public interface Model {
/**
* Returns list of elements annotated by the {@link MiriamData}.
- *
+ *
* @param miriamData
* {@link MiriamData}
* @return list of elements
@@ -296,30 +306,16 @@ public interface Model {
/**
* Returns list of elements with given name.
- *
+ *
* @param name
* name of the element
* @return list of elements with given name
*/
List<Element> getElementsByName(String name);
- /**
- *
- * @param height
- * new {@link ModelData#height}
- */
- void setHeight(int height);
-
- /**
- *
- * @param width
- * new {@link ModelData#width}
- */
- void setWidth(int width);
-
/**
* Returns {@link Element} for given database identifier.
- *
+ *
* @param dbId
* element database identifier ({@link Element#id})
* @return {@link Element} for a given id
@@ -328,7 +324,7 @@ public interface Model {
/**
* Returns {@link Reaction} for given database identifier.
- *
+ *
* @param dbId
* reaction database identifier ({@link Reaction#id})
* @return {@link Reaction} for a given id
@@ -337,25 +333,18 @@ public interface Model {
/**
* Returns sorted by size list of compartments.
- *
+ *
* @return list of compartment sorted by size
*/
List<Compartment> getSortedCompartments();
/**
* Returns list of elements sorted by the size.
- *
+ *
* @return list of elements sorted by the size
*/
List<Element> getElementsSortedBySize();
- /**
- *
- * @param project
- * new {@link ModelData#project}
- */
- void setProject(Project project);
-
/**
*
* @return {@link ModelData#project}
@@ -363,11 +352,11 @@ public interface Model {
Project getProject();
/**
- *
- * @param elements
- * new {@link ModelData#elements} collection
+ *
+ * @param project
+ * new {@link ModelData#project}
*/
- void setElements(Set<Element> elements);
+ void setProject(Project project);
/**
* @return the modelData
@@ -380,9 +369,17 @@ public interface Model {
*/
Integer getId();
+ /**
+ * Sets database identifier of the model.
+ *
+ * @param id
+ * database identifier
+ */
+ void setId(int id);
+
/**
* Adds submodel connection.
- *
+ *
* @param submodel
* submodel to add
*/
@@ -390,21 +387,21 @@ public interface Model {
/**
* Returns set of submodel connections.
- *
+ *
* @return collection of submodels
*/
Collection<ModelSubmodelConnection> getSubmodelConnections();
/**
* Returns name of the model.
- *
+ *
* @return name of the model
*/
String getName();
/**
* Sets name of the model.
- *
+ *
* @param name
* name of the model
*/
@@ -413,7 +410,7 @@ public interface Model {
/**
* Returns {@link Model submodel} by the {@link ModelData#id database
* identifier} given in the parameter.
- *
+ *
* @param idObject
* the {@link ModelData#id database identifier} that identifies
* submodel
@@ -425,14 +422,14 @@ public interface Model {
/**
* Returns set of connections that point to this model. Be very carefoul with
* using this function as the implementation forces lazy loading of the maps.
- *
+ *
* @return set of connections that point to this model
*/
Collection<SubmodelConnection> getParentModels();
/**
* Returns connection to a submodel identified by connection name.
- *
+ *
* @param name
* name of the connection
* @return connection to a submodel identified by connection name
@@ -441,7 +438,7 @@ public interface Model {
/**
* Returns connection to a submodel identified by connection identifier.
- *
+ *
* @param id
* id of the connection
* @return connection to a submodel identified by connection identifier
@@ -450,7 +447,7 @@ public interface Model {
/**
* Returns submodel identified by submodel identifier.
- *
+ *
* @param identifier
* identifier of the model
* @return submodel identified by identifier
@@ -459,7 +456,7 @@ public interface Model {
/**
* Returns collection of {@link Model submodels}.
- *
+ *
* @return collection of {@link Model submodels}
*/
Collection<Model> getSubmodels();
@@ -467,7 +464,7 @@ public interface Model {
/**
* Returns {@link Model submodel} identified by the {@link ModelData#name model
* name}. It returns this 'parent' object when the names matches.
- *
+ *
* @param name
* name of the submodel that should be returned
* @return {@link Model submodel} identified by the {@link ModelData#name model
@@ -475,14 +472,6 @@ public interface Model {
*/
Model getSubmodelByName(String name);
- /**
- * Sets database identifier of the model.
- *
- * @param id
- * database identifier
- */
- void setId(int id);
-
/**
* Return list of all {@link BioEntity} in the map. This includes all
* {@link Reaction reactions} and {@link Element elements}.
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 4fdff6e9ab..2055171f78 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
@@ -1,29 +1,16 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.CalendarComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.ListComparator;
-import lcsb.mapviewer.common.comparator.SetComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.comparator.*;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
-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.kinetics.*;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
import lcsb.mapviewer.model.map.reaction.Reaction;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index 0e07da18b9..aba2d8751c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -1,40 +1,20 @@
package lcsb.mapviewer.model.map.model;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-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.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderColumn;
-import javax.persistence.Transient;
+import java.util.*;
+
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlTransient;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.*;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
@@ -311,16 +291,7 @@ public class ModelData implements Serializable {
}
/**
- *
- * @param elements
- * new {@link #elements} collection
- */
- public void setElements(Set<Element> elements) {
- this.elements = elements;
- }
-
- /**
- *
+ *
* @return {@link #project}
*/
public Project getProject() {
@@ -328,7 +299,7 @@ public class ModelData implements Serializable {
}
/**
- *
+ *
* @param project
* new {@link #project}
*/
@@ -336,27 +307,9 @@ public class ModelData implements Serializable {
this.project = project;
}
- /**
- *
- * @param width
- * new {@link #width}
- */
- public void setWidth(int width) {
- setWidth(Double.valueOf(width));
- }
-
- /**
- *
- * @param height
- * new {@link #height}
- */
- public void setHeight(int height) {
- setHeight(Double.valueOf(height));
- }
-
/**
* Adds reactions to model.
- *
+ *
* @param reactions2
* list of reaction to add
*/
@@ -368,7 +321,7 @@ public class ModelData implements Serializable {
/**
* Adds collection of {@link Layer layers} to the model data.
- *
+ *
* @param layers
* objets to add
*/
@@ -380,7 +333,7 @@ public class ModelData implements Serializable {
/**
* Adds {@link ElementGroup} to the model data.
- *
+ *
* @param elementGroup
* object to add
*/
@@ -390,7 +343,7 @@ public class ModelData implements Serializable {
/**
* Adds {@link BlockDiagram} to the model data.
- *
+ *
* @param blockDiagram
* object to add
*/
@@ -400,7 +353,7 @@ public class ModelData implements Serializable {
/**
* Removes {@link Element} from the model.
- *
+ *
* @param element
* element to remove
*/
@@ -419,7 +372,7 @@ public class ModelData implements Serializable {
/**
* Removes reaction from model.
- *
+ *
* @param reaction
* reaction to remove
*/
@@ -512,6 +465,15 @@ public class ModelData implements Serializable {
return elements;
}
+ /**
+ *
+ * @param elements
+ * new {@link #elements} collection
+ */
+ public void setElements(Set<Element> elements) {
+ this.elements = elements;
+ }
+
/**
* @return the layers
* @see #layers
@@ -554,6 +516,15 @@ public class ModelData implements Serializable {
return width;
}
+ /**
+ *
+ * @param width
+ * new {@link #width}
+ */
+ public void setWidth(int width) {
+ setWidth(Double.valueOf(width));
+ }
+
/**
* @param width
* the width to set
@@ -571,6 +542,15 @@ public class ModelData implements Serializable {
return height;
}
+ /**
+ *
+ * @param height
+ * new {@link #height}
+ */
+ public void setHeight(int height) {
+ setHeight(Double.valueOf(height));
+ }
+
/**
* @param height
* the height to set
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 0d6a451085..8592b4abe5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -1,33 +1,20 @@
package lcsb.mapviewer.model.map.model;
-import java.util.ArrayList;
-import java.util.Calendar;
-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.logging.log4j.*;
+import java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.*;
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.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.model.map.species.*;
/**
* This class implements {@link Model} interface. It's is very simple
@@ -131,6 +118,16 @@ public class ModelFullIndexed implements Model {
modelData.setWidth(width);
}
+ @Override
+ public void setWidth(String text) {
+ modelData.setWidth(Double.parseDouble(text));
+ }
+
+ @Override
+ public void setWidth(int width) {
+ setWidth(Double.valueOf(width));
+ }
+
@Override
public double getHeight() {
return modelData.getHeight();
@@ -142,13 +139,13 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void setWidth(String text) {
- modelData.setWidth(Double.parseDouble(text));
+ public void setHeight(String text) {
+ modelData.setHeight(Double.parseDouble(text));
}
@Override
- public void setHeight(String text) {
- modelData.setHeight(Double.parseDouble(text));
+ public void setHeight(int height) {
+ setHeight(Double.valueOf(height));
}
@Override
@@ -156,6 +153,11 @@ public class ModelFullIndexed implements Model {
return modelData.getElements();
}
+ @Override
+ public void setElements(Set<Element> elements) {
+ this.modelData.setElements(elements);
+ }
+
@SuppressWarnings("unchecked")
@Override
public <T extends Element> T getElementByElementId(String elementId) {
@@ -205,6 +207,11 @@ public class ModelFullIndexed implements Model {
}
}
+ @Override
+ public String getNotes() {
+ return modelData.getNotes();
+ }
+
@Override
public void setNotes(String notes) {
if (notes != null && notes.contains("<html")) {
@@ -214,111 +221,100 @@ public class ModelFullIndexed implements Model {
}
@Override
- public String getNotes() {
- return modelData.getNotes();
+ public Reaction getReactionByReactionId(String idReaction) {
+ return reactionByReactionId.get(idReaction);
}
@Override
- public void setElements(Set<Element> elements) {
- this.modelData.setElements(elements);
+ public void addLayers(Collection<Layer> layers) {
+ for (Layer layer : layers) {
+ addLayer(layer);
+ }
}
@Override
- public Reaction getReactionByReactionId(String idReaction) {
- return reactionByReactionId.get(idReaction);
+ public void addElementGroup(ElementGroup elementGroup) {
+ modelData.addElementGroup(elementGroup);
}
@Override
- public Project getProject() {
- return modelData.getProject();
+ public void addBlockDiagream(BlockDiagram blockDiagram) {
+ modelData.addBlockDiagream(blockDiagram);
}
@Override
- public void setProject(Project project) {
- modelData.setProject(project);
+ public String getIdModel() {
+ return modelData.getIdModel();
}
@Override
- public List<Element> getElementsSortedBySize() {
- List<Element> sortedElements = new ArrayList<>();
- sortedElements.addAll(getElements());
- Collections.sort(sortedElements, Element.SIZE_COMPARATOR);
- return sortedElements;
+ public void setIdModel(String idModel) {
+ this.modelData.setIdModel(idModel);
}
@Override
- public List<Compartment> getSortedCompartments() {
- List<Compartment> result = getCompartments();
- Collections.sort(result, Element.SIZE_COMPARATOR);
- return result;
+ public int getTileSize() {
+ return modelData.getTileSize();
}
@Override
- public Reaction getReactionByDbId(Integer dbId) {
- return reactionByDbId.get(dbId);
+ public void setTileSize(int tileSize) {
+ this.modelData.setTileSize(tileSize);
}
- @SuppressWarnings("unchecked")
@Override
- public <T extends Element> T getElementByDbId(Integer dbId) {
- return (T) elementByDbId.get(dbId);
+ public int getZoomLevels() {
+ return modelData.getZoomLevels();
}
@Override
- public void setWidth(int width) {
- setWidth(Double.valueOf(width));
+ public void setZoomLevels(int zoomLevels) {
+ this.modelData.setZoomLevels(zoomLevels);
}
@Override
- public void setHeight(int height) {
- setHeight(Double.valueOf(height));
+ public void removeReaction(Reaction reaction) {
+ modelData.removeReaction(reaction);
+ reactionByReactionId.remove(reaction.getIdReaction());
+ reactionByDbId.remove(reaction.getId());
}
@Override
- public Set<BioEntity> getElementsByAnnotation(MiriamData miriamData) {
- Set<BioEntity> result = new HashSet<>();
- for (Element element : getElements()) {
- for (MiriamData md : element.getMiriamData()) {
- if (md.equals(miriamData)) {
- result.add(element);
- }
- }
- }
+ public void removeElement(Element element) {
+ modelData.removeElement(element);
+ elementByElementId.remove(element.getElementId());
+ elementByDbId.remove(element.getId());
- for (Reaction element : getReactions()) {
- for (MiriamData md : element.getMiriamData()) {
- if (md.equals(miriamData)) {
- result.add(element);
- }
- }
+ if (element.getCompartment() != null) {
+ Compartment ca = element.getCompartment();
+ ca.removeElement(element);
}
- return result;
- }
-
- @Override
- public void addReactions(List<Reaction> reactions2) {
- for (Reaction reaction : reactions2) {
- addReaction(reaction);
+ if (element instanceof Species) {
+ Species al = (Species) element;
+ if (al.getComplex() != null) {
+ Complex ca = ((Species) element).getComplex();
+ ca.removeElement(al);
+ }
}
}
@Override
- public Collection<Complex> getComplexList() {
- List<Complex> result = new ArrayList<>();
+ public Collection<Species> getNotComplexSpeciesList() {
+ List<Species> result = new ArrayList<>();
for (Element element : modelData.getElements()) {
- if (element instanceof Complex) {
- result.add((Complex) element);
+ if (element instanceof Species && !(element instanceof Complex)) {
+ result.add((Species) element);
}
}
return result;
}
@Override
- public Collection<Species> getNotComplexSpeciesList() {
+ public List<Species> getSpeciesList() {
List<Species> result = new ArrayList<>();
for (Element element : modelData.getElements()) {
- if (element instanceof Species && !(element instanceof Complex)) {
+ if (element instanceof Species) {
result.add((Species) element);
}
}
@@ -326,77 +322,90 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addLayers(Collection<Layer> layers) {
- for (Layer layer : layers) {
- addLayer(layer);
+ public Collection<Complex> getComplexList() {
+ List<Complex> result = new ArrayList<>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Complex) {
+ result.add((Complex) element);
+ }
}
+ return result;
}
@Override
- public void addElementGroup(ElementGroup elementGroup) {
- modelData.addElementGroup(elementGroup);
- }
-
- @Override
- public void addBlockDiagream(BlockDiagram blockDiagram) {
- modelData.addBlockDiagream(blockDiagram);
+ public void addReactions(List<Reaction> reactions2) {
+ for (Reaction reaction : reactions2) {
+ addReaction(reaction);
+ }
}
@Override
- public void removeElement(Element element) {
- modelData.removeElement(element);
- elementByElementId.remove(element.getElementId());
- elementByDbId.remove(element.getId());
-
- if (element.getCompartment() != null) {
- Compartment ca = element.getCompartment();
- ca.removeElement(element);
+ public Set<BioEntity> getElementsByAnnotation(MiriamData miriamData) {
+ Set<BioEntity> result = new HashSet<>();
+ for (Element element : getElements()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (md.equals(miriamData)) {
+ result.add(element);
+ }
+ }
}
- if (element instanceof Species) {
- Species al = (Species) element;
- if (al.getComplex() != null) {
- Complex ca = ((Species) element).getComplex();
- ca.removeElement(al);
+ for (Reaction element : getReactions()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (md.equals(miriamData)) {
+ result.add(element);
+ }
}
}
+
+ return result;
}
@Override
- public void removeReaction(Reaction reaction) {
- modelData.removeReaction(reaction);
- reactionByReactionId.remove(reaction.getIdReaction());
- reactionByDbId.remove(reaction.getId());
+ public List<Element> getElementsByName(String name) {
+ List<Element> result = new ArrayList<>();
+ for (Element element : getElements()) {
+ if (element.getName().equalsIgnoreCase(name)) {
+ result.add(element);
+ }
+ }
+ return result;
}
+ @SuppressWarnings("unchecked")
@Override
- public int getZoomLevels() {
- return modelData.getZoomLevels();
+ public <T extends Element> T getElementByDbId(Integer dbId) {
+ return (T) elementByDbId.get(dbId);
}
@Override
- public void setZoomLevels(int zoomLevels) {
- this.modelData.setZoomLevels(zoomLevels);
+ public Reaction getReactionByDbId(Integer dbId) {
+ return reactionByDbId.get(dbId);
}
@Override
- public int getTileSize() {
- return modelData.getTileSize();
+ public List<Compartment> getSortedCompartments() {
+ List<Compartment> result = getCompartments();
+ Collections.sort(result, Element.SIZE_COMPARATOR);
+ return result;
}
@Override
- public void setTileSize(int tileSize) {
- this.modelData.setTileSize(tileSize);
+ public List<Element> getElementsSortedBySize() {
+ List<Element> sortedElements = new ArrayList<>();
+ sortedElements.addAll(getElements());
+ Collections.sort(sortedElements, Element.SIZE_COMPARATOR);
+ return sortedElements;
}
@Override
- public String getIdModel() {
- return modelData.getIdModel();
+ public Project getProject() {
+ return modelData.getProject();
}
@Override
- public void setIdModel(String idModel) {
- this.modelData.setIdModel(idModel);
+ public void setProject(Project project) {
+ modelData.setProject(project);
}
@Override
@@ -409,6 +418,11 @@ public class ModelFullIndexed implements Model {
return modelData.getId();
}
+ @Override
+ public void setId(int id) {
+ modelData.setId(id);
+ }
+
@Override
public void addSubmodelConnection(ModelSubmodelConnection submodel) {
modelData.addSubmodel(submodel);
@@ -508,11 +522,6 @@ public class ModelFullIndexed implements Model {
return null;
}
- @Override
- public void setId(int id) {
- modelData.setId(id);
- }
-
@Override
public List<BioEntity> getBioEntities() {
List<BioEntity> result = new ArrayList<>();
@@ -521,28 +530,6 @@ public class ModelFullIndexed implements Model {
return result;
}
- @Override
- public List<Element> getElementsByName(String name) {
- List<Element> result = new ArrayList<>();
- for (Element element : getElements()) {
- if (element.getName().equalsIgnoreCase(name)) {
- result.add(element);
- }
- }
- return result;
- }
-
- @Override
- public List<Species> getSpeciesList() {
- List<Species> result = new ArrayList<>();
- for (Element element : modelData.getElements()) {
- if (element instanceof Species) {
- result.add((Species) element);
- }
- }
- return result;
- }
-
@Override
public Double getDefaultCenterX() {
return modelData.getDefaultCenterX();
@@ -675,6 +662,18 @@ public class ModelFullIndexed implements Model {
}
}
+ @Override
+ public void addAuthor(Author author) {
+ modelData.addAuthor(author);
+ }
+
+ @Override
+ public void addAuthors(Collection<Author> authors) {
+ for (Author author : authors) {
+ addAuthor(author);
+ }
+ }
+
@Override
public List<Author> getAuthors() {
return modelData.getAuthors();
@@ -700,18 +699,6 @@ public class ModelFullIndexed implements Model {
return modelData.getModificationDates();
}
- @Override
- public void addAuthor(Author author) {
- modelData.addAuthor(author);
- }
-
- @Override
- public void addAuthors(Collection<Author> authors) {
- for (Author author : authors) {
- addAuthor(author);
- }
- }
-
@Override
public void addModificationDates(Collection<Calendar> modificationDates) {
for (Calendar calendar : modificationDates) {
@@ -723,7 +710,7 @@ public class ModelFullIndexed implements Model {
public Set<Drawable> getDrawables() {
Set<Drawable> result = new HashSet<>();
result.addAll(getBioEntities());
- for (Layer layer: getLayers()) {
+ for (Layer layer : getLayers()) {
result.addAll(layer.getDrawables());
}
return result;
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 2638ad9a5a..db9df4c50f 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
@@ -2,10 +2,7 @@ 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 javax.persistence.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -20,11 +17,6 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@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
@@ -32,7 +24,10 @@ public class ModelSubmodelConnection extends SubmodelConnection {
return o1.getId() - o2.getId();
}
};
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Super (parent) model.
*/
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 2d7849907c..0ee6af2da9 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 9cf64cd9ac..3db3ce897a 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
@@ -2,21 +2,10 @@ package lcsb.mapviewer.model.map.model;
import java.io.Serializable;
-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 org.apache.logging.log4j.*;
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This abstract class defines connection between models. It points to submodel
@@ -171,6 +160,17 @@ public abstract class SubmodelConnection implements Serializable {
submodel.getParentModels().add(this);
}
+ /**
+ * Sets submodel to which this connection points to.
+ *
+ * @param submodel
+ * submodel to set.
+ * @see #submodel
+ */
+ public void setSubmodel(Model submodel) {
+ setSubmodel(submodel.getModelData());
+ }
+
/**
* @return the id
* @see #id
@@ -188,17 +188,6 @@ public abstract class SubmodelConnection implements Serializable {
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.
*
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 947b83716e..155a588f5c 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 7647ab8578..ed55e999d6 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
@@ -2,4 +2,3 @@
* 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/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/package-info.java
index b5520bf31f..cf76bdb9d7 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 +1,5 @@
/**
- * Provides data structure for
- * {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} 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 902c25f151..33f7cc81cc 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
@@ -4,4 +4,3 @@
* 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 9edfb40959..6c9b5e8a94 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
@@ -2,19 +2,7 @@ package lcsb.mapviewer.model.map.reaction;
import java.io.Serializable;
-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 javax.persistence.*;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
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 97077d96c5..c1c14cd4dc 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 53856fec5d..fe85562262 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -17,51 +18,51 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("AND_OPERATOR_NODE")
public class AndOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(AndOperator.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * 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();
- }
+ /**
+ * Default constructor.
+ */
+ public AndOperator() {
+ super();
+ }
- @Override
- public String getOperatorText() {
- return "&";
- }
+ @Override
+ public String getOperatorText() {
+ return "&";
+ }
- @Override
- public String getSBGNOperatorText() {
- return "AND";
- }
+ @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());
- }
- }
+ @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 7859ae764e..3886db32c4 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -19,46 +20,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("ASSOCIATION_OPERATOR_NODE")
public class AssociationOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(AssociationOperator.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * 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();
- }
+ /**
+ * Default constructor.
+ */
+ public AssociationOperator() {
+ super();
+ }
- @Override
- public String getOperatorText() {
- return "&";
- }
+ @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());
- }
- }
+ @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 462044be1d..2c6fe8678f 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -18,46 +19,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("DISSOCIATION_OPERATOR_NODE")
public class DissociationOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 5527d7a4e2..33999b74e5 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
@@ -18,47 +18,47 @@ import lcsb.mapviewer.model.map.species.Species;
@Entity
@DiscriminatorValue("MODIFIER_NODE")
public class Modifier extends ReactionNode {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- protected Modifier() {
- super();
- }
+ /**
+ * 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 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);
- }
+ /**
+ * 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());
- }
- }
+ @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 13a7f475f4..94c85733b3 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -17,46 +18,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@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 = LogManager.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());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 ce0d9e1412..edb31556a1 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
@@ -1,16 +1,11 @@
package lcsb.mapviewer.model.map.reaction;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
+import javax.persistence.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
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 2acb49363b..2a82eab580 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -24,7 +25,7 @@ public class NodeOperatorComparator extends Comparator<NodeOperator> {
* Epsilon value used for comparison of doubles.
*/
private double epsilon;
-
+
private boolean ignoreLayout;
/**
@@ -43,10 +44,6 @@ public class NodeOperatorComparator extends Comparator<NodeOperator> {
this(epsilon, false);
}
- protected Comparator<?> getParentComparator() {
- return new AbstractNodeComparator(epsilon, ignoreLayout);
- }
-
/**
* Default constructor.
*/
@@ -54,6 +51,10 @@ public class NodeOperatorComparator extends Comparator<NodeOperator> {
this(Configuration.EPSILON);
}
+ protected Comparator<?> getParentComparator() {
+ return new AbstractNodeComparator(epsilon, ignoreLayout);
+ }
+
@Override
protected int internalCompare(NodeOperator arg0, NodeOperator arg1) {
AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon, ignoreLayout);
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 21613a239b..ff4f1b4158 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -18,51 +19,51 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("OR_OPERATOR_NODE")
public class OrOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(OrOperator.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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);
- }
+ /**
+ * 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();
- }
+ /**
+ * Default constructor.
+ */
+ public OrOperator() {
+ super();
+ }
- @Override
- public String getOperatorText() {
- return "|";
- }
-
- @Override
- public String getSBGNOperatorText() {
- return "OR";
- }
+ @Override
+ public String getOperatorText() {
+ return "|";
+ }
- @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());
- }
- }
+ @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 110dcddb57..9c98d7a92f 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
@@ -18,51 +18,51 @@ import lcsb.mapviewer.model.map.species.Species;
@DiscriminatorValue("PRODUCT_NODE")
public class Product extends ReactionNode {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- public Product() {
- super();
- }
+ /**
+ * 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(Element element) {
- super(element);
- if (element==null) {
- throw new InvalidArgumentException("Element cannot be null");
- }
- }
+ /**
+ * 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(Element element) {
+ super(element);
+ if (element == null) {
+ throw new InvalidArgumentException("Element cannot be null");
+ }
+ }
- /**
- * Constructor that initialize the product with data from parameter.
- *
- * @param original
- * original product used for data initalization
- */
- protected Product(Product original) {
- super(original);
- }
+ /**
+ * 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());
- }
- }
+ @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 aadfb454e2..b9180904ef 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
@@ -18,50 +18,50 @@ import lcsb.mapviewer.model.map.species.Species;
@DiscriminatorValue("REACTANT_NODE")
public class Reactant extends ReactionNode {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- */
- public Reactant() {
- super();
- }
+ /**
+ * 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(Element element) {
- super(element);
- if (element==null) {
- throw new InvalidArgumentException("Element cannot be null");
- }
- }
+ /**
+ * 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(Element element) {
+ super(element);
+ if (element == null) {
+ throw new InvalidArgumentException("Element cannot be null");
+ }
+ }
- /**
- * Constructor that initialize the reactant with data from parameter.
- *
- * @param original
- * original reactant used for data initalization
- */
- public Reactant(Reactant original) {
- super(original);
- }
+ /**
+ * 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());
- }
- }
+ @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 7288924b23..64a886593f 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
@@ -2,34 +2,9 @@ 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.OrderColumn;
+import java.util.*;
+
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlTransient;
import org.apache.logging.log4j.LogManager;
@@ -45,9 +20,7 @@ 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.TwoProductReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -79,11 +52,6 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
@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.
@@ -94,7 +62,10 @@ public class Reaction implements BioEntity {
return reaction1.getIdReaction().compareTo(reaction2.getIdReaction());
}
};
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@@ -443,28 +414,9 @@ public class Reaction implements BioEntity {
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() {
@@ -479,28 +431,34 @@ public class Reaction implements BioEntity {
/**
* Removes modifier.
- *
+ *
* @param modifier
* modifier to remove
*/
public void removeModifier(Modifier modifier) {
nodes.remove(modifier);
+ } @Override
+ public String getVisibilityLevel() {
+ return visibilityLevel;
}
/**
* Removes {@link AbstractNode}.
- *
+ *
* @param node
* node to remove
*/
public void removeNode(AbstractNode node) {
nodes.remove(node);
+ } @Override
+ public void setVisibilityLevel(String visibilityLevel) {
+ this.visibilityLevel = visibilityLevel;
}
/**
* 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
*/
@@ -510,7 +468,7 @@ public class Reaction implements BioEntity {
/**
* 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,
@@ -525,22 +483,9 @@ public class Reaction implements BioEntity {
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() {
@@ -553,23 +498,6 @@ public class Reaction implements BioEntity {
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
@@ -587,27 +515,23 @@ public class Reaction implements BioEntity {
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();
+ } /**
+ * 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());
+ }
}
/**
@@ -619,20 +543,6 @@ public class Reaction implements BioEntity {
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
@@ -662,23 +572,6 @@ public class Reaction implements BioEntity {
}
}
- /**
- * @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)) {
@@ -689,20 +582,19 @@ public class Reaction implements BioEntity {
}
}
- /**
- * Sets model where the reaction is located.
- *
- * @param model2
- * model where the reaction is located
- */
- public void setModel(Model model2) {
- this.model = model2.getModelData();
+ @Override
+ public String getName() {
+ return name;
}
- @XmlTransient
@Override
- public Model getModel() {
- return model.getModel();
+ public String getNotes() {
+ return notes;
+ }
+
+ @Override
+ public void setNotes(String notes) {
+ this.notes = notes;
}
@Override
@@ -715,6 +607,23 @@ public class Reaction implements BioEntity {
this.symbol = symbol;
}
+ /**
+ * @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;
+ }
+
@Override
public String getAbbreviation() {
return abbreviation;
@@ -725,14 +634,68 @@ public class Reaction implements BioEntity {
this.abbreviation = abbreviation;
}
- @Override
- public String getFormula() {
- return formula;
+ /**
+ * @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;
+ }
+
+ /**
+ * Returns short string describing type of the reaction.
+ *
+ * @return short string describing type of the reaction
+ */
+ public String getStringType() {
+ return "Generic Reaction";
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public ModelData getModelData() {
+ return model;
+ } /**
+ * Sets model where the reaction is located.
+ *
+ * @param model2
+ * model where the reaction is located
+ */
+ public void setModel(Model model2) {
+ this.model = model2.getModelData();
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModelData(ModelData model) {
+ this.model = model;
+ } @XmlTransient
@Override
- public void setFormula(String formula) {
- this.formula = formula;
+ public Model getModel() {
+ return model.getModel();
}
/**
@@ -775,6 +738,9 @@ public class Reaction implements BioEntity {
*/
public Double getUpperBound() {
return upperBound;
+ } @Override
+ public String getFormula() {
+ return formula;
}
/**
@@ -784,6 +750,9 @@ public class Reaction implements BioEntity {
*/
public void setUpperBound(Double upperBound) {
this.upperBound = upperBound;
+ } @Override
+ public void setFormula(String formula) {
+ this.formula = formula;
}
/**
@@ -820,26 +789,9 @@ public class Reaction implements BioEntity {
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
*/
@@ -847,16 +799,6 @@ public class Reaction implements BioEntity {
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;
}
@@ -875,6 +817,11 @@ public class Reaction implements BioEntity {
this.z = z;
}
+ @Override
+ public String getElementId() {
+ return getIdReaction();
+ }
+
@Override
public double getSize() {
return 0;
@@ -891,5 +838,29 @@ public class Reaction implements BioEntity {
public void setLine(PolylineData line) {
this.line = line;
+ } @Override
+ public void setVisibilityLevel(Integer zoomLevelVisibility) {
+ if (zoomLevelVisibility == null) {
+ this.visibilityLevel = null;
+ } else {
+ this.visibilityLevel = zoomLevelVisibility + "";
+ }
+
}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
}
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 39d0259ebc..f6249b7feb 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
@@ -5,12 +5,7 @@ import org.apache.logging.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.SetComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
+import lcsb.mapviewer.common.comparator.*;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
@@ -32,7 +27,7 @@ public class ReactionComparator extends Comparator<Reaction> {
* Epsilon value used for comparison of doubles.
*/
private double epsilon;
-
+
private boolean ignoreLayout;
/**
@@ -46,7 +41,7 @@ public class ReactionComparator extends Comparator<Reaction> {
this.epsilon = epsilon;
this.ignoreLayout = ignoreLayout;
}
-
+
public ReactionComparator(double epsilon) {
this(epsilon, false);
}
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 85f99be6a6..f5ba4ab033 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -92,7 +90,7 @@ public abstract class ReactionNode extends AbstractNode {
public void setStoichiometry(Double stoichiometry) {
this.stoichiometry = stoichiometry;
}
-
+
@Override
public String toString() {
return new ElementUtils().getElementTag(this);
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 2e8323b300..72721cc921 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -47,10 +48,6 @@ public class ReactionNodeComparator extends Comparator<ReactionNode> {
this(epsilon, false);
}
- protected Comparator<?> getParentComparator() {
- return new AbstractNodeComparator(epsilon, ignoreLayout);
- }
-
/**
* Default constructor.
*/
@@ -58,6 +55,10 @@ public class ReactionNodeComparator extends Comparator<ReactionNode> {
this(Configuration.EPSILON);
}
+ protected Comparator<?> getParentComparator() {
+ return new AbstractNodeComparator(epsilon, ignoreLayout);
+ }
+
@Override
protected int internalCompare(ReactionNode arg0, ReactionNode arg1) {
AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon, ignoreLayout);
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 4affd22bac..ca7f2f0556 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -18,46 +19,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("SPLIT_OPERATOR_NODE")
public class SplitOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 b9850c2681..79c25e3e29 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -18,46 +19,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("TRUNCATION_OPERATOR_NODE")
public class TruncationOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 ae3f63f81b..39fbebeceb 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.reaction;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -18,46 +19,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@DiscriminatorValue("UNKNOWN_OPERATOR_NODE")
public class UnknownOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.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());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.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 bd371e82b9..518019086e 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
@@ -1,7 +1,7 @@
/**
* 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
+ * 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
@@ -9,4 +9,3 @@
*
*/
package lcsb.mapviewer.model.map.reaction;
-
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 806f1943bb..65a2aa74a6 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
@@ -3,4 +3,3 @@
* (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/AntisenseRna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 088eac1a13..ef7b4e8ebe 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -3,23 +3,14 @@ package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
+import javax.persistence.*;
import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.*;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
-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.SpeciesWithCodingRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationSite;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Entity representing antisense rna element on the map.
@@ -118,11 +109,6 @@ public class AntisenseRna extends Species
return regions;
}
- @Override
- public List<ModificationResidue> getModificationResidues() {
- return getRegions();
- }
-
/**
* @param regions
* the regions to set
@@ -132,6 +118,11 @@ public class AntisenseRna extends Species
this.regions = regions;
}
+ @Override
+ public List<ModificationResidue> getModificationResidues() {
+ return getRegions();
+ }
+
@Override
public String getStringType() {
return "Antisense RNA";
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 d50acfca12..6d4f0be4df 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.species;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 064397dd0e..cabe5500d3 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
+import javax.persistence.*;
/**
* Entity representing chemical element on the map.
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 b6c41465cf..960d18c77b 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -37,11 +38,6 @@ public class ChemicalComparator extends Comparator<Chemical> {
addSubClassComparator(new SimpleMoleculeComparator(epsilon));
}
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
/**
* Default constructor.
*/
@@ -49,6 +45,11 @@ public class ChemicalComparator extends Comparator<Chemical> {
this(Configuration.EPSILON);
}
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
@Override
protected int internalCompare(Chemical arg0, Chemical arg1) {
StringComparator stringComparator = new StringComparator();
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 673f30044b..4c3e4c4e70 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
@@ -1,16 +1,11 @@
package lcsb.mapviewer.model.map.species;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
+import javax.persistence.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
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 980548937b..07af665d13 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.species;
import java.util.HashMap;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -39,11 +40,6 @@ public class ComplexComparator extends Comparator<Complex> {
this.epsilon = epsilon;
}
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
/**
* Default constructor.
*/
@@ -51,6 +47,11 @@ public class ComplexComparator extends Comparator<Complex> {
this(Configuration.EPSILON);
}
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
@Override
protected int internalCompare(Complex arg0, Complex arg1) {
ElementComparator elementComparator = new ElementComparator(epsilon);
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 533decd1db..83535c256e 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -35,11 +36,6 @@ public class DegradedComparator extends Comparator<Degraded> {
this.epsilon = epsilon;
}
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
/**
* Default constructor.
*/
@@ -47,6 +43,11 @@ public class DegradedComparator extends Comparator<Degraded> {
this(Configuration.EPSILON);
}
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
@Override
protected int internalCompare(Degraded arg0, Degraded arg1) {
return 0;
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 3b6e6ae294..2f5ca405a8 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index b12449a841..631dc6a158 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -1,52 +1,27 @@
package lcsb.mapviewer.model.map.species;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashSet;
+import java.util.*;
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.OrderColumn;
+
+import javax.persistence.*;
import javax.xml.bind.annotation.XmlTransient;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.layout.graphics.Glyph;
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.*;
/**
* Abstract class representing objects in the model. Elements are objects that
@@ -62,21 +37,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
@DiscriminatorValue("GENERIC")
public abstract class Element implements BioEntity, Serializable, SbmlArgument {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default font size for element description.
- */
- private static final double DEFAULT_FONT_SIZE = 12.0;
-
- /**
- * Maximum length of the valid synonym name.
- */
- private static final int MAX_SYNONYM_LENGTH = 255;
-
/**
* Comparator of elements that takes into consideration size (width*height) of
* elements.
@@ -96,7 +56,18 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
}
};
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ /**
+ * Default font size for element description.
+ */
+ private static final double DEFAULT_FONT_SIZE = 12.0;
+ /**
+ * Maximum length of the valid synonym name.
+ */
+ private static final int MAX_SYNONYM_LENGTH = 255;
/**
* Default class logger.
*/
@@ -307,16 +278,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
}
- /**
- * Adds list of former symbol to the object.
- *
- * @param formerSymbols
- * list of former symbols to add
- */
- public void addFormerSymbols(List<String> formerSymbols) {
- this.formerSymbols.addAll(formerSymbols);
- }
-
/**
* Empty constructor required by hibernate.
*/
@@ -332,36 +293,13 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * Parse and set x coordinate from string.
- *
- * @param string
- * text representing x coordinate
- * @see x
- */
- public void setX(String string) {
- setX(Double.parseDouble(string));
- }
-
- /**
- * Parse and set y coordinate from string.
- *
- * @param string
- * text representing y coordinate
- * @see y
- */
- public void setY(String string) {
- this.y = Double.parseDouble(string);
- }
-
- /**
- * Parse and set font size.
+ * Adds list of former symbol to the object.
*
- * @param string
- * text representing font size
- * @see fontSize
+ * @param formerSymbols
+ * list of former symbols to add
*/
- public void setFontSize(String string) {
- this.fontSize = Double.parseDouble(string);
+ public void addFormerSymbols(List<String> formerSymbols) {
+ this.formerSymbols.addAll(formerSymbols);
}
/**
@@ -405,56 +343,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.height += increaseSize * 2;
}
- /**
- * Parse and set width.
- *
- * @param string
- * text representing width
- * @see width
- */
- public void setWidth(String string) {
- try {
- width = Double.parseDouble(string);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid width format: " + string, e);
- }
- }
-
- /**
- * Parse and set height.
- *
- * @param string
- * text representing height
- * @see height
- */
- public void setHeight(String string) {
- try {
- height = Double.parseDouble(string);
- } catch (Exception e) {
- throw new InvalidArgumentException("Invalid height format: " + string, e);
- }
- }
-
- /**
- *
- * @param width
- * the width value to set
- * @see #width
- */
- public void setWidth(int width) {
- this.width = (double) width;
- }
-
- /**
- *
- * @param height
- * the height value to set
- * @see #height
- */
- public void setHeight(int height) {
- this.height = (double) height;
- }
-
/**
* This method computes the distance between point and the element. It assumes
* that element is a rectangle.
@@ -506,13 +394,11 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
return new Rectangle2D.Double(x, y, width, height);
}
- /**
- * Returns size of the element in square units.
- *
- * @return size of the element
- */
- public double getSize() {
- return getWidth() * getHeight();
+ public void setBorder(Rectangle2D border) {
+ setX(border.getX());
+ setY(border.getY());
+ setWidth(border.getWidth());
+ setHeight(border.getHeight());
}
/**
@@ -540,38 +426,32 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * Makes a copy of the element.
- *
- * @return copy of the element
+ * @return the x
+ * @see #x
*/
- public abstract Element copy();
+ public Double getX() {
+ return x;
+ }
/**
+ * Parse and set x coordinate from string.
*
- * @param x
- * the x value to set
+ * @param string
+ * text representing x coordinate
* @see x
*/
- public void setX(int x) {
- setX((double) x);
+ public void setX(String string) {
+ setX(Double.parseDouble(string));
}
/**
*
- * @param y
- * the y value to set
- * @see y
- */
- public void setY(int y) {
- setY((double) y);
- }
-
- /**
- * @return the x
- * @see #x
+ * @param x
+ * the x value to set
+ * @see x
*/
- public Double getX() {
- return x;
+ public void setX(int x) {
+ setX((double) x);
}
/**
@@ -591,6 +471,27 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
return y;
}
+ /**
+ * Parse and set y coordinate from string.
+ *
+ * @param string
+ * text representing y coordinate
+ * @see y
+ */
+ public void setY(String string) {
+ this.y = Double.parseDouble(string);
+ }
+
+ /**
+ *
+ * @param y
+ * the y value to set
+ * @see y
+ */
+ public void setY(int y) {
+ setY((double) y);
+ }
+
/**
* @param y
* the y to set
@@ -598,7 +499,12 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public void setY(Double y) {
this.y = y;
- }
+ } /**
+ * Makes a copy of the element.
+ *
+ * @return copy of the element
+ */
+ public abstract Element copy();
/**
* @return the width
@@ -608,6 +514,31 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
return width;
}
+ /**
+ * Parse and set width.
+ *
+ * @param string
+ * text representing width
+ * @see width
+ */
+ public void setWidth(String string) {
+ try {
+ width = Double.parseDouble(string);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid width format: " + string, e);
+ }
+ }
+
+ /**
+ *
+ * @param width
+ * the width value to set
+ * @see #width
+ */
+ public void setWidth(int width) {
+ this.width = (double) width;
+ }
+
/**
* @param width
* the width to set
@@ -625,6 +556,31 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
return height;
}
+ /**
+ * Parse and set height.
+ *
+ * @param string
+ * text representing height
+ * @see height
+ */
+ public void setHeight(String string) {
+ try {
+ height = Double.parseDouble(string);
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Invalid height format: " + string, e);
+ }
+ }
+
+ /**
+ *
+ * @param height
+ * the height value to set
+ * @see #height
+ */
+ public void setHeight(int height) {
+ this.height = (double) height;
+ }
+
/**
* @param height
* the height to set
@@ -643,45 +599,32 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param fontSize
- * the fontSize to set
- * @see #fontSize
+ * Parse and set font size.
+ *
+ * @param string
+ * text representing font size
+ * @see fontSize
*/
- public void setFontSize(Double fontSize) {
- this.fontSize = fontSize;
- }
-
- @Override
- public String getElementId() {
- return elementId;
+ public void setFontSize(String string) {
+ this.fontSize = Double.parseDouble(string);
}
/**
- * @param elementId
- * the elementId to set
- * @see #elementId
+ * @param fontSize
+ * the fontSize to set
+ * @see #fontSize
*/
- public void setElementId(String elementId) {
- this.elementId = elementId;
- }
-
- @Override
- public String getVisibilityLevel() {
- return visibilityLevel;
- }
-
- @Override
- public void setVisibilityLevel(String visibilityLevel) {
- this.visibilityLevel = visibilityLevel;
+ public void setFontSize(Double fontSize) {
+ this.fontSize = fontSize;
}
- @Override
- public void setVisibilityLevel(Integer visibilityLevel) {
- if (visibilityLevel == null) {
- this.visibilityLevel = null;
- } else {
- this.visibilityLevel = visibilityLevel + "";
- }
+ /**
+ * @param fontSize
+ * the fontSize to set
+ * @see #fontSize
+ */
+ public void setFontSize(int fontSize) {
+ setFontSize((double) fontSize);
}
/**
@@ -707,6 +650,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public Compartment getCompartment() {
return compartment;
+ } @Override
+ public String getVisibilityLevel() {
+ return visibilityLevel;
}
/**
@@ -721,23 +667,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
formerCompartment.removeElement(this);
}
this.compartment = compartment;
- }
-
- /**
- * @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 void setVisibilityLevel(String visibilityLevel) {
+ this.visibilityLevel = visibilityLevel;
}
/**
@@ -746,6 +678,13 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public Color getColor() {
return color;
+ } @Override
+ public void setVisibilityLevel(Integer visibilityLevel) {
+ if (visibilityLevel == null) {
+ this.visibilityLevel = null;
+ } else {
+ this.visibilityLevel = visibilityLevel + "";
+ }
}
/**
@@ -774,19 +713,12 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.transparencyLevel = transparencyLevel;
}
- @XmlTransient
- @Override
- public Model getModel() {
- return model.getModel();
- }
-
/**
- * @param model
- * the model to set
- * @see #model
+ * @return the searchIndexes
+ * @see #searchIndexes
*/
- public void setModel(Model model) {
- this.model = model.getModelData();
+ public List<SearchIndex> getSearchIndexes() {
+ return searchIndexes;
}
/**
@@ -802,14 +734,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.searchIndexes.addAll(searchIndexes);
}
- /**
- * @return the searchIndexes
- * @see #searchIndexes
- */
- public List<SearchIndex> getSearchIndexes() {
- return searchIndexes;
- }
-
/**
* @return the submodel
* @see #submodel
@@ -830,15 +754,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
}
- /**
- * @param fontSize
- * the fontSize to set
- * @see #fontSize
- */
- public void setFontSize(int fontSize) {
- setFontSize((double) fontSize);
- }
-
/**
* Checks if element contains a {@link LayerText}.
*
@@ -863,23 +778,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
searchIndexes.add(searchIndex);
}
- /**
- * @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
@@ -895,40 +793,68 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public void setFullName(String fullName) {
this.fullName = fullName;
+ } @XmlTransient
+ @Override
+ public Model getModel() {
+ return model.getModel();
}
/**
- * @return the abbreviation
- * @see #abbreviation
+ * @return the formerSymbols
+ * @see #formerSymbols
*/
- public String getAbbreviation() {
- return abbreviation;
+ public List<String> getFormerSymbols() {
+ return formerSymbols;
+ } /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModel(Model model) {
+ this.model = model.getModelData();
}
/**
- * @param abbreviation
- * the abbreviation to set
- * @see #abbreviation
+ * @param formerSymbols
+ * the formerSymbols to set
+ * @see #formerSymbols
*/
- public void setAbbreviation(String abbreviation) {
- this.abbreviation = abbreviation;
+ public void setFormerSymbols(List<String> formerSymbols) {
+ this.formerSymbols = formerSymbols;
}
/**
- * @return the formula
- * @see #formula
+ * @return the miriamData
+ * @see #miriamData
*/
- public String getFormula() {
- return formula;
+ public Set<MiriamData> getMiriamData() {
+ return miriamData;
}
/**
- * @param formula
- * the formula to set
- * @see #formula
+ * @param miriamData
+ * the miriamData to set
+ * @see #miriamData
*/
- public void setFormula(String formula) {
- this.formula = formula;
+ public void setMiriamData(Set<MiriamData> miriamData) {
+ this.miriamData = miriamData;
+ }
+
+ @Override
+ public void addMiriamData(Collection<MiriamData> miriamData) {
+ for (MiriamData md : miriamData) {
+ addMiriamData(md);
+ }
+ }
+
+ @Override
+ public void addMiriamData(MiriamData md) {
+ if (this.miriamData.contains(md)) {
+ logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getElementId()
+ + " already exists. Ignoring...");
+ } else {
+ this.miriamData.add(md);
+ }
}
/**
@@ -948,12 +874,67 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
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;
+ }
+
+ @Override
+ public String getNotes() {
+ return notes;
+ }
+
+ @Override
+ public void setNotes(String notes) {
+ if (notes != null) {
+ if (notes.contains("</html>")) {
+ throw new InvalidArgumentException("Notes cannot contain html tags...");
+ }
+ }
+ this.notes = notes;
+ }
+
+ /**
+ * @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 synonyms
* @see #synonyms
*/
public List<String> getSynonyms() {
return synonyms;
+ } /**
+ * @return the formula
+ * @see #formula
+ */
+ public String getFormula() {
+ return formula;
}
/**
@@ -963,40 +944,30 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public void setSynonyms(List<String> synonyms) {
this.synonyms = synonyms;
- }
-
- /**
- * @return the formerSymbols
- * @see #formerSymbols
- */
- public List<String> getFormerSymbols() {
- return formerSymbols;
- }
-
- /**
- * @param formerSymbols
- * the formerSymbols to set
- * @see #formerSymbols
+ } /**
+ * @param formula
+ * the formula to set
+ * @see #formula
*/
- public void setFormerSymbols(List<String> formerSymbols) {
- this.formerSymbols = formerSymbols;
+ public void setFormula(String formula) {
+ this.formula = formula;
}
/**
- * @return the miriamData
- * @see #miriamData
+ * @return the abbreviation
+ * @see #abbreviation
*/
- public Set<MiriamData> getMiriamData() {
- return miriamData;
+ public String getAbbreviation() {
+ return abbreviation;
}
/**
- * @param miriamData
- * the miriamData to set
- * @see #miriamData
+ * @param abbreviation
+ * the abbreviation to set
+ * @see #abbreviation
*/
- public void setMiriamData(Set<MiriamData> miriamData) {
- this.miriamData = miriamData;
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
}
/**
@@ -1017,38 +988,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
- @Override
- public void addMiriamData(Collection<MiriamData> miriamData) {
- for (MiriamData md : miriamData) {
- addMiriamData(md);
- }
- }
-
- @Override
- public void addMiriamData(MiriamData md) {
- if (this.miriamData.contains(md)) {
- logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getElementId()
- + " already exists. Ignoring...");
- } else {
- this.miriamData.add(md);
- }
- }
-
- @Override
- public String getNotes() {
- return notes;
- }
-
- @Override
- public void setNotes(String notes) {
- if (notes != null) {
- if (notes.contains("</html>")) {
- throw new InvalidArgumentException("Notes cannot contain html tags...");
- }
- }
- this.notes = notes;
- }
-
/**
* Adds former symbol to the object.
*
@@ -1077,13 +1016,6 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.fontColor = fontColor;
}
- public void setBorder(Rectangle2D border) {
- setX(border.getX());
- setY(border.getY());
- setWidth(border.getWidth());
- setHeight(border.getHeight());
- }
-
@Override
public Integer getZ() {
return z;
@@ -1094,6 +1026,29 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.z = z;
}
+ @Override
+ public String getElementId() {
+ return elementId;
+ }
+
+ /**
+ * Returns size of the element in square units.
+ *
+ * @return size of the element
+ */
+ public double getSize() {
+ return getWidth() * getHeight();
+ }
+
+ /**
+ * @param elementId
+ * the elementId to set
+ * @see #elementId
+ */
+ public void setElementId(String elementId) {
+ this.elementId = elementId;
+ }
+
public Glyph getGlyph() {
return glyph;
}
@@ -1101,4 +1056,20 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
public void setGlyph(Glyph glyph) {
this.glyph = glyph;
}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
}
\ No newline at end of file
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 4fc14abe8a..6c3485ab98 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
@@ -1,15 +1,11 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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.IntegerComparator;
-import lcsb.mapviewer.common.comparator.SetComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
+import lcsb.mapviewer.common.comparator.*;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
@@ -90,7 +86,6 @@ public class ElementComparator extends Comparator<Element> {
return integerComparator.compare(arg0.getZ(), arg1.getZ());
}
-
if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
index 729c75d53b..61338acf7d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
@@ -3,26 +3,16 @@ package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
+import javax.persistence.*;
import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-import org.apache.logging.log4j.*;
-import org.hibernate.annotations.Cascade;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.hibernate.annotations.*;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
-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.RegulatoryRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithCodingRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationSite;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithRegulatoryRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithTranscriptionSite;
-import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Entity representing gene element on the map.
@@ -32,16 +22,15 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
*/
@Entity
@DiscriminatorValue("GENE")
-public class Gene extends Species implements SpeciesWithCodingRegion, SpeciesWithModificationSite, SpeciesWithRegulatoryRegion, SpeciesWithTranscriptionSite {
-
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(Gene.class);
+public class Gene extends Species implements SpeciesWithCodingRegion, SpeciesWithModificationSite,
+ SpeciesWithRegulatoryRegion, SpeciesWithTranscriptionSite {
/**
- *
+ *
*/
private static final long serialVersionUID = 1L;
-
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(Gene.class);
/**
* List of modifications for the Gene.
*/
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 566af4a352..f4de2b378e 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.species;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 d49c07d7b0..3977bc2314 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 9cd67ad455..362f1c5eeb 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 bdcc6c159a..944fb038ae 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 398feb5823..779da7f128 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
@@ -47,7 +48,6 @@ public class PhenotypeComparator extends Comparator<Phenotype> {
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 31d26cd609..81bec9f3e7 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
@@ -3,20 +3,13 @@ package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
+import javax.persistence.*;
import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.*;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.model.map.species.field.BindingRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.Residue;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithBindingRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithResidue;
+
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Entity representing protein element on the map.
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 67140df7bb..b2930d68d8 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.species;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 d00fc3f2bb..1639255c1c 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
index d34d431b1c..31d86122f0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
@@ -3,23 +3,14 @@ package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
+import javax.persistence.*;
import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.*;
import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
-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.SpeciesWithCodingRegion;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationSite;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Entity representing rna element on the map.
@@ -29,7 +20,8 @@ import lcsb.mapviewer.model.map.species.field.SpeciesWithProteinBindingDomain;
*/
@Entity
@DiscriminatorValue("RNA")
-public class Rna extends Species implements SpeciesWithCodingRegion, SpeciesWithProteinBindingDomain, SpeciesWithModificationSite {
+public class Rna extends Species
+ implements SpeciesWithCodingRegion, SpeciesWithProteinBindingDomain, SpeciesWithModificationSite {
/**
*
@@ -89,12 +81,12 @@ public class Rna extends Species implements SpeciesWithCodingRegion, SpeciesWith
public void addCodingRegion(CodingRegion codingRegion) {
this.addModificationResidue(codingRegion);
}
-
+
@Override
public void addProteinBindingDomain(ProteinBindingDomain codingRegion) {
this.addModificationResidue(codingRegion);
}
-
+
@Override
public void addModificationSite(ModificationSite codingRegion) {
this.addModificationResidue(codingRegion);
@@ -116,11 +108,6 @@ public class Rna extends Species implements SpeciesWithCodingRegion, SpeciesWith
public List<ModificationResidue> getRegions() {
return regions;
}
-
- @Override
- public List<ModificationResidue> getModificationResidues() {
- return getRegions();
- }
/**
* @param regions
@@ -131,6 +118,11 @@ public class Rna extends Species implements SpeciesWithCodingRegion, SpeciesWith
this.regions = regions;
}
+ @Override
+ public List<ModificationResidue> getModificationResidues() {
+ return getRegions();
+ }
+
@Override
public String getStringType() {
return "RNA";
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 7c98838f50..2576cc6517 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
@@ -3,7 +3,8 @@ package lcsb.mapviewer.model.map.species;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 8f812206d9..67b1a8c73c 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 819aafc076..22b065e41a 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
@@ -3,16 +3,10 @@ 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.logging.log4j.*;
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -405,15 +399,6 @@ public abstract class Species extends Element {
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
@@ -423,12 +408,12 @@ public abstract class Species extends Element {
}
/**
- * @param hypothetical
- * the hypothetical to set
- * @see #hypothetical
+ * @param uniprots
+ * set of uniprot records for this species
+ * @see #uniprots
*/
- public void setHypothetical(Boolean hypothetical) {
- this.hypothetical = hypothetical;
+ public void setUniprots(Set<UniprotRecord> uniprots) {
+ this.uniprots = uniprots;
}
/**
@@ -441,7 +426,7 @@ public abstract class Species extends Element {
/**
* Is species hypothetical or not.
- *
+ *
* @return <code>true</code> if species is hypothetical, <code>false</code>
* otherwise
*/
@@ -452,6 +437,15 @@ public abstract class Species extends Element {
return hypothetical;
}
+ /**
+ * @param hypothetical
+ * the hypothetical to set
+ * @see #hypothetical
+ */
+ public void setHypothetical(Boolean hypothetical) {
+ this.hypothetical = hypothetical;
+ }
+
public boolean isBoundaryCondition() {
if (boundaryCondition == null) {
return false;
@@ -478,14 +472,14 @@ public abstract class Species extends Element {
return constant;
}
- public SbmlUnitType getSubstanceUnits() {
- return substanceUnits;
- }
-
public void setConstant(Boolean constant) {
this.constant = constant;
}
+ public SbmlUnitType getSubstanceUnits() {
+ return substanceUnits;
+ }
+
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 fccb26a474..5aed73eaf2 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
@@ -5,11 +5,7 @@ import org.apache.logging.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;
+import lcsb.mapviewer.common.comparator.*;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
/**
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 b3c798ecb4..1b9be69249 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
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 bea3bf1427..1f56fbef15 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
index 2f693653e6..e924219f67 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
@@ -2,10 +2,7 @@ package lcsb.mapviewer.model.map.species.field;
import java.text.DecimalFormat;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
+import javax.persistence.*;
@Entity
@DiscriminatorValue("ABSTRACT_SITE_MODIFICATION")
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
index bef43a4b25..997f416da2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
@@ -5,7 +5,8 @@ import java.io.Serializable;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Protein;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
index 57368aa998..7d0565be2c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
@@ -5,13 +5,11 @@ import java.io.Serializable;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
/**
* This structure contains information about Coding Region for one of the
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
index c40bafa2e2..1741b30c70 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
@@ -3,21 +3,10 @@ package lcsb.mapviewer.model.map.species.field;
import java.awt.geom.Point2D;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-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.JoinColumn;
-import javax.persistence.ManyToOne;
-
-import org.apache.logging.log4j.*;
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Type;
import lcsb.mapviewer.common.exception.NotImplementedException;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
index 52b13b5865..ca28fe522d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
@@ -4,10 +4,7 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
/**
* This structure contains information about Modification Site for one of the
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
index 2aaa570b36..23e0415049 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
@@ -117,6 +117,22 @@ public enum ModificationState {
this.abbreviation = abbreviation;
}
+ /**
+ * Returns {@link ModificationState} identified by the full name.
+ *
+ * @param name
+ * full name of the state
+ * @return {@link ModificationState} identified by the full name
+ */
+ public static ModificationState getByName(String name) {
+ for (ModificationState state : values()) {
+ if (state.getFullName().equalsIgnoreCase(name)) {
+ return state;
+ }
+ }
+ return null;
+ }
+
/**
* @return the fullName
* @see #fullName
@@ -133,20 +149,4 @@ public enum ModificationState {
return abbreviation;
}
- /**
- * Returns {@link ModificationState} identified by the full name.
- *
- * @param name
- * full name of the state
- * @return {@link ModificationState} identified by the full name
- */
- public static ModificationState getByName(String name) {
- for (ModificationState state : values()) {
- if (state.getFullName().equalsIgnoreCase(name)) {
- return state;
- }
- }
- return null;
- }
-
}
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 22240b09b6..bbc560cb07 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
@@ -51,17 +51,9 @@ public enum PositionToCompartment {
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}
@@ -74,4 +66,12 @@ public enum PositionToCompartment {
}
return null;
}
+
+ /**
+ * @return the stringName
+ * @see #stringName
+ */
+ public String getStringName() {
+ return stringName;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
index cd1f1f3657..b9f14a7de7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
@@ -5,12 +5,11 @@ import java.io.Serializable;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
/**
* This structure contains information about Protein Binding Domain for one of
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
index b6fcc4ba3f..e7d769273c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
@@ -5,7 +5,8 @@ import java.io.Serializable;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Gene;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationSite.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationSite.java
index 2cc929dde2..eeb4446dc7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationSite.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationSite.java
@@ -8,6 +8,6 @@ public interface SpeciesWithModificationSite extends SpeciesWithModificationResi
* @param codingRegion
* {@link ModificationSite } to add
*/
- void addModificationSite (ModificationSite modificationSite );
+ void addModificationSite(ModificationSite modificationSite);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithResidue.java
index 46a1c305ee..61224fee90 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithResidue.java
@@ -1,8 +1,7 @@
package lcsb.mapviewer.model.map.species.field;
/**
- * Interface implemented by species that support {@link Residue}
- * modification.
+ * Interface implemented by species that support {@link Residue} modification.
*
* @author Piotr Gawron
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
index 6eaa87c618..2d37bb17eb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
@@ -4,13 +4,7 @@ import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
-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.*;
import lcsb.mapviewer.common.exception.NotImplementedException;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java
index bf7b7f3ab1..32dfa15609 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java
@@ -5,7 +5,8 @@ import java.io.Serializable;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Gene;
@@ -59,20 +60,9 @@ public class TranscriptionSite extends AbstractRegionModification implements Ser
this.active = original.getActive();
}
- @Override
- public void update(AbstractRegionModification mr) {
- TranscriptionSite original = (TranscriptionSite) mr;
- if (original.getDirection() != null) {
- this.direction = original.getDirection();
- }
- if (original.getActive() != null) {
- this.active = original.getActive();
- }
- }
-
/**
* Creates a copy of current object.
- *
+ *
* @return copy of the object
*/
public TranscriptionSite copy() {
@@ -104,4 +94,15 @@ public class TranscriptionSite extends AbstractRegionModification implements Ser
public String toString() {
return super.toString() + "," + getActive() + "," + getDirection();
}
+
+ @Override
+ public void update(AbstractRegionModification mr) {
+ TranscriptionSite original = (TranscriptionSite) mr;
+ if (original.getDirection() != null) {
+ this.direction = original.getDirection();
+ }
+ if (original.getActive() != null) {
+ this.active = original.getActive();
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
index b735554f7a..8e13690030 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
@@ -1,19 +1,9 @@
package lcsb.mapviewer.model.map.species.field;
import java.io.Serializable;
-import java.util.Collection;
-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.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
+import java.util.*;
+
+import javax.persistence.*;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -140,6 +130,14 @@ public class UniprotRecord implements Serializable {
this.uniprotId = uniprotId;
}
+ /**
+ * @return the species
+ * @see #species
+ */
+ public Species getSpecies() {
+ return species;
+ }
+
/**
* @param species
* species to which this uniprot record belongs
@@ -150,11 +148,11 @@ public class UniprotRecord implements Serializable {
}
/**
- * @return the species
- * @see #species
+ * @return the structures
+ * @see #structures
*/
- public Species getSpecies() {
- return species;
+ public Set<Structure> getStructures() {
+ return structures;
}
/**
@@ -166,14 +164,6 @@ public class UniprotRecord implements Serializable {
this.structures = structures;
}
- /**
- * @return the structures
- * @see #structures
- */
- public Set<Structure> getStructures() {
- return structures;
- }
-
public void addStructures(Collection<Structure> structures) {
this.structures.addAll(structures);
}
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 4769fddc83..cb5feef627 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
@@ -3,13 +3,7 @@ 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.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import javax.persistence.*;
/**
* This object describe single search event entry. It's used for gathering some
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 c1e9adffde..f67a1ed035 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
@@ -2,4 +2,3 @@
* 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 76cf68c54a..7034400d7d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/package-info.java
@@ -6,16 +6,15 @@
* 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>
+ * {@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).
+ * 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 9a7500d061..b94d12d594 100644
--- a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
@@ -1,18 +1,9 @@
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 java.util.*;
+
+import javax.persistence.*;
import lcsb.mapviewer.common.comparator.IntegerComparator;
@@ -25,11 +16,6 @@ import lcsb.mapviewer.common.comparator.IntegerComparator;
@Entity
public class Plugin implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
public static final Comparator<? super Plugin> ID_COMPARATOR = new Comparator<Plugin>() {
@Override
@@ -37,7 +23,10 @@ public class Plugin implements Serializable {
return new IntegerComparator().compare(o1.getId(), o2.getId());
}
};
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
/**
* Unique database identifier.
*/
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 057bf3f38a..dc3f631604 100644
--- a/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
@@ -2,13 +2,7 @@ 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.*;
import lcsb.mapviewer.model.user.User;
diff --git a/model/src/main/java/lcsb/mapviewer/model/security/Privilege.java b/model/src/main/java/lcsb/mapviewer/model/security/Privilege.java
index b9e0e3731d..34679a80f5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/security/Privilege.java
+++ b/model/src/main/java/lcsb/mapviewer/model/security/Privilege.java
@@ -34,11 +34,15 @@ public class Privilege implements Serializable {
}
@Override
- public String toString() {
+ public int hashCode() {
+ if (type == null) {
+ return 0;
+ }
+
if (isObjectPrivilege()) {
- return type.name() + ":" + objectId;
+ return Objects.hash(type, objectId);
} else {
- return type.name();
+ return type.hashCode();
}
}
@@ -54,15 +58,11 @@ public class Privilege implements Serializable {
}
@Override
- public int hashCode() {
- if (type == null) {
- return 0;
- }
-
+ public String toString() {
if (isObjectPrivilege()) {
- return Objects.hash(type, objectId);
+ return type.name() + ":" + objectId;
} else {
- return type.hashCode();
+ return type.name();
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index a20b2bd24d..5f0234b09d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -216,7 +216,8 @@ public enum ConfigurationElementType {
DEFAULT_WRITE_PROJECT("Default user privilege for: " + PrivilegeType.WRITE_PROJECT.getDescription(), "false",
ConfigurationElementEditType.BOOLEAN, false, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
- DEFAULT_CAN_CREATE_OVERLAYS("Default user privilege for: " + PrivilegeType.CAN_CREATE_OVERLAYS.getDescription(), "true",
+ DEFAULT_CAN_CREATE_OVERLAYS("Default user privilege for: " + PrivilegeType.CAN_CREATE_OVERLAYS.getDescription(),
+ "true",
ConfigurationElementEditType.BOOLEAN, false, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
SHOW_REACTION_TYPE("Show reaction type", "true", ConfigurationElementEditType.BOOLEAN, false,
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 2c5c863b00..dacbc2c443 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java
@@ -2,12 +2,7 @@ package lcsb.mapviewer.model.user;
import java.io.Serializable;
-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.*;
/**
* This class represents one configurable parameter of the system.
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 354c2d091e..981f594fb4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.user;
-import java.awt.Color;
+import java.awt.*;
import java.io.Serializable;
import java.util.*;
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 0be86fc4ef..566a10e604 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
@@ -1,21 +1,12 @@
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.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 org.apache.logging.log4j.*;
+import java.util.*;
+
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
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 a0bbe8bf31..49088f1daf 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java
@@ -4,13 +4,7 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.Entity;
-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.*;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
@@ -142,6 +136,16 @@ public class UserClassAnnotators implements Serializable {
this.className = className;
}
+ /**
+ * Sets {@link #className}.
+ *
+ * @param clazz
+ * new {@link #className} value
+ */
+ public void setClassName(Class<?> clazz) {
+ setClassName(clazz.getCanonicalName());
+ }
+
/**
* @return the annotators
* @see #annotators
@@ -167,16 +171,6 @@ public class UserClassAnnotators implements Serializable {
fixAnnotatorsOrder();
}
- /**
- * 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}.
*
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 65c9eea443..9d75f1d499 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java
@@ -1,24 +1,12 @@
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.OrderColumn;
-
-import org.apache.logging.log4j.*;
+import java.util.*;
+
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.MiriamType;
@@ -136,6 +124,16 @@ public class UserClassRequiredAnnotations implements Serializable {
this.className = className;
}
+ /**
+ * Sets {@link #className}.
+ *
+ * @param clazz
+ * new {@link #className} value
+ */
+ public void setClassName(Class<?> clazz) {
+ setClassName(clazz.getCanonicalName());
+ }
+
/**
* @return the id
* @see #id
@@ -153,16 +151,6 @@ public class UserClassRequiredAnnotations implements Serializable {
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}.
*
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 97907dd6aa..3dfd5eeb72 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java
@@ -1,22 +1,9 @@
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.OrderColumn;
+import java.util.*;
+
+import javax.persistence.*;
import lcsb.mapviewer.model.map.MiriamType;
@@ -132,6 +119,16 @@ public class UserClassValidAnnotations implements Serializable {
this.className = className;
}
+ /**
+ * Sets {@link #className} value.
+ *
+ * @param clazz
+ * new {@link #className} value
+ */
+ public void setClassName(Class<?> clazz) {
+ setClassName(clazz.getCanonicalName());
+ }
+
/**
* @return the id
* @see #id
@@ -149,16 +146,6 @@ public class UserClassValidAnnotations implements Serializable {
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}.
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java b/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java
index 4b1dffd79d..1d933adf9e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java
@@ -2,14 +2,7 @@ package lcsb.mapviewer.model.user;
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.JoinColumn;
-import javax.persistence.ManyToOne;
+import javax.persistence.*;
/**
* This class defines GUI preference for the {@link User}.
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorConfigParameter.java b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorConfigParameter.java
index cf798a17be..1b37d2435d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorConfigParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorConfigParameter.java
@@ -2,10 +2,7 @@ package lcsb.mapviewer.model.user.annotator;
import java.io.Serializable;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
+import javax.persistence.*;
import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorData.java b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorData.java
index ee31625762..7b07e43df1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorData.java
@@ -4,14 +4,7 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-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.OneToMany;
-import javax.persistence.OrderBy;
+import javax.persistence.*;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorInputParameter.java b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorInputParameter.java
index 4d21e4bf7e..68e4cd2613 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorInputParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorInputParameter.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.model.user.annotator;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
+import javax.persistence.*;
import lcsb.mapviewer.model.map.MiriamType;
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorOutputParameter.java b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorOutputParameter.java
index 1bfbaa5297..9ed5bd4f5f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorOutputParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorOutputParameter.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.model.user.annotator;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
+import javax.persistence.*;
import lcsb.mapviewer.model.map.MiriamType;
@@ -33,7 +30,7 @@ public class AnnotatorOutputParameter extends AnnotatorParameter {
*/
protected AnnotatorOutputParameter() {
}
-
+
public AnnotatorOutputParameter(BioEntityField field) {
this.field = field;
}
@@ -51,8 +48,8 @@ public class AnnotatorOutputParameter extends AnnotatorParameter {
}
@Override
- public String toString() {
- return "[" + field + "," + identifierType + "]";
+ public int hashCode() {
+ return this.toString().hashCode();
}
@Override
@@ -62,9 +59,9 @@ public class AnnotatorOutputParameter extends AnnotatorParameter {
}
return this.toString().equals(o.toString());
}
-
+
@Override
- public int hashCode() {
- return this.toString().hashCode();
+ public String toString() {
+ return "[" + field + "," + identifierType + "]";
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameter.java b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameter.java
index 431da35b7d..3e456cef74 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameter.java
@@ -2,16 +2,7 @@ package lcsb.mapviewer.model.user.annotator;
import java.io.Serializable;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-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.ManyToOne;
+import javax.persistence.*;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/annotator/BioEntityField.java b/model/src/main/java/lcsb/mapviewer/model/user/annotator/BioEntityField.java
index 117be90f93..40d9e06b01 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/annotator/BioEntityField.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/annotator/BioEntityField.java
@@ -31,7 +31,7 @@ public enum BioEntityField {
private BioEntityField(String fieldName) {
this.fieldName = fieldName;
}
-
+
public static String getFieldValueForBioEntity(BioEntity bioEntity, BioEntityField field) {
if (field.equals(ABBREVIATION)) {
return bioEntity.getAbbreviation();
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 d5dd86f858..18182990e2 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
@@ -2,4 +2,3 @@
* Contains structures used for modeling users, privileges, etc.
*/
package lcsb.mapviewer.model.user;
-
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 5d50a196b5..a3dbe51f35 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -1,12 +1,6 @@
package lcsb.mapviewer.modelutils.map;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -50,10 +44,28 @@ public final class ElementUtils {
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(ElementUtils.class);
+ /**
+ * @param elementClasses
+ * the elementClasses to set
+ * @see #elementClasses
+ */
+ protected static void setElementClasses(Map<String, Class<? extends Element>> elementClasses) {
+ ElementUtils.elementClasses = elementClasses;
+ }
+
+ /**
+ * @param reactionClasses
+ * the reactionClasses to set
+ * @see #reactionClasses
+ */
+ protected static void setReactionClasses(Map<String, Class<? extends Reaction>> reactionClasses) {
+ ElementUtils.reactionClasses = reactionClasses;
+ }
+
/**
* This method return tag that identifies {@link BioEntity}. This tag should be
* used in warning messages.
- *
+ *
* @param element
* tag for this element is created
* @return tag that identifies element
@@ -65,7 +77,7 @@ public final class ElementUtils {
/**
* This method return tag that identifies {@link BioEntity}. This tag should be
* used in warning messages.
- *
+ *
* @param element
* tag for this element is created
* @param annotator
@@ -90,7 +102,7 @@ public final class ElementUtils {
/**
* Returns {@link #annotatedObjectTree}.
- *
+ *
* @return {@link #annotatedObjectTree}
*/
public ClassTreeNode getAnnotatedElementClassTree() {
@@ -146,7 +158,7 @@ public final class ElementUtils {
/**
* Returns list of classes that extends {@link Element} class, but don't have
* children (leaves in the hierarchy tree).
- *
+ *
* @return list of classes that extends {@link Element} class, but don't have
* children (leaves in the hierarchy tree)
*/
@@ -209,7 +221,7 @@ public final class ElementUtils {
/**
* Returns a {@link Class} that extends {@link BioEntity} for a given name.
- *
+ *
* @param name
* name of the class
* @return {@link Class} that extends {@link BioEntity} for a given name
@@ -227,7 +239,7 @@ public final class ElementUtils {
/**
* Return list of {@link Reaction} classes that are available in the system.
- *
+ *
* @return list of {@link Reaction} classes that are available in the system
*/
public List<Class<? extends Reaction>> getAvailableReactionSubclasses() {
@@ -240,24 +252,6 @@ public final class ElementUtils {
return result;
}
- /**
- * @param elementClasses
- * the elementClasses to set
- * @see #elementClasses
- */
- protected static void setElementClasses(Map<String, Class<? extends Element>> elementClasses) {
- ElementUtils.elementClasses = elementClasses;
- }
-
- /**
- * @param reactionClasses
- * the reactionClasses to set
- * @see #reactionClasses
- */
- protected static void setReactionClasses(Map<String, Class<? extends Reaction>> reactionClasses) {
- ElementUtils.reactionClasses = reactionClasses;
- }
-
public String getElementTag(ReactionNode node) {
String reactionPrefix = "";
if (node.getReaction() != null) {
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
index dce61de4bc..984a8b7140 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
@@ -2,14 +2,7 @@ package lcsb.mapviewer.modelutils.map;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-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;
+import lcsb.mapviewer.model.map.species.*;
/**
* List of {@link BioEntity} that must be annotated with at least one
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 1e96e287fb..7e3ed7cb18 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
@@ -2,4 +2,3 @@
* 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 d7ed5099a5..6ef867cda0 100644
--- a/model/src/test/java/lcsb/mapviewer/AllTests.java
+++ b/model/src/test/java/lcsb/mapviewer/AllTests.java
@@ -1,12 +1,12 @@
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;
+import lcsb.mapviewer.model.AllModelTests;
+import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
+
@RunWith(Suite.class)
@SuiteClasses({ AllModelTests.class,
AllMapUtilTests.class,
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
index 0d4cdcdfeb..5e5d48ef9b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
@@ -2,29 +2,27 @@ package lcsb.mapviewer.model;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ProjectStatusTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (ProjectStatus type : ProjectStatus.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (ProjectStatus type : ProjectStatus.values()) {
+ assertNotNull(type);
- // for coverage tests
- ProjectStatus.valueOf(type.name());
- type.toString();
- }
- }
+ // 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 6a5fb5d27d..ef69150a42 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.*;
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 5eca526011..fdd791b623 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
@@ -6,10 +6,10 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ BigFileEntryTest.class,
- CacheQueryTest.class,
- CacheTypeTest.class,
- UploadedFileEntryTest.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 049e72efca..1807d22551 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/BigFileEntryTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/BigFileEntryTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.Calendar;
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 8c1daeff24..48de8af108 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/CacheQueryTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/CacheQueryTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.util.Calendar;
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 77bd9d8ecc..c551027e18 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/CacheTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/CacheTypeTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 8f3f0f4e75..345308362e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
@@ -6,11 +6,11 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ ArrowTypeDataComparatorTest.class,
- ArrowTypeDataTest.class,
- ArrowTypeTest.class,
- LineTypeTest.class,
- PolylineDataTest.class,
- PolylineDataComparatorTest.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 764446834e..dd03bcfc5f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 6a5dc9213e..edacbfa029 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 d8701436b3..82a482f222 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 +1,27 @@
package lcsb.mapviewer.model.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ArrowTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (ArrowType type : ArrowType.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (ArrowType type : ArrowType.values()) {
+ assertNotNull(type);
- // for coverage tests
- ArrowType.valueOf(type.toString());
- }
- }
+ // 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 8d16c8f510..e8f8d280b0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/LineTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/LineTypeTest.java
@@ -2,29 +2,27 @@ package lcsb.mapviewer.model.graphics;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class LineTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (LineType type : LineType.values()) {
- assertNotNull(type);
- assertNotNull(type.getStroke());
+ @Test
+ public void testValidValues() {
+ for (LineType type : LineType.values()) {
+ assertNotNull(type);
+ assertNotNull(type.getStroke());
- // for coverage tests
- LineType.valueOf(type.toString());
- }
- }
+ // 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 e01b64d290..3572aa0414 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import org.junit.*;
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 c2478f76a9..b79771ae7d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.model.graphics;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.*;
import java.util.ArrayList;
import java.util.List;
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 c18826c304..b21e990c59 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.awt.geom.Point2D;
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 17e609addf..ff88ca6c04 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamRelationTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamRelationTypeTest.java
@@ -3,36 +3,34 @@ 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;
+import org.junit.*;
public class MiriamRelationTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (MiriamRelationType type : MiriamRelationType.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (MiriamRelationType type : MiriamRelationType.values()) {
+ assertNotNull(type);
- // for coverage tests
- MiriamRelationType.valueOf(type.toString());
- assertNotNull(type.getStringRepresentation());
+ // for coverage tests
+ MiriamRelationType.valueOf(type.toString());
+ assertNotNull(type.getStringRepresentation());
- }
- }
+ }
+ }
- @Test
- public void testGetTypeByString() {
- assertNull(MiriamRelationType.getTypeByStringRepresentation("DSfsdfs"));
- assertNotNull(MiriamRelationType.getTypeByStringRepresentation("bqbiol:occures"));
- }
+ @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 647b22bcc3..a3905139c5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeNameComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeNameComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
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 3dd25d4491..e0956ea0be 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageComparatorTest.java
@@ -1,12 +1,12 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class OverviewImageComparatorTest extends ModelTestFunctions {
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 0373063248..72a9bd49fb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
@@ -1,12 +1,12 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class OverviewImageLinkComparatorTest extends ModelTestFunctions {
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 7d03e3da8f..355d70f952 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
@@ -8,7 +8,6 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class OverviewImageLinkTest extends ModelTestFunctions {
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 3de5cdfaae..7761a75329 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
@@ -11,7 +12,6 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class OverviewImageTest extends ModelTestFunctions {
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 acd59e7d1a..59fb3837c8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
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 fff035e5f8..bfffc1d1fc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkTest.java
@@ -1,12 +1,11 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class OverviewLinkTest extends ModelTestFunctions {
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 b6a85d55f2..d2adb4fa62 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 7cb33dff1a..23efe21c6d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewSearchLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewSearchLinkTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 c7475b44e6..fe7f0b30e0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/SearchIndexTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/SearchIndexTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 8fab2b8b02..a3855e0d1b 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
@@ -6,14 +6,14 @@ 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,
+ 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 6ecb713c70..fad7793d50 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 1659c72abf..744def3b48 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import org.apache.logging.log4j.LogManager;
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 1b079db050..ebcb694688 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 afe846f021..097f5b3e20 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 a71eeb7e1b..255738b934 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 bf76defcf6..bcc0b4c321 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java
index f01d92e601..17b8e15c30 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 58d1b1201d..7c114cfaab 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.compartment;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
index 51d54bf708..339af44301 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
@@ -15,7 +15,7 @@ import org.junit.runners.Suite.SuiteClasses;
SbmlUnitComparatorTest.class,
SbmlUnitTypeFactorTest.class,
SbmlUnitTypeFactorComparatorTest.class,
- })
+})
public class AllKineticsTests {
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java
index f733ad8795..840a875694 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.kinetics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java
index 8e22d3bd72..8ff3c5fda3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java
@@ -17,7 +17,7 @@ public class SbmlKineticsTest {
kinetics.addParameter(parameter);
assertEquals(kinetics.getParameters().iterator().next(), parameter);
}
-
+
@Test
public void testAddFunction() {
SbmlFunction function = new SbmlFunction("");
@@ -27,7 +27,7 @@ public class SbmlKineticsTest {
assertEquals(1, kinetics.getArguments().size());
assertEquals(kinetics.getArguments().iterator().next(), function);
}
-
+
@Test
public void testGetArguments() {
SbmlParameter parameter = new SbmlParameter("k1");
@@ -39,16 +39,16 @@ public class SbmlKineticsTest {
@Test
public void testAddElement() {
Element protein = new GenericProtein("s1");
-
+
SbmlKinetics kinetics = new SbmlKinetics();
kinetics.addElement(protein);
assertEquals(kinetics.getArguments().get(0), protein);
}
-
+
@Test
public void testSetDefinition() {
String definition = "<lambda><bvar><ci> x </ci></bvar></lambda>";
-
+
SbmlKinetics kinetics = new SbmlKinetics();
kinetics.setDefinition(definition);
assertEquals(definition, kinetics.getDefinition());
@@ -66,6 +66,4 @@ public class SbmlKineticsTest {
assertEquals(0, comparator.compare(copy, kinetics));
}
-
-
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java
index e803cbd9ca..d452fc291e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.kinetics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.Test;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java
index 861d98a596..17a0a82a11 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.kinetics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.Test;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java
index 284f89a936..e392f1a519 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.kinetics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.Test;
@@ -39,7 +40,8 @@ public class SbmlUnitComparatorTest {
public void testCompareUnitTypes() {
SbmlUnit parameter = createUnit();
SbmlUnit parameter2 = createUnit();
- parameter.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 1, 1));;
+ parameter.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 1, 1));
+ ;
assertTrue(0 != comparator.compare(parameter, parameter2));
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java
index 83ec875f1f..494e0396e2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.kinetics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.Test;
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 a0c2e8cc67..d2c96db83c 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
@@ -8,17 +8,17 @@ 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,
+ 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 6c57476266..591cf782ce 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
-import java.awt.Color;
+import java.awt.*;
import java.util.ArrayList;
import java.util.List;
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 c362be4c24..1ecba9d5de 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 1077458009..0c61764e9f 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
@@ -11,7 +11,6 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class GeneVariationColorSchemaTest extends ModelTestFunctions {
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 bd9c5b0f5e..aeaf2a290b 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
@@ -1,13 +1,12 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class GeneVariationTest extends ModelTestFunctions {
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 8b8be18c9b..3de4e0dbc2 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 ecbf480532..181292d795 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 7517897fd9..46aa2da065 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
@@ -2,29 +2,27 @@ package lcsb.mapviewer.model.map.layout;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class LayoutStatusTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (LayoutStatus type : LayoutStatus.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (LayoutStatus type : LayoutStatus.values()) {
+ assertNotNull(type);
- // for coverage tests
- LayoutStatus.valueOf(type.toString());
- assertNotNull(type.getCommonName());
- }
- }
+ // 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 c898f57198..cc037a25e6 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
@@ -10,7 +10,6 @@ import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class LayoutTest extends ModelTestFunctions {
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 c914d44e5f..2b90b82c27 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
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 b9182eee56..6c1937cf0e 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 1b4c5c817b..2a9bfd244b 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 +1,32 @@
package lcsb.mapviewer.model.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ReferenceGenomeTypeTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ assertNotNull(type);
- // for coverage tests
- ReferenceGenomeType.valueOf(type.toString());
- assertNotNull(type.getHomepage());
- }
- }
+ // 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 6c08e4c7f1..aea5168b67 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
@@ -6,13 +6,13 @@ 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,
+ 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 70ddddbe43..56ad191b17 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 d6f37724b1..42b7f4346f 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.mockito.Mockito;
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 971a65b5ba..b9f6e09693 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
@@ -2,7 +2,7 @@ package lcsb.mapviewer.model.map.layout.graphics;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 5c3c1f6e84..491885d019 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.mockito.Mockito;
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 d89cd63f29..6f5fa07785 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
@@ -2,7 +2,7 @@ package lcsb.mapviewer.model.map.layout.graphics;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 6d0233362e..ba66652055 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.mockito.Mockito;
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 7251f41bdf..b0100ab974 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
@@ -6,15 +6,15 @@ 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,
+ 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 cd76b150b5..66936298e4 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.mockito.Mockito;
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 da061855ec..3f17299da5 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
@@ -8,7 +8,6 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class ElementSubmodelConnectionTest extends ModelTestFunctions {
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 5c201cd3aa..99e40cc5a1 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
@@ -1,7 +1,8 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Mockito.when;
import java.util.Calendar;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index 0f4f321b6c..b0fe7f6665 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -471,34 +471,34 @@ public class ModelFullIndexedTest extends ModelTestFunctions {
public void testGetters() {
Model model = new ModelFullIndexed(null);
- double width = 12.0;
- int widthInt = 12;
- String widthStr = "12.0";
- double height = 13.0;
- String heightStr = "13.0";
- int heightInt = 13;
- Set<Element> elements = new HashSet<>();
- int zoomLevels = 98;
- int tileSize = 1024;
- String idModel = "model_ID";
-
- model.setWidth(widthStr);
- assertEquals(width, model.getWidth(), Configuration.EPSILON);
- model.setWidth(0.0);
- model.setWidth(width);
- assertEquals(width, model.getWidth(), Configuration.EPSILON);
- model.setWidth(0.0);
- model.setWidth(widthInt);
- assertEquals(width, model.getWidth(), Configuration.EPSILON);
-
- model.setHeight(heightStr);
- assertEquals(height, model.getHeight(), Configuration.EPSILON);
- model.setHeight(0.0);
- model.setHeight(height);
- assertEquals(height, model.getHeight(), Configuration.EPSILON);
- model.setHeight(0.0);
- model.setHeight(heightInt);
- assertEquals(height, model.getHeight(), Configuration.EPSILON);
+ double width = 12.0;
+ int widthInt = 12;
+ String widthStr = "12.0";
+ double height = 13.0;
+ String heightStr = "13.0";
+ int heightInt = 13;
+ Set<Element> elements = new HashSet<>();
+ int zoomLevels = 98;
+ int tileSize = 1024;
+ String idModel = "model_ID";
+
+ model.setWidth(widthStr);
+ assertEquals(width, model.getWidth(), Configuration.EPSILON);
+ model.setWidth(0.0);
+ model.setWidth(width);
+ assertEquals(width, model.getWidth(), Configuration.EPSILON);
+ model.setWidth(0.0);
+ model.setWidth(widthInt);
+ assertEquals(width, model.getWidth(), Configuration.EPSILON);
+
+ model.setHeight(heightStr);
+ assertEquals(height, model.getHeight(), Configuration.EPSILON);
+ model.setHeight(0.0);
+ model.setHeight(height);
+ assertEquals(height, model.getHeight(), Configuration.EPSILON);
+ model.setHeight(0.0);
+ model.setHeight(heightInt);
+ assertEquals(height, model.getHeight(), Configuration.EPSILON);
model.setElements(elements);
assertEquals(elements, model.getElements());
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 90dc66bf24..f6ad4c6110 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 ad99e667a2..7c529ec2d0 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
@@ -8,7 +9,6 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
public class ModelSubmodelConnectionTest extends ModelTestFunctions {
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 88330e931c..9903d48c99 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 202a2f1996..50d04b87c1 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
@@ -2,29 +2,27 @@ package lcsb.mapviewer.model.map.model;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class SubmodelTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (SubmodelType type : SubmodelType.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (SubmodelType type : SubmodelType.values()) {
+ assertNotNull(type);
- // for coverage tests
- SubmodelType.valueOf(type.toString());
- assertNotNull(type.getCommonName());
- }
- }
+ // 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 e2533ce33f..ec897a1f83 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
@@ -6,12 +6,12 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CatalysisTest.class,
- InhibitionTest.class,
- ModulationTest.class,
- PhysicalStimulationTest.class,
- TriggerTest.class,
- UnknownCatalysisTest.class,
- UnknownInhibitionTest.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 5b149190ac..27f4153c13 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 52775701ec..d83e8e7dac 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 cb0231984a..1da8e7ec43 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 e20499a2f3..be85348aff 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 f5c6524aef..e7c44be2a3 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 e708b26dc7..0eba189132 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 7a9e707905..c944de9fd2 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.modifier;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 a4b850daa8..eafe33164f 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 4f7ccaa125..91b03aba7b 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
@@ -1,30 +1,30 @@
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;
+import lcsb.mapviewer.model.map.reaction.type.AllReactionTypeTests;
+
@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,
+ 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/AssociationOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AssociationOperatorTest.java
index 406c3fcbca..82dc3caf4d 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 7738614412..772703cf78 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 603d7bbe74..36b37a8411 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 c5dd68f2a1..7d8d00f2c6 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 8f5d37ff02..c8f648c080 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
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 73a6e2ee50..caf7496987 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
@@ -4,27 +4,27 @@ 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();
- }
+ /**
+ *
+ */
+ 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/OrOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/OrOperatorTest.java
index 570a5b6e98..bb47ea5eca 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 27de69631a..11170ed9e0 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 3d3c1aa3a3..4c9c5aa6ab 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 2cb92cb915..5db7e0201d 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
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 6d8ff0496c..bbecd9f08d 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
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 aea738e451..97a0533bcf 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 29b6fdfcf9..e3d67141a1 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 4e182a1413..7c9098e0bd 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 2a3c6954a8..cf4f510fc6 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 4c71a76c5d..32a5414546 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 485be3d4df..99efaf8469 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 0e19c70bf1..4ad4a51a17 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 626447a36a..7c85c396e4 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 7c4de9b4b3..e3eaad75fc 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
@@ -2,28 +2,26 @@ 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;
+import org.junit.*;
public class ReactionRectTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (ReactionRect type : ReactionRect.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (ReactionRect type : ReactionRect.values()) {
+ assertNotNull(type);
- // for coverage tests
- ReactionRect.valueOf(type.toString());
- assertNotNull(type.getText());
- }
- }
+ // 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 3af121e9e7..6aec927f84 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 2e36146965..f9681af47b 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 dc6e20698e..4331b85da2 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 63766df9cd..b3fd9c916f 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 a5a0efa99e..3bb4f8c5da 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 797f530353..8fb71e5575 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 550d971357..fcc1c8fe19 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 172e3a1b5e..c4ad3b3e20 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 41657d5ef4..d3c45b037d 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 f6064bf915..5386451043 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 fdd9447caf..ebb0109c4a 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 3a2f2787cc..3eef31750f 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 19392e6655..b7b511b0ca 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 181de50eb1..90ae71aa3f 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction.type;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 41464b30cc..c5661e83dd 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
@@ -8,41 +8,41 @@ 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,
+ 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 00f1684306..78c1b4efae 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
index d43b90d1bd..1c7f41e502 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 9d509a9d6f..469f78df26 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 b0d7480a51..60ba2db455 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
@@ -1,9 +1,10 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Mockito.when;
-import java.awt.Color;
+import java.awt.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
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 cb686002ab..97cd264159 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 24aff10c4b..08fcd8f987 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 68ee746e1e..0955b845b9 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 ae3b3a1b05..a6bfc06b34 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 70f973bfc1..642e38d177 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 a9b75ad52a..48d6f03c0e 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
@@ -1,14 +1,14 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.compartment.Compartment;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
index f39b00f3c9..735efdffb8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
index ca3450c307..41a44d7b12 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 7f874e1c43..ce5e45b294 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 aa6c24c5c1..5a4ca72142 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 0ad7b0f6d4..5c9d716b5d 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 871c361273..f079732e7b 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 9cf4a3d73f..144415e1d6 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 7cf6596007..9b80ff2a07 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 fe9d66fe14..4710736e83 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 5b8535329d..06ac3a0ade 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
index 2307b594ad..a0c3b2b7f3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
index af692fc075..8fd69b5dc0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 74bc63f06c..014bce4dfe 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 52977e3d1b..89a40be818 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
index 7d5209461f..3ba5523be0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
@@ -73,7 +74,7 @@ public class RnaComparatorTest extends ModelTestFunctions {
return result;
}
- @Test(expected=NotImplementedException.class)
+ @Test(expected = NotImplementedException.class)
public void testInvalid() {
Rna object = Mockito.mock(Rna.class);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
index 2d742662d2..d46b948073 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.ArrayList;
import java.util.List;
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 06b77a459a..4c06b26fad 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 6d88a38983..a408c3e8d7 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 7751e2b5fd..df3283922c 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.mockito.Mockito;
@@ -120,7 +121,7 @@ public class SpeciesComparatorTest extends ModelTestFunctions {
assertTrue(comparator.compare(species2, species1) != 0);
}
- @Test(expected=NotImplementedException.class)
+ @Test(expected = NotImplementedException.class)
public void testException() {
Species mock = Mockito.mock(Species.class);
comparator.compare(mock, mock);
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 2dff3ef1f2..99130fc40e 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
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 feea3071a8..f48697810c 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 fbaad1d3c1..bcd6accc0d 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 324249ff10..5d38a4da94 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
import org.mockito.Mockito;
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 ed3e6cf75b..f62e5a00d3 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 48eca26298..009b8980fc 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
@@ -6,12 +6,12 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CodingRegionTest.class,
- ModificationStateTest.class,
- ResidueTest.class,
- PositionToCompartmentTest.class,
- ProteinBindingDomainTest.class,
- StructureTest.class,
- UniprotRecordTest.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/CodingRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/CodingRegionTest.java
index cff6502b20..5745fa28f3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/CodingRegionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/CodingRegionTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species.field;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.awt.geom.Point2D;
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 3de4dbaae7..7bd6fa181a 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
@@ -3,38 +3,34 @@ 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;
+import org.junit.*;
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"));
- }
+ @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 dabb973bd6..0383f2f6f9 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
@@ -3,37 +3,33 @@ 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;
+import org.junit.*;
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"));
- }
+ @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/species/field/ResidueTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
index 4c2b7c8658..f7ab37f9e9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
@@ -3,10 +3,7 @@ package lcsb.mapviewer.model.map.species.field;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java
index 2014473d37..283f273e44 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/StructureTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species.field;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.util.HashSet;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java
index 26e3aa41a8..31ca26e835 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/UniprotRecordTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species.field;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.junit.*;
import org.mockito.Mockito;
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 e212af7b9b..683daea3c1 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
@@ -6,7 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ SearchHistoryTest.class,
- SearchTypeTest.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 08b7e0ee0a..60b8b0fc61 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.statistics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.Calendar;
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 0d0ed2796f..f42d6430de 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
@@ -2,27 +2,25 @@ package lcsb.mapviewer.model.map.statistics;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class SearchTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (SearchType type : SearchType.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (SearchType type : SearchType.values()) {
+ assertNotNull(type);
- // for coverage tests
- SearchType.valueOf(type.toString());
- }
- }
+ // for coverage tests
+ SearchType.valueOf(type.toString());
+ }
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/security/PrivilegeTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/security/PrivilegeTypeTest.java
index b2fdca855b..e205574de2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/security/PrivilegeTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/security/PrivilegeTypeTest.java
@@ -2,30 +2,27 @@ package lcsb.mapviewer.model.security;
import static org.junit.Assert.assertNotNull;
-import lcsb.mapviewer.model.security.PrivilegeType;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class PrivilegeTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (PrivilegeType type : PrivilegeType.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (PrivilegeType type : PrivilegeType.values()) {
+ assertNotNull(type);
- // for coverage tests
- PrivilegeType.valueOf(type.toString());
- assertNotNull(type.getDescription());
- }
- }
+ // for coverage tests
+ PrivilegeType.valueOf(type.toString());
+ assertNotNull(type.getDescription());
+ }
+ }
}
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 39d37832c9..2d8683dd51 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 +1,28 @@
package lcsb.mapviewer.model.user;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ConfigurationElementEditTypeTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValues() {
- for (ConfigurationElementEditType type: ConfigurationElementEditType.values()){
- assertNotNull(ConfigurationElementEditType.valueOf(type.toString()));
- }
- }
+ @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 2c9d683b50..03f2f6a1fd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementTypeTest.java
@@ -2,30 +2,28 @@ package lcsb.mapviewer.model.user;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class ConfigurationElementTypeTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (ConfigurationElementType type : ConfigurationElementType.values()) {
- assertNotNull(type);
+ @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());
- }
- }
+ // 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 e9d088ff51..e6a1dcae75 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.user;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.*;
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 b5c9dba438..c09b67b2eb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserAnnotationSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserAnnotationSchemaTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.user;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 3d60065c91..4d1e39ea7c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserClassAnnotatorsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserClassAnnotatorsTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.user;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 3c243c43f7..1a09a76273 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.model.user;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
-import java.awt.Color;
+import java.awt.*;
import java.util.HashSet;
import java.util.Set;
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameterTest.java b/model/src/test/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameterTest.java
index 175c41627e..751e922b2c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameterTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/annotator/AnnotatorParameterTest.java
@@ -1,10 +1,8 @@
package lcsb.mapviewer.model.user.annotator;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
import org.junit.Test;
@@ -19,13 +17,13 @@ public class AnnotatorParameterTest {
p2.setOrderPosition(1);
AnnotatorParameter p3 = new AnnotatorConfigParameter();
p3.setOrderPosition(12);
-
+
list.add(p1);
list.add(p2);
list.add(p3);
-
+
Collections.sort(list);
-
+
assertEquals(p2, list.get(0));
assertEquals(p1, list.get(1));
assertEquals(p3, list.get(2));
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 16ddd95d33..662f73e50a 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
@@ -6,8 +6,8 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ ClassTreeNodeTest.class,
- ElementUtilsTest.class,
- RequireAnnotationMapTest.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 0b80b693bc..e80bb05371 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.modelutils.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
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 9c30c4cea4..f73ec178db 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMapTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMapTest.java
@@ -2,28 +2,26 @@ package lcsb.mapviewer.modelutils.map;
import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
public class RequireAnnotationMapTest {
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testValidValues() {
- for (RequireAnnotationMap type : RequireAnnotationMap.values()) {
- assertNotNull(type);
+ @Test
+ public void testValidValues() {
+ for (RequireAnnotationMap type : RequireAnnotationMap.values()) {
+ assertNotNull(type);
- // for coverage tests
- RequireAnnotationMap.valueOf(type.toString());
- }
- }
+ // 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 e08ed1dfa0..23dccfe8cc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/Activator.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/Activator.java
@@ -14,21 +14,21 @@ import org.pathvisio.desktop.plugin.Plugin;
public class Activator implements BundleActivator {
- /**
- * CellDesigner plugin for pathvisio.
- */
- private ImportExport plugin;
+ /**
+ * 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 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();
- }
- }
+ @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 bb5e4a1bfe..f9279eb532 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.wikipathway;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.io.PrintWriter;
+import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
@@ -12,10 +9,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.apache.logging.log4j.core.LoggerContext;
-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.core.model.*;
import org.pathvisio.desktop.PvDesktop;
import org.pathvisio.desktop.plugin.Plugin;
@@ -33,180 +27,180 @@ import lcsb.mapviewer.wikipathway.XML.ModelToGPML;
*
*/
public class ImportExport implements Plugin {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.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 {
- LoggerContext context = (org.apache.logging.log4j.core.LoggerContext) LogManager.getContext(false);
- File file = new File("log4j2.properties");
- context.setConfigLocation(file.toURI());
- } 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<LogEvent> 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 {
- MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
- try {
- 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);
-
- MinervaLoggerAppender.unregisterLogEventStorage(appender);
- warnings.addAll(appender.getWarnings());
- return pathway;
- } catch (Exception e) {
- logger.error(e, e);
- throw new ConverterException(e);
- } finally {
- MinervaLoggerAppender.unregisterLogEventStorage(appender);
- }
- }
-
- @Override
- public boolean isCorrectType(File arg0) {
- return true;
- }
-
- @Override
- public List<String> getWarnings() {
- List<String> result = new ArrayList<>();
- for (LogEvent event : warnings) {
- result.add(event.getMessage().getFormattedMessage());
- }
- 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 {
- MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
- try {
- pathway.writeToXml(new File("tmp.gpml"), false);
- model = new GPMLToModel().getModel("tmp.gpml");
-
- MinervaLoggerAppender.unregisterLogEventStorage(appender);
- warnings = createWarnings(appender);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(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 {
- MinervaLoggerAppender.unregisterLogEventStorage(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(MinervaLoggerAppender appender) {
- List<String> warnings = new ArrayList<>();
- for (LogEvent event : appender.getWarnings()) {
- warnings.add(event.getMessage().getFormattedMessage().replaceAll("\n", "_NEW_LINE_"));
- }
- return warnings;
- }
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.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 {
+ LoggerContext context = (org.apache.logging.log4j.core.LoggerContext) LogManager.getContext(false);
+ File file = new File("log4j2.properties");
+ context.setConfigLocation(file.toURI());
+ } 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<LogEvent> warnings = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public ImportCellDesigner() {
+ }
+
+ @Override
+ public String getName() {
+ return "CellDesigner";
+ }
+
+ @Override
+ public String[] getExtensions() {
+ return importExtensions;
+ }
+
+ @Override
+ public List<String> getWarnings() {
+ List<String> result = new ArrayList<>();
+ for (LogEvent event : warnings) {
+ result.add(event.getMessage().getFormattedMessage());
+ }
+ return result;
+ }
+
+ @Override
+ public boolean isCorrectType(File arg0) {
+ return true;
+ }
+
+ @Override
+ public Pathway doImport(File file) throws ConverterException {
+ MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
+ try {
+ 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);
+
+ MinervaLoggerAppender.unregisterLogEventStorage(appender);
+ warnings.addAll(appender.getWarnings());
+ return pathway;
+ } catch (Exception e) {
+ logger.error(e, e);
+ throw new ConverterException(e);
+ } finally {
+ MinervaLoggerAppender.unregisterLogEventStorage(appender);
+ }
+ }
+ }
+
+ /**
+ * 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 getName() {
+ return "CellDesigner";
+ }
+
+ @Override
+ public String[] getExtensions() {
+ return exportExtensions;
+ }
+
+ @Override
+ public List<String> getWarnings() {
+ return warnings;
+ }
+
+ @Override
+ public void doExport(File file, Pathway pathway) throws ConverterException {
+ MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
+ try {
+ pathway.writeToXml(new File("tmp.gpml"), false);
+ model = new GPMLToModel().getModel("tmp.gpml");
+
+ MinervaLoggerAppender.unregisterLogEventStorage(appender);
+ warnings = createWarnings(appender);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.model2String(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 {
+ MinervaLoggerAppender.unregisterLogEventStorage(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(MinervaLoggerAppender appender) {
+ List<String> warnings = new ArrayList<>();
+ for (LogEvent event : appender.getWarnings()) {
+ warnings.add(event.getMessage().getFormattedMessage().replaceAll("\n", "_NEW_LINE_"));
+ }
+ 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 877f7cf6d3..0296f8a1e1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
@@ -1,24 +1,16 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.wikipathway.model.biopax.*;
/**
* Parser of Biopax data from the gpml file.
@@ -28,237 +20,237 @@ import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
*/
public class BiopaxParser {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger(BiopaxParser.class);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = LogManager.getLogger(BiopaxParser.class);
- /**
- * Hash used for next {@link BiopaxPublication} processed by parser.
- */
- private Integer hash = 1;
+ /**
+ * 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<>();
+ /**
+ * 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;
- }
+ /**
+ * 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();
+ /**
+ * 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;
- }
+ 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();
+ /**
+ * 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(XmlParser.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;
- }
+ result.setReferenceId(XmlParser.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 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);
- }
+ /**
+ * 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");
+ /**
+ * 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();
- }
+ 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();
- }
+ /**
+ * 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());
- }
- }
+ /**
+ * 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;
- }
+ /**
+ * 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 46ad82cf91..1d2a3e863e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
@@ -20,19 +20,19 @@ import lcsb.mapviewer.converter.ConverterException;
*/
public class CyclicEdgeException extends ConverterException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 96bb89c3e5..445bf4de09 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
@@ -3,19 +3,16 @@ package lcsb.mapviewer.wikipathway.XML;
import java.awt.geom.Rectangle2D;
import java.util.Collection;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
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;
+import lcsb.mapviewer.wikipathway.model.*;
/**
* Parser class that creates {@link DataNode} objects from Xml {@link Element
@@ -26,175 +23,175 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
- /**
- * Default claass logger.
- */
- private final Logger logger = LogManager.getLogger(DataNodeParser.class);
+ /**
+ * Default claass logger.
+ */
+ private final Logger logger = LogManager.getLogger(DataNodeParser.class);
- /**
- * PArser used to process references.
- */
- private final ReferenceParser referenceParser = new ReferenceParser();
+ /**
+ * 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"));
+ @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;
- }
- }
+ 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;
- }
- }
- }
+ 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;
- }
+ 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));
- }
+ @Override
+ public String toXml(DataNode node) throws ConverterException {
+ throw new NotImplementedException();
+ }
- /**
- * 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(Collection<DataNode> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
- @Override
- public String toXml(DataNode node) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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));
+ }
- @Override
- public String toXml(Collection<DataNode> list) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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;
+ }
+ }
}
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 d848563e24..7a534a2272 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
@@ -2,10 +2,9 @@ package lcsb.mapviewer.wikipathway.XML;
import java.util.Collection;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -22,71 +21,72 @@ import lcsb.mapviewer.wikipathway.model.Edge;
*/
public class EdgeLineParser extends ElementGpmlParser<Edge> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(EdgeLineParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(EdgeLineParser.class);
- /**
- * Parser used to parse typical {@link Edge} xml nodes.
- */
- private final EdgeParser edgeParser = new EdgeParser();
+ /**
+ * 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());
- }
- }
+ /**
+ * 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;
- }
+ 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(Edge node) throws ConverterException {
+ throw new NotImplementedException();
+ }
- @Override
- public String toXml(Collection<Edge> list) 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 dc083bad42..d1d4c91cb6 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
@@ -2,14 +2,11 @@ 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 java.util.*;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
@@ -17,12 +14,7 @@ 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;
+import lcsb.mapviewer.wikipathway.model.*;
/**
* Parser class that creates {@link Edge} objects from Xml {@link Element node}.
@@ -32,548 +24,547 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
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 = LogManager.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();
- }
+ /**
+ * 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;
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(EdgeParser.class);
+ /**
+ * 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();
+
+ /**
+ * 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;
+ }
+
+ @Override
+ public String toXml(Edge node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<Edge> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * 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;
+ }
+ }
}
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 7cde314e72..d1e6398aaa 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
@@ -1,21 +1,17 @@
package lcsb.mapviewer.wikipathway.XML;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
+import java.awt.*;
+import java.util.*;
import java.util.List;
-import java.util.Set;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterException;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-
/**
* Generic parser for GPML xml structures.
*
@@ -26,114 +22,113 @@ import org.w3c.dom.Node;
*/
public abstract class ElementGpmlParser<T> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.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);
+ /**
+ * Color that should be used when we have transparent color.
+ */
+ private static final Color TRANSPARENT_COLOR = new Color(0, 0, 0, 0);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.getLogger(ElementGpmlParser.class);
- /**
- * 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;
+ /**
+ * 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 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;
+ /**
+ * 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;
- }
+ /**
+ * 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
- }
+ /**
+ * 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;
- }
+ /**
+ * 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 90367ca264..8b14d6f2a5 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.wikipathway.XML;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.map.model.Model;
@@ -16,36 +14,36 @@ import lcsb.mapviewer.wikipathway.model.Graph;
*/
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 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);
- }
+ /**
+ * 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 671ebacb11..4563d839db 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -2,42 +2,21 @@ 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.logging.log4j.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import java.util.*;
+
+import javax.xml.parsers.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
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;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.wikipathway.model.*;
/**
* This class allows to parse
@@ -48,610 +27,617 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public class GpmlParser {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.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 stored
- */
- 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 stored
- * @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;
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.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 stored
+ */
+ 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 stored
+ * @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 3e6d5c26f5..bfb0819c05 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
@@ -2,13 +2,12 @@ package lcsb.mapviewer.wikipathway.XML;
import java.awt.font.TextAttribute;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import lcsb.mapviewer.wikipathway.model.*;
/**
* Parser used for extracting common data (from gpml file) for all elements
@@ -20,58 +19,59 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public abstract class GraphicalPathwayElementParser<T extends GraphicalPathwayElement> extends ElementGpmlParser<T> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(GraphicalPathwayElementParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.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;
- }
+ /**
+ * 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 ed81e3e0ae..0382aefb37 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/InvalidElbowConnectorException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/InvalidElbowConnectorException.java
@@ -12,19 +12,19 @@ import lcsb.mapviewer.converter.ConverterException;
*/
public class InvalidElbowConnectorException extends ConverterException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 82af92ce1b..c3c91d277e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
@@ -3,10 +3,9 @@ package lcsb.mapviewer.wikipathway.XML;
import java.awt.geom.Rectangle2D;
import java.util.Collection;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -24,155 +23,156 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public class LabelParser extends GraphicalPathwayElementParser<Label> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(LabelParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.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"));
+ @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;
- }
- }
+ 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;
- }
- }
- }
+ 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;
- }
+ 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));
- }
+ @Override
+ public String toXml(Label node) throws ConverterException {
+ throw new NotImplementedException();
+ }
- /**
- * 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(Collection<Label> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
- @Override
- public String toXml(Label node) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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));
+ }
- @Override
- public String toXml(Collection<Label> list) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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;
+ }
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 2f335d27f1..8b56cec964 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -1,16 +1,9 @@
package lcsb.mapviewer.wikipathway.XML;
-import java.awt.Color;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
+import java.awt.*;
+import java.awt.geom.*;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.LogManager;
@@ -29,55 +22,18 @@ import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.OvalCompartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-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.compartment.*;
+import lcsb.mapviewer.model.map.layout.graphics.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-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.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.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
-import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-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.GenericProtein;
-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.species.field.AbstractSiteModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationSite;
-import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
+import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
-import lcsb.mapviewer.wikipathway.model.DataNode;
-import lcsb.mapviewer.wikipathway.model.Edge;
-import lcsb.mapviewer.wikipathway.model.Graph;
-import lcsb.mapviewer.wikipathway.model.GraphicalPathwayElement;
-import lcsb.mapviewer.wikipathway.model.Group;
-import lcsb.mapviewer.wikipathway.model.Interaction;
-import lcsb.mapviewer.wikipathway.model.InteractionMapping;
+import lcsb.mapviewer.wikipathway.model.*;
import lcsb.mapviewer.wikipathway.model.Label;
-import lcsb.mapviewer.wikipathway.model.PathwayElement;
import lcsb.mapviewer.wikipathway.model.Shape;
-import lcsb.mapviewer.wikipathway.model.State;
import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
import lcsb.mapviewer.wikipathway.utils.Geo;
@@ -89,44 +45,22 @@ import lcsb.mapviewer.wikipathway.utils.Geo;
*/
public class ModelContructor {
- /**
- * CellDesigner util class used for retrieving information about modifier
- * graphics.
- */
- private ModifierTypeUtils mtu = new ModifierTypeUtils();
-
/**
* Default color used by complexes.
*/
private static final Color DEFAULT_COMPLEX_ALIAS_COLOR = new Color(102, 255, 255);
-
/**
* How much of central line is used by and operator that joins reactants.
*/
private static final int AND_OPERATOR_CENTRAL_LINE_RATIO = 10;
-
/**
* How much of central line is used by split operator that split products.
*/
private static final int SPLIT_OPERATOR_CENTRAL_LINE_RATIO = 10;
-
/**
* Epsilon used for double comparison.
*/
private static final double EPSILON = 1e-6;
-
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.getLogger(ModelContructor.class);
-
- /**
- * Parser used for extracting {@link MiriamData references} from GPML model.
- */
- private BiopaxParser biopaxParser = new BiopaxParser();
-
- private PointTransformation pt = new PointTransformation();
-
/**
* List of {@link Shape#shape shapes} that are not supported to be part of a
* {@link Complex complex}.
@@ -147,6 +81,21 @@ public class ModelContructor {
INALID_COMPLEX_SHAPE_CHILDREN.add("Hexagon");
}
+ /**
+ * CellDesigner util class used for retrieving information about modifier
+ * graphics.
+ */
+ private ModifierTypeUtils mtu = new ModifierTypeUtils();
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(ModelContructor.class);
+ /**
+ * Parser used for extracting {@link MiriamData references} from GPML model.
+ */
+ private BiopaxParser biopaxParser = new BiopaxParser();
+ private PointTransformation pt = new PointTransformation();
+
/**
* This function splits {@link PolylineData} into two parts. It also assumes
* that last segment on the left part is equal to the length of the first
@@ -222,37 +171,9 @@ public class ModelContructor {
return new Pair<PolylineData, PolylineData>(p1, p2);
}
- /**
- * Support class to send less parameters in functions.
- *
- * @author Jan Badura
- */
- private final class Data {
- /**
- * Map between graphId and aliases created from gpml elements.
- */
- private Map<String, Element> id2alias;
-
- /**
- * Default layer.
- */
- private Layer layer;
-
- /**
- * Default constructor.
- */
- private Data() {
- id2alias = new HashMap<String, Element>();
- layer = new Layer();
- layer.setVisible(true);
- layer.setLayerId("1");
- layer.setName("defaultLayer");
- }
- }
-
/**
* This function creates Species from DataNode.
- *
+ *
* @param dataNode
* object from which species is created
* @param data
@@ -294,7 +215,7 @@ public class ModelContructor {
/**
* This function adds ComplexSpecies to model from graph. ComplexName is set as
* groupId from .gpml
- *
+ *
* @param model
* to this model complexes will be added
* @param graph
@@ -329,7 +250,7 @@ public class ModelContructor {
/**
* This function adds Species, TextLabels, Compartments and Shapes from graph.
- *
+ *
* @param model
* model to which species will be added
* @param graph
@@ -433,7 +354,7 @@ public class ModelContructor {
* {@link ModificationResidue} in element might have slightly off coordinates
* (due to different symbol shapes). For that we need to align them to match our
* model.
- *
+ *
* @param species
*/
protected void adjustModificationCoordinates(Element species) {
@@ -461,7 +382,7 @@ public class ModelContructor {
/**
* Creates {@link LayerRect} object from {@link Shape}.
- *
+ *
* @param shape
* source gpml object to be transformed
* @return {@link LayerRect} obtained from {@link Shape} object
@@ -479,7 +400,7 @@ public class ModelContructor {
/**
* Creates {@link LayerOval} object from {@link Shape}.
- *
+ *
* @param shape
* source gpml object to be transformed
* @return {@link LayerOval} obtained from {@link Shape} object
@@ -497,7 +418,7 @@ public class ModelContructor {
/**
* Creates {@link LayerText} from {@link Label}.
- *
+ *
* @param label
* object from which result will be created
* @return {@link LayerText} from {@link Label}
@@ -521,7 +442,7 @@ public class ModelContructor {
/**
* Creates alias for {@link GraphicalPathwayElement}. Type of the alias is
* defined by the parameter {@link Species}
- *
+ *
* @param gpmlElement
* object from which alias will be create
* @param alias
@@ -553,7 +474,7 @@ public class ModelContructor {
/**
* Creates {@link Unknown species} from {@link Label}.
- *
+ *
* @param label
* original label from which output should be created
* @return {@link Unknown} object created from input {@link Label}
@@ -568,7 +489,7 @@ public class ModelContructor {
/**
* Creates {@link Unknown species} from {@link Shape}.
- *
+ *
* @param shape
* original label from which output should be created
* @return {@link Unknown} object created from input {@link Label}
@@ -583,7 +504,7 @@ public class ModelContructor {
/**
* This function add Species to right Complexes.
- *
+ *
* @param graph
* gpml data model
* @param data
@@ -632,7 +553,7 @@ public class ModelContructor {
/**
* This function creates {@link Reaction} from {@link Interaction} from graph.
- *
+ *
* @param interaction
* gpml interaction
* @param graph
@@ -812,7 +733,7 @@ public class ModelContructor {
/**
* Creates {@link Reactant} from gpml edge.
- *
+ *
* @param data
* ...
* @param e
@@ -845,7 +766,7 @@ public class ModelContructor {
/**
* Creates {@link Product} from gpml edge.
- *
+ *
* @param data
* ...
* @param e
@@ -876,7 +797,7 @@ public class ModelContructor {
/**
* Creates {@link Modifier} from gpml edge.
- *
+ *
* @param data
* ...
* @param e
@@ -914,7 +835,7 @@ public class ModelContructor {
/**
* Creates {@link Reaction} for a given class type.
- *
+ *
* @param reactionType
* type of reaction to create
* @return new instance of the reactionType
@@ -930,7 +851,7 @@ public class ModelContructor {
/**
* Creates {@link Modifier} for a given class type.
- *
+ *
* @param modifierType
* type of modifier in reaction to create
* @param alias
@@ -948,13 +869,13 @@ public class ModelContructor {
/**
* This function creates {@link Model} from {@link Graph}.
- *
+ *
* @param graph
* object with data obtained from gpml
* @return {@link Model} object representing gpml
* @throws ConverterException
* exception thrown when conversion from graph couldn't be performed
- *
+ *
*/
public Model getModel(Graph graph) throws ConverterException {
try {
@@ -1019,7 +940,7 @@ public class ModelContructor {
/**
* Method that put {@link Species aliases} that are not assigned into any
* {@link Compartment} into a proper compartment.
- *
+ *
* @param model
* model where aliases will be modified
*/
@@ -1049,7 +970,7 @@ public class ModelContructor {
/**
* Removes empty complexes (with size 0) from model.
- *
+ *
* @param model
* model where operation is performed
*/
@@ -1082,7 +1003,7 @@ public class ModelContructor {
/**
* Tries to find a name to assign to complexes if complexes don't contain them.
- *
+ *
* @param model
* model where complexes are placed
*/
@@ -1112,7 +1033,7 @@ public class ModelContructor {
/**
* Tries to find a name to assign to compartments if comparments don't contain
* them.
- *
+ *
* @param model
* model where compartments are placed
*/
@@ -1141,7 +1062,7 @@ public class ModelContructor {
/**
* Creates list of {@link LayerLine} in the model from gpml model.
- *
+ *
* @param graph
* gpml model
* @return list of {@link LayerLine}
@@ -1157,7 +1078,7 @@ public class ModelContructor {
/**
* By default gpml doesn't offer information about compartments structure. This
* function fixes assignments to compartment and compartment aliases.
- *
+ *
* @param model
* model where assignments are fixed.
*/
@@ -1191,4 +1112,32 @@ public class ModelContructor {
}
}
}
+
+ /**
+ * Support class to send less parameters in functions.
+ *
+ * @author Jan Badura
+ */
+ private final class Data {
+ /**
+ * Map between graphId and aliases created from gpml elements.
+ */
+ private Map<String, Element> id2alias;
+
+ /**
+ * Default layer.
+ */
+ private Layer layer;
+
+ /**
+ * Default constructor.
+ */
+ private Data() {
+ id2alias = new HashMap<String, Element>();
+ layer = new Layer();
+ layer.setVisible(true);
+ layer.setLayerId("1");
+ layer.setName("defaultLayer");
+ }
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 0e4ba28f7e..929b4db2df 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -5,7 +5,8 @@ import java.awt.geom.Rectangle2D;
import java.util.HashSet;
import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterException;
@@ -15,25 +16,8 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
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.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.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.reaction.*;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.wikipathway.utils.Geo;
/**
@@ -44,39 +28,33 @@ import lcsb.mapviewer.wikipathway.utils.Geo;
*/
public class ModelToGPML {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger(ModelToGPML.class);
-
/**
* Maximum distance between point and line. ???
*/
private static final double DIS_FOR_LINE = 3.0;
-
/**
* This value define margin of the group border. Rectangle border will be
* resized by this value in every direction.
*/
private static final int GROUP_RECTANGLE_BORDER_MARGIN = 8;
-
/**
* First id value used for generating identifiers during conversion.
*/
private static final int INITIAL_ID_VALUE = 10000;
-
+ /**
+ * Maximum distance between point and rectangle. ???
+ */
+ private static final double DIS_FOR_REP = 9.0;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = LogManager.getLogger(ModelToGPML.class);
/**
* Counter used for generating identifiers if identifiers aren't provided by the
* gpml model.
*/
private int idCounter = INITIAL_ID_VALUE;
-
- /**
- * Maximum distance between point and rectangle. ???
- */
- private static final double DIS_FOR_REP = 9.0;
-
/**
* Parser used to convert from/to xml {@link MiriamData} annotations.
*/
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 1d1e037c73..614829c670 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
@@ -2,15 +2,14 @@ package lcsb.mapviewer.wikipathway.XML;
import java.util.Collection;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import lcsb.mapviewer.wikipathway.model.*;
/**
* Parser class that creates {@link PointData} objects from Xml {@link Element
@@ -21,48 +20,48 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public class PointDataParser extends ElementGpmlParser<PointData> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(PointDataParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.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 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(PointData node) throws ConverterException {
+ throw new NotImplementedException();
+ }
- @Override
- public String toXml(Collection<PointData> list) 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 ec6a06d01e..f2efd4e5da 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
@@ -2,20 +2,16 @@ package lcsb.mapviewer.wikipathway.XML;
import java.util.Collection;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.MinervaLoggerAppender;
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.model.map.*;
import lcsb.mapviewer.wikipathway.model.ReferenceMapping;
/**
@@ -27,136 +23,137 @@ import lcsb.mapviewer.wikipathway.model.ReferenceMapping;
*/
public class ReferenceParser extends ElementGpmlParser<MiriamData> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(ReferenceParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.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);
- }
- }
+ /**
+ * 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;
- }
- }
+ @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;
- }
- }
- }
+ 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;
- }
+ 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(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) {
- MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
- try {
- result.append(toXml(md));
- if (appender.getWarnings().size() > 0) {
- counter--;
- }
- } finally {
- MinervaLoggerAppender.unregisterLogEventStorage(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();
- }
+ @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) {
+ MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
+ try {
+ result.append(toXml(md));
+ if (appender.getWarnings().size() > 0) {
+ counter--;
+ }
+ } finally {
+ MinervaLoggerAppender.unregisterLogEventStorage(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 21aa6c627f..532fdd97c2 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
@@ -4,10 +4,9 @@ import java.awt.font.TextAttribute;
import java.awt.geom.Rectangle2D;
import java.util.Collection;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -26,171 +25,171 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(ShapeParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.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;
- }
- }
+ @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;
- }
+ 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;
- }
- }
+ @Override
+ public String toXml(Shape node) throws ConverterException {
+ throw new NotImplementedException();
+ }
- /**
- * 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(Collection<Shape> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
- @Override
- public String toXml(Shape node) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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;
+ }
+ }
- @Override
- public String toXml(Collection<Shape> list) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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));
+ }
}
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 c31cf5f56b..99deb50bad 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
@@ -2,20 +2,16 @@ package lcsb.mapviewer.wikipathway.XML;
import java.util.Collection;
-import org.apache.logging.log4j.*;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.*;
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;
+import lcsb.mapviewer.wikipathway.model.*;
/**
* Parser class that creates {@link State} objects from Xml {@link Element node}
@@ -26,146 +22,146 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
*/
public class StateParser extends ElementGpmlParser<State> {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(StateParser.class);
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(StateParser.class);
- /**
- * Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
- * references} from GPML model.
- */
- private ReferenceParser referenceParser = new ReferenceParser();
+ /**
+ * 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;
- }
- }
+ @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;
- }
+ 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;
- }
- }
- }
+ @Override
+ public String toXml(State node) throws ConverterException {
+ throw new NotImplementedException();
+ }
- /**
- * 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(Collection<State> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
- @Override
- public String toXml(State node) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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;
+ }
+ }
+ }
- @Override
- public String toXml(Collection<State> list) throws ConverterException {
- throw new NotImplementedException();
- }
+ /**
+ * 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;
+ }
+ }
}
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 f531fc0925..b4d755fd5b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
@@ -3,27 +3,27 @@ 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.
+ * 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);
- }
+ /**
+ *
+ */
+ 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 c070d7c60a..cd281aac89 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownChildClassException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownChildClassException.java
@@ -11,20 +11,19 @@ import lcsb.mapviewer.converter.ConverterException;
*/
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);
- }
+ /**
+ *
+ */
+ 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 6cc97d1d02..27a270b765 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownMergingMethodException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownMergingMethodException.java
@@ -11,19 +11,19 @@ import lcsb.mapviewer.converter.ConverterException;
*/
public class UnknownMergingMethodException extends ConverterException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 1cbdfb96fc..c7465a0f2a 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
@@ -2,4 +2,3 @@
* 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 73f39e5788..480dfef4fe 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
@@ -14,201 +14,201 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
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;
- }
+ /**
+ *
+ */
+ 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 53e55ce336..2fddb3e568 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
@@ -9,72 +9,72 @@ package lcsb.mapviewer.wikipathway.model;
*/
public enum Direction {
- /**
- * North.
- */
- NORTH(Axis.NORTH_SOUTH),
+ /**
+ * North.
+ */
+ NORTH(Axis.NORTH_SOUTH),
- /**
- * East.
- */
- EAST(Axis.EAST_WEST),
+ /**
+ * East.
+ */
+ EAST(Axis.EAST_WEST),
- /**
- * South.
- */
- SOUTH(Axis.NORTH_SOUTH),
+ /**
+ * South.
+ */
+ SOUTH(Axis.NORTH_SOUTH),
- /**
- * West.
- */
- WEST(Axis.EAST_WEST);
+ /**
+ * West.
+ */
+ WEST(Axis.EAST_WEST);
- /**
- * Defines axis in which direction lies (either {@link Axis#NORTH_SOUTH} or
- * {@link Axis#EAST_WEST}).
- */
- private Axis axis;
+ /**
+ * 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;
- }
+ /**
+ * 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).
- */
+ /**
+ * @return the axis
+ * @see #axis
+ */
+ public Axis getAxis() {
+ return axis;
+ }
- EAST_WEST;
- }
+ /**
+ * 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];
+ }
- /**
- * @return the axis
- * @see #axis
- */
- public Axis getAxis() {
- return 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).
+ */
- /**
- * 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];
- }
+ EAST_WEST;
+ }
}
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 062fbb0090..7baa8a54aa 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.wikipathway.model;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashSet;
+import java.util.*;
import java.util.List;
-import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -24,446 +23,448 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
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 = LogManager.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;
- }
+ /**
+ *
+ */
+ 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 = LogManager.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 524c0b7e1a..3775bf5f8e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
@@ -8,128 +8,128 @@ package lcsb.mapviewer.wikipathway.model;
*/
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);
- }
+ /**
+ * 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;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return 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 8eab165591..1fc70aa044 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
@@ -8,66 +8,66 @@ package lcsb.mapviewer.wikipathway.model;
*/
public enum GpmlLineConnectorType {
- /**
- * Line is a curve.
- */
- CURVED("Curved"),
+ /**
+ * Line is a curve.
+ */
+ CURVED("Curved"),
- /**
- * Line is constructed from list of perpendicular segments.
- */
- ELBOW("Elbow"),
+ /**
+ * Line is constructed from list of perpendicular segments.
+ */
+ ELBOW("Elbow"),
- /**
- * It's a straight line from start point to the end point.
- */
- STRAIGHT("Straight"),
+ /**
+ * It's a straight line from start point to the end point.
+ */
+ STRAIGHT("Straight"),
- /**
- * Line is constructoed from list of segement lines.
- */
- SEGMENTED("Segmented");
+ /**
+ * Line is constructoed from list of segement lines.
+ */
+ SEGMENTED("Segmented");
- /**
- * String used in gpml to identify this specific connection type.
- */
- private String gpmlName;
+ /**
+ * 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;
- }
+ /**
+ * 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);
+ }
- /**
- * 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);
- }
+ /**
+ * @return the gpmlName
+ * @see #gpmlName
+ */
+ public String getGpmlName() {
+ return 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 60a07ccd7d..d8fa12c162 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
@@ -9,77 +9,77 @@ import lcsb.mapviewer.model.graphics.LineType;
*
*/
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;
+ /**
+ * Sold line (global representation: {@link LineType#SOLID}).
+ */
+ SOLID(null, LineType.SOLID),
- /**
- * Which {@link LineType} in our model should be used for this GPML line type.
- */
- private LineType correspondingGlobalLineType;
+ /**
+ * Dashed line (global representation: {@link LineType#DASHED}).
+ */
+ DASHED("Broken", LineType.DASHED);
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #gpmlString}
- * @param globalLineType
- * {@link #correspondingGlobalLineType}
- */
- GpmlLineType(String gpmlString, LineType globalLineType) {
- this.gpmlString = gpmlString;
- this.correspondingGlobalLineType = globalLineType;
- }
+ /**
+ * String in GPML format representig this type.
+ */
+ private String gpmlString;
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
+ /**
+ * Which {@link LineType} in our model should be used for this GPML line type.
+ */
+ private LineType correspondingGlobalLineType;
- /**
- * @return the correspondingGlobalLineType
- * @see #correspondingGlobalLineType
- */
- public LineType getCorrespondingGlobalLineType() {
- return correspondingGlobalLineType;
- }
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param globalLineType
+ * {@link #correspondingGlobalLineType}
+ */
+ GpmlLineType(String gpmlString, LineType globalLineType) {
+ this.gpmlString = gpmlString;
+ this.correspondingGlobalLineType = globalLineType;
+ }
- /**
- * 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);
- }
+ /**
+ * 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);
+ }
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * @return the correspondingGlobalLineType
+ * @see #correspondingGlobalLineType
+ */
+ public LineType getCorrespondingGlobalLineType() {
+ return correspondingGlobalLineType;
+ }
}
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 79370f35ab..a0879d2eb7 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
@@ -10,127 +10,126 @@ import lcsb.mapviewer.model.map.species.field.ModificationState;
*/
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;
- }
+ /**
+ * 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);
+
+ /**
+ * 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;
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param correspondingModificationState
+ * {@link #correspondingModificationState}
+ */
+ GpmlModificationType(String gpmlString, ModificationState correspondingModificationState) {
+ this.gpmlString = gpmlString;
+ this.correspondingModificationState = correspondingModificationState;
+ }
+
+ /**
+ * 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 gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * @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 feccb7c7fc..f7a72157c4 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
@@ -8,80 +8,79 @@ package lcsb.mapviewer.wikipathway.model;
*/
public enum GpmlStateType {
- /**
- * Gpml type representing "GTP"
- * {@link lcsb.mapviewer.model.map.species.Protein#structuralState state of
- * Protein}.
- */
- GTP("GTP", "GTP"),
+ /**
+ * 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");
+ /**
+ * 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;
- /**
- * String in GPML format representig this type.
- */
- private String gpmlString;
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param stringRepresenation
+ * {@link #stringRepresenation}
+ */
+ GpmlStateType(String gpmlString, String stringRepresenation) {
+ this.gpmlString = gpmlString;
+ this.stringRepresenation = stringRepresenation;
+ }
- /**
- * String that should be used in our representation.
- */
- private String stringRepresenation;
+ /**
+ * 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 gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
+ /**
+ * @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;
- }
+ /**
+ * @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 e967340cf5..e789c9debc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
@@ -1,17 +1,14 @@
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 java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
-import org.apache.logging.log4j.*;
-
/**
* This class models nodes and reaction from PathVisio for easy(?) conversion to
* Model.
@@ -21,563 +18,562 @@ import org.apache.logging.log4j.*;
*/
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 = LogManager.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;
- }
+ /**
+ *
+ */
+ 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 = LogManager.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 a16f5337f1..2bb2c2bd46 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.wikipathway.model;
-import java.awt.Color;
+import java.awt.*;
import java.awt.font.TextAttribute;
import java.awt.geom.Rectangle2D;
import java.util.HashMap;
@@ -18,236 +18,237 @@ import lcsb.mapviewer.model.graphics.LineType;
*/
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;
- }
+ /**
+ *
+ */
+ 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 954b92053a..16160000c5 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
@@ -11,125 +11,127 @@ import java.util.Set;
*
*/
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;
- }
+
+ /**
+ *
+ */
+ 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 69f9081aa7..563536b9f0 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.wikipathway.model;
-import java.awt.Color;
+import java.awt.*;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashSet;
+import java.util.*;
import java.util.List;
-import java.util.Set;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
@@ -18,373 +16,373 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
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;
- }
+ /**
+ *
+ */
+ 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 d8570ebf06..413dab8be1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
@@ -1,24 +1,9 @@
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;
+import lcsb.mapviewer.model.map.modifier.*;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
/**
* This class contains mapping between gpml interactions and CellDesigner model
@@ -39,476 +24,479 @@ import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
*/
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;
- }
+ /**
+ * 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);
+ }
+
+ /**
+ * 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 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;
+ }
+
+ /**
+ * @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 0f1ff697dc..d6ba71d23c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
@@ -8,165 +8,165 @@ package lcsb.mapviewer.wikipathway.model;
*/
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;
- }
+ /**
+ *
+ */
+ 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 2076bccc08..ec6a8877ec 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
@@ -10,190 +10,190 @@ package lcsb.mapviewer.wikipathway.model;
*/
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;
- }
+ /**
+ * 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 665c44527d..4b0a7263e8 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
@@ -9,9 +9,9 @@ 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
+ * <li>{@link GraphicalPathwayElement}, representing elemnts with some graphical
* representation</li>
- * <li> {@link Group}, representing just groups of elements</li>
+ * <li>{@link Group}, representing just groups of elements</li>
* </ul>
*
* @author Jan Badura
@@ -19,149 +19,147 @@ import java.util.List;
*/
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);
- }
+ /**
+ *
+ */
+ 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;
+ }
+
+ /**
+ * @param graphId
+ * the graphId to set
+ * @see #graphId
+ */
+ void setGraphId(String graphId) {
+ this.graphId = 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();
+
+ /**
+ * 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 c05084ce6c..a651e4af3e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.wikipathway.model;
import java.awt.geom.Point2D;
import java.io.Serializable;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Class that defines infgomration about point stored in gpml structures.
@@ -13,189 +14,190 @@ import org.apache.logging.log4j.*;
*/
public class PointData implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Defdault clas logger.
- */
- private final transient Logger logger = LogManager.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;
- }
- }
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Defdault clas logger.
+ */
+ private final transient Logger logger = LogManager.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 9db45a737d..e0067fabbd 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
@@ -11,260 +11,260 @@ import lcsb.mapviewer.model.map.MiriamType;
*/
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;
- }
+ /**
+ * {@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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public MiriamType getType() {
+ return type;
+ }
}
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 db68dc2c69..8755fc2ebc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
@@ -8,217 +8,217 @@ package lcsb.mapviewer.wikipathway.model;
*/
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;
- }
+ /**
+ *
+ */
+ 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;
+ }
+
+ @Override
+ public String getWarningPrefix() {
+ return "[" + getShape() + " " + getGraphId() + "]\t";
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * @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 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 7447a82d5f..23bdb2e653 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
@@ -17,243 +17,245 @@ import lcsb.mapviewer.model.map.species.field.ModificationState;
*/
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;
- }
+ /**
+ *
+ */
+ 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 f648725fbb..a5af942d9b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/UnknownTypeException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/UnknownTypeException.java
@@ -10,19 +10,19 @@ import lcsb.mapviewer.converter.ConverterException;
*/
public class UnknownTypeException extends ConverterException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ 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);
- }
+ /**
+ * 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 3cd84eb8e5..48b8c782c2 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
@@ -1,15 +1,12 @@
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 java.util.*;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.*;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
/**
* Element containg all biopax information parsed from gpml file.
@@ -19,74 +16,74 @@ import org.apache.logging.log4j.*;
*/
public class BiopaxData implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final transient Logger logger = LogManager.getLogger(BiopaxData.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final transient Logger logger = LogManager.getLogger(BiopaxData.class);
- /**
- * List of {@link BiopaxPublication publications}.
- */
- private Map<String, BiopaxPublication> publications = new HashMap<String, BiopaxPublication>();
+ /**
+ * 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>();
+ /**
+ * 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();
- }
+ /**
+ * @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);
- }
+ /**
+ * @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);
- }
+ /**
+ * 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;
- }
+ /**
+ * @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);
- }
+ /**
+ * @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 53804781d7..e7aabeee53 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
@@ -10,76 +10,75 @@ import java.io.Serializable;
*
*/
public class BiopaxOpenControlledVocabulary implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * ???
- */
- private String id;
-
- /**
- * ???
- */
- private String term;
-
- /**
- * ???
- */
- private String ontology;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * @return the id
- * @see #id
- */
- public String getId() {
- return id;
- }
+ /**
+ * ???
+ */
+ private String id;
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(String id) {
- this.id = id;
- }
+ /**
+ * ???
+ */
+ private String term;
- /**
- * @return the term
- * @see #term
- */
- public String getTerm() {
- return term;
- }
+ /**
+ * ???
+ */
+ private String ontology;
- /**
- * @param term
- * the term to set
- * @see #term
- */
- public void setTerm(String term) {
- this.term = term;
- }
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * @return the ontology
- * @see #ontology
- */
- public String getOntology() {
- return ontology;
- }
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
- /**
- * @param ontology
- * the ontology to set
- * @see #ontology
- */
- public void setOntology(String ontology) {
- this.ontology = ontology;
- }
+ /**
+ * @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 cb561ad58e..7960830511 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
@@ -9,164 +9,163 @@ import java.io.Serializable;
*
*/
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;
- }
+
+ /**
+ *
+ */
+ 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 fd3c232c66..59a6d62ae6 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
@@ -4,4 +4,3 @@
*
*/
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 bd59db6b13..64a4c19f86 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
@@ -2,14 +2,13 @@
* 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
+ * <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} -
+ * <li>{@link lcsb.mapviewer.wikipathway.model.Interaction Interaction} -
* description of single interaction in the model,</li>
- * <li> {@link lcsb.mapviewer.wikipathway.model.PathwayElement PathwayElement} -
+ * <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 24f302e3bc..fa582dca17 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/package-info.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/package-info.java
@@ -2,9 +2,9 @@
* 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>.
+ * 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 3101d56c6f..71d92007b1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.wikipathway.utils;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
+import java.awt.geom.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -16,311 +14,312 @@ import lcsb.mapviewer.model.graphics.PolylineData;
*/
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;
- }
+ /**
+ * 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 491c5ebef4..52d16874d7 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
@@ -2,4 +2,3 @@
* 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 fee29d20bc..281011ebeb 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
@@ -9,13 +9,13 @@ 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,
+ 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 6cbde646a3..2569ea3c2f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.wikipathway;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
index 097555f416..4e9b4a2cd5 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.wikipathway;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Line2D;
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
index fd2df0a77e..8143060695 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
@@ -1,61 +1,38 @@
package lcsb.mapviewer.wikipathway;
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-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.io.*;
import java.net.URL;
import java.net.URLConnection;
import java.nio.charset.StandardCharsets;
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.parsers.*;
+import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.junit.*;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.w3c.dom.*;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
+import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
public abstract class WikipathwaysTestFunctions {
- private Logger logger = LogManager.getLogger(WikipathwaysTestFunctions.class);
-
+ protected static double EPSILON = Configuration.EPSILON;
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
- protected static double EPSILON = Configuration.EPSILON;
-
+ private Logger logger = LogManager.getLogger(WikipathwaysTestFunctions.class);
private DocumentBuilder db;
private MinervaLoggerAppender appender;
@@ -241,7 +218,7 @@ public abstract class WikipathwaysTestFunctions {
protected Model serializeModelOverCellDesignerParser(Model model1)
throws InconsistentModelException, InvalidInputDataExecption {
- for (BioEntity bioEntity: model1.getBioEntities()) {
+ for (BioEntity bioEntity : model1.getBioEntities()) {
bioEntity.setZ(null);
}
new ZIndexPopulator().populateZIndex(model1);
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 563d471d1f..f52b49dddb 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
@@ -6,16 +6,16 @@ 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,
+ 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/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index f4036a7d22..c77b5b4552 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.wikipathway.XML;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import java.io.FileInputStream;
@@ -16,6 +16,7 @@ import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
public class BugTest extends WikipathwaysTestFunctions {
Logger logger = LogManager.getLogger(BugTest.class);
+ private ModelComparator mc = new ModelComparator(1.0);
@Test
public void testBug319() throws Exception {
@@ -25,8 +26,6 @@ public class BugTest extends WikipathwaysTestFunctions {
assertEquals(1, getWarnings().size());
}
- private ModelComparator mc = new ModelComparator(1.0);
-
@Test
public void testBug328() throws Exception {
String filename = "testFiles/bugs/error_328.gpml";
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 42428c7f96..2f44e6873d 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.wikipathway.XML;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import java.awt.Color;
+import java.awt.*;
import java.util.Collection;
import org.junit.*;
@@ -16,7 +16,7 @@ public class ElementGpmlParserTest extends WikipathwaysTestFunctions {
ElementGpmlParser<Object> parser = new ElementGpmlParser<Object>() {
@Override
- public String toXml(Collection<Object> list) throws ConverterException {
+ public Object parse(Element node) throws ConverterException {
throw new NotImplementedException();
}
@@ -26,7 +26,7 @@ public class ElementGpmlParserTest extends WikipathwaysTestFunctions {
}
@Override
- public Object parse(Element node) throws ConverterException {
+ public String toXml(Collection<Object> list) throws ConverterException {
throw new NotImplementedException();
}
};
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 2cd7b571ad..14f6aeb0f9 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.wikipathway.XML;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.junit.*;
import org.w3c.dom.Element;
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 ea147500f9..2d960c9302 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.wikipathway.XML;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
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 0f351c613d..385d524ffe 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.wikipathway.XML;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
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 85605eee81..11c6fb1cf4 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.wikipathway.XML;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import org.junit.After;
import org.junit.Test;
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 1446fc6e25..4f8a696a79 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.wikipathway.XML;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.junit.After;
import org.junit.Test;
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 940702b474..59cc0c9ddb 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;
+import lcsb.mapviewer.wikipathway.model.biopax.AllBiopaxTests;
+
@RunWith(Suite.class)
@SuiteClasses({ AllBiopaxTests.class,
- DataNodeTest.class,
- EdgeTest.class,
- GraphTest.class,
- GroupTest.class,
- InteractionTest.class,
- LabelTest.class,
- PointDataTest.class,
- ShapeTest.class,
- StateTest.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/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java b/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
index 5d898b0ee0..c480231a2a 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
@@ -22,55 +22,56 @@ import org.springframework.context.support.ClassPathXmlApplicationContext;
*/
public final class ApplicationContextLoader {
- /**
- * Application context used by the application.
- */
- private static ConfigurableApplicationContext applicationContext;
+ /**
+ * Application context used by the application.
+ */
+ private static ConfigurableApplicationContext applicationContext;
- /**
- * Default constructor. Prevents instatiation.
- */
- private ApplicationContextLoader() {
+ /**
+ * Default constructor. Prevents instatiation.
+ */
+ private ApplicationContextLoader() {
- }
+ }
- /**
- *
- * @return {@link #applicationContext}
- */
- public static ConfigurableApplicationContext getApplicationContext() {
- return applicationContext;
- }
+ /**
+ *
+ * @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();
- }
+ /**
+ *
+ * @param applicationContext
+ * {@link #applicationContext} to set
+ */
+ public static void setApplicationContext(ConfigurableApplicationContext applicationContext) {
+ ApplicationContextLoader.applicationContext = applicationContext;
+ }
- /**
- * 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);
- }
+ /**
+ * 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();
+ }
- /**
- *
- * @param applicationContext
- * {@link #applicationContext} to set
- */
- public static void setApplicationContext(ConfigurableApplicationContext applicationContext) {
- ApplicationContextLoader.applicationContext = applicationContext;
- }
+ /**
+ * 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);
+ }
}
\ No newline at end of file
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/ConfigurationHolder.java b/persist/src/main/java/lcsb/mapviewer/persist/ConfigurationHolder.java
index 3cb7f0f5bb..4109640856 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/ConfigurationHolder.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/ConfigurationHolder.java
@@ -7,41 +7,41 @@ import org.springframework.stereotype.Service;
@Service
@PropertySources({
- @PropertySource("classpath:db.properties"),
- @PropertySource(value = "file:/etc/minerva/db.properties", ignoreResourceNotFound = true)
+ @PropertySource("classpath:db.properties"),
+ @PropertySource(value = "file:/etc/minerva/db.properties", ignoreResourceNotFound = true)
})
public class ConfigurationHolder {
- @Value("${database.uri}")
- private String dbUri;
+ @Value("${database.uri}")
+ private String dbUri;
- @Value("${database.username}")
- private String dbUsername;
+ @Value("${database.username}")
+ private String dbUsername;
- @Value("${database.password}")
- private String dbPassword;
+ @Value("${database.password}")
+ private String dbPassword;
- public String getDbUri() {
- return dbUri;
- }
+ public String getDbUri() {
+ return dbUri;
+ }
- public void setDbUri(String dbUri) {
- this.dbUri = dbUri;
- }
+ public void setDbUri(String dbUri) {
+ this.dbUri = dbUri;
+ }
- public String getDbUsername() {
- return dbUsername;
- }
+ public String getDbUsername() {
+ return dbUsername;
+ }
- public void setDbUsername(String dbUsername) {
- this.dbUsername = dbUsername;
- }
+ public void setDbUsername(String dbUsername) {
+ this.dbUsername = dbUsername;
+ }
- public String getDbPassword() {
- return dbPassword;
- }
+ public String getDbPassword() {
+ return dbPassword;
+ }
- public void setDbPassword(String dbPassword) {
- this.dbPassword = dbPassword;
- }
+ public void setDbPassword(String dbPassword) {
+ this.dbPassword = dbPassword;
+ }
}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java b/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java
index 145bb45498..a2aae037b9 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.persist;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.boot.model.naming.Identifier;
import org.hibernate.boot.model.naming.ImplicitEntityNameSource;
import org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy;
@@ -17,10 +18,8 @@ public class CustomImplicitNamingStrategy extends SpringImplicitNamingStrategy {
*
*/
private static final long serialVersionUID = 1L;
-
- Logger logger = LogManager.getLogger(CustomImplicitNamingStrategy.class);
-
private static final String TABLE_NAME_SUFFIX = "Table";
+ Logger logger = LogManager.getLogger(CustomImplicitNamingStrategy.class);
@Override
public Identifier determinePrimaryTableName(ImplicitEntityNameSource source) {
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
index 5225b1ca80..535d6848e4 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.persist;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Observable;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -37,18 +35,11 @@ public class DbUtils extends Observable {
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(DbUtils.class);
-
- /**
- * Hibernate session factory.
- */
- private SessionFactory sessionFactory;
-
/**
* 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:
@@ -60,6 +51,10 @@ public class DbUtils extends Observable {
* </ol>
*/
private static Map<Long, Boolean> autoFlushForThread = new HashMap<>();
+ /**
+ * Hibernate session factory.
+ */
+ private SessionFactory sessionFactory;
/**
* Constructor
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java b/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java
index 8b87a2a294..bbc5ea6c6b 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.persist;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Component;
@@ -17,52 +18,52 @@ import org.springframework.transaction.annotation.Transactional;
@Component
public class SpringApplicationContext implements ApplicationContextAware {
- /**
- * Default logger for this class.
- */
- private static Logger logger = LogManager.getLogger(SpringApplicationContext.class);
+ /**
+ * Default logger for this class.
+ */
+ private static Logger logger = LogManager.getLogger(SpringApplicationContext.class);
- /**
- * {@link ApplicationContext} used by the Spring framework.
- */
- private static ApplicationContext context;
+ /**
+ * {@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) {
+ beanName = beanName.substring(0, 1).toLowerCase() + beanName.substring(1);
+ return context.getBean(beanName);
+ }
+
+ /**
+ *
+ * @return {@link #context}
+ */
+ public static ApplicationContext getApplicationContext() {
+ return 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) {
- beanName = beanName.substring(0, 1).toLowerCase() + beanName.substring(1);
- 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/SpringPersistConfig.java b/persist/src/main/java/lcsb/mapviewer/persist/SpringPersistConfig.java
index 546335ef10..06918a4891 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/SpringPersistConfig.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/SpringPersistConfig.java
@@ -1,73 +1,73 @@
package lcsb.mapviewer.persist;
-import com.zaxxer.hikari.HikariDataSource;
+import java.util.Properties;
+
+import javax.sql.DataSource;
+
import org.hibernate.SessionFactory;
import org.hibernate.cfg.Environment;
import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.*;
import org.springframework.jdbc.datasource.init.DataSourceInitializer;
import org.springframework.jdbc.datasource.init.DatabasePopulator;
import org.springframework.orm.hibernate5.HibernateTransactionManager;
import org.springframework.orm.hibernate5.LocalSessionFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
-import javax.sql.DataSource;
-import java.util.Properties;
+import com.zaxxer.hikari.HikariDataSource;
@Configuration
@EnableTransactionManagement
-@ComponentScan(basePackages = {"lcsb.mapviewer.persist"})
+@ComponentScan(basePackages = { "lcsb.mapviewer.persist" })
public class SpringPersistConfig {
- @Bean
- public ConfigurationHolder config() {
- return new ConfigurationHolder();
- }
+ @Bean
+ public ConfigurationHolder config() {
+ return new ConfigurationHolder();
+ }
- @Bean(destroyMethod = "close")
- public HikariDataSource dataSource(ConfigurationHolder config) {
- HikariDataSource dataSource = new HikariDataSource();
- dataSource.setDriverClassName("org.postgresql.Driver");
- dataSource.setJdbcUrl(config.getDbUri());
- dataSource.setUsername(config.getDbUsername());
- dataSource.setPassword(config.getDbPassword());
- dataSource.setIdleTimeout(30000);
- dataSource.setMaximumPoolSize(40);
- dataSource.setMinimumIdle(10);
- dataSource.setConnectionTestQuery("select 1");
- return dataSource;
- }
+ @Bean(destroyMethod = "close")
+ public HikariDataSource dataSource(ConfigurationHolder config) {
+ HikariDataSource dataSource = new HikariDataSource();
+ dataSource.setDriverClassName("org.postgresql.Driver");
+ dataSource.setJdbcUrl(config.getDbUri());
+ dataSource.setUsername(config.getDbUsername());
+ dataSource.setPassword(config.getDbPassword());
+ dataSource.setIdleTimeout(30000);
+ dataSource.setMaximumPoolSize(40);
+ dataSource.setMinimumIdle(10);
+ dataSource.setConnectionTestQuery("select 1");
+ return dataSource;
+ }
- @Bean
- public LocalSessionFactoryBean sessionFactory(DataSource dataSource) {
- Properties props = new Properties();
- props.setProperty(Environment.DIALECT, "org.hibernate.dialect.PostgreSQL95Dialect");
- props.setProperty(Environment.SHOW_SQL, "false");
- LocalSessionFactoryBean factoryBean = new LocalSessionFactoryBean();
- factoryBean.setDataSource(dataSource);
- factoryBean.setHibernateProperties(props);
- factoryBean.setPackagesToScan("lcsb.mapviewer.model");
- factoryBean.setImplicitNamingStrategy(new CustomImplicitNamingStrategy());
- factoryBean.setPhysicalNamingStrategy(new SpringPhysicalNamingStrategy());
- return factoryBean;
- }
+ @Bean
+ public LocalSessionFactoryBean sessionFactory(DataSource dataSource) {
+ Properties props = new Properties();
+ props.setProperty(Environment.DIALECT, "org.hibernate.dialect.PostgreSQL95Dialect");
+ props.setProperty(Environment.SHOW_SQL, "false");
+ LocalSessionFactoryBean factoryBean = new LocalSessionFactoryBean();
+ factoryBean.setDataSource(dataSource);
+ factoryBean.setHibernateProperties(props);
+ factoryBean.setPackagesToScan("lcsb.mapviewer.model");
+ factoryBean.setImplicitNamingStrategy(new CustomImplicitNamingStrategy());
+ factoryBean.setPhysicalNamingStrategy(new SpringPhysicalNamingStrategy());
+ return factoryBean;
+ }
- @Bean
- public HibernateTransactionManager transactionManager(SessionFactory sessionFactory) {
- HibernateTransactionManager transactionManager = new HibernateTransactionManager();
- transactionManager.setSessionFactory(sessionFactory);
- return transactionManager;
- }
+ @Bean
+ public HibernateTransactionManager transactionManager(SessionFactory sessionFactory) {
+ HibernateTransactionManager transactionManager = new HibernateTransactionManager();
+ transactionManager.setSessionFactory(sessionFactory);
+ return transactionManager;
+ }
- @Bean
- public DataSourceInitializer dataSourceInitializer(DataSource dataSource, DatabasePopulator databasePopulator) {
- DataSourceInitializer initializer = new DataSourceInitializer();
- initializer.setDataSource(dataSource);
- initializer.setDatabasePopulator(databasePopulator);
- initializer.setEnabled(true);
- return initializer;
- }
+ @Bean
+ public DataSourceInitializer dataSourceInitializer(DataSource dataSource, DatabasePopulator databasePopulator) {
+ DataSourceInitializer initializer = new DataSourceInitializer();
+ initializer.setDataSource(dataSource);
+ initializer.setDatabasePopulator(databasePopulator);
+ initializer.setEnabled(true);
+ return initializer;
+ }
}
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 3ccc22f2a8..5cb391fb19 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
@@ -2,9 +2,7 @@ package lcsb.mapviewer.persist.dao;
import java.util.List;
-import javax.persistence.criteria.CriteriaBuilder;
-import javax.persistence.criteria.CriteriaQuery;
-import javax.persistence.criteria.Root;
+import javax.persistence.criteria.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -46,10 +44,16 @@ public abstract class BaseDao<T> {
* Class of the object that DAO works on.
*/
private Class<T> clazz;
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
/**
* Default constructor.
- *
+ *
* @param theClass
* class of the object that DAO will work on
*/
@@ -59,27 +63,20 @@ public abstract class BaseDao<T> {
/**
* 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<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.
*
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 244f38544f..f28d3fa6d0 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/ConfigurationDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/ConfigurationDao.java
@@ -1,9 +1,10 @@
package lcsb.mapviewer.persist.dao;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
import org.springframework.stereotype.Repository;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+
/**
* Data access object class for Configuration objects.
*
@@ -13,42 +14,41 @@ import org.springframework.stereotype.Repository;
@Repository
public class ConfigurationDao extends BaseDao<ConfigurationOption> {
- /**
- * Default constructor.
- */
- public ConfigurationDao() {
- super(ConfigurationOption.class);
- }
+ /**
+ * 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 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();
- }
- }
+ /**
+ * 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/cache/BigFileEntryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDao.java
index fca6757cfb..fb3466fdd9 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
@@ -2,11 +2,12 @@ package lcsb.mapviewer.persist.dao.cache;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Repository;
import lcsb.mapviewer.model.cache.BigFileEntry;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for cached values.
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 b5b63df58e..bf3dc41300 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
@@ -2,10 +2,11 @@ package lcsb.mapviewer.persist.dao.cache;
import java.util.List;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.cache.CacheQuery;
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for cached values.
@@ -15,46 +16,47 @@ import org.springframework.stereotype.Repository;
*/
@Repository
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());
- }
+
+ /**
+ * 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 9f92af8c70..1c7f5263ed 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
@@ -2,12 +2,13 @@ package lcsb.mapviewer.persist.dao.cache;
import java.util.List;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.apache.logging.log4j.*;
-import org.springframework.stereotype.Repository;
-
/**
* Data access object for cached values.
*
@@ -16,32 +17,32 @@ import org.springframework.stereotype.Repository;
*/
@Repository
public class CacheTypeDao extends BaseDao<CacheType> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(CacheTypeDao.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(CacheTypeDao.class);
- /**
- * Default constructor.
- */
- public CacheTypeDao() {
- super(CacheType.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);
- }
+ /**
+ * 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 897c5a5fc3..76abc6bcfe 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
@@ -1,10 +1,11 @@
package lcsb.mapviewer.persist.dao.cache;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Repository;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for cached values.
@@ -14,23 +15,23 @@ import org.springframework.stereotype.Repository;
*/
@Repository
public class UploadedFileEntryDao extends BaseDao<UploadedFileEntry> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(UploadedFileEntryDao.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(UploadedFileEntryDao.class);
- /**
- * Default constructor.
- */
- public UploadedFileEntryDao() {
- super(UploadedFileEntry.class, "removed");
- }
+ /**
+ * Default constructor.
+ */
+ public UploadedFileEntryDao() {
+ super(UploadedFileEntry.class, "removed");
+ }
- @Override
- public void delete(UploadedFileEntry entry) {
- entry.setRemoved(true);
- update(entry);
- }
+ @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 f2f2f5f53c..6f912da125 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
@@ -2,4 +2,3 @@
* 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 2f428b692f..aefd24ce5d 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.persist.dao.graphics;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for {@link PolylineDao} class.
@@ -13,11 +14,11 @@ import org.springframework.stereotype.Repository;
@Repository
public class PolylineDao extends BaseDao<PolylineData> {
- /**
- * Default constructor.
- */
- public PolylineDao() {
- super(PolylineData.class);
- }
+ /**
+ * 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 ae5ee40a47..87d3b407ab 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
@@ -2,4 +2,3 @@
* 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/map/CommentDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/CommentDao.java
index 64535fe2f2..b8150dcb89 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
@@ -3,14 +3,15 @@ package lcsb.mapviewer.persist.dao.map;
import java.util.ArrayList;
import java.util.List;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Repository;
+
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.logging.log4j.*;
-import org.springframework.stereotype.Repository;
-
/**
* Data access object class for Comment objects.
*
@@ -19,117 +20,117 @@ import org.springframework.stereotype.Repository;
*/
@Repository
public class CommentDao extends BaseDao<Comment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(CommentDao.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(CommentDao.class);
- /**
- * Default constructor.
- */
- public CommentDao() {
- super(Comment.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 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_id", modelId);
- List<Comment> result = new ArrayList<Comment>();
- if (deleted != null) {
- for (Comment comment : comments) {
- if (comment.isDeleted() == deleted) {
- result.add(comment);
- }
- }
- } else {
- result = comments;
- }
+ /**
+ * 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_id", 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;
- }
+ 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);
- }
+ /**
+ * 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 5190ed5644..dcced37ff2 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
@@ -2,9 +2,7 @@ package lcsb.mapviewer.persist.dao.map;
import java.util.List;
-import javax.persistence.criteria.CriteriaBuilder;
-import javax.persistence.criteria.CriteriaQuery;
-import javax.persistence.criteria.Root;
+import javax.persistence.criteria.*;
import org.springframework.stereotype.Repository;
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 0d027da0fe..28b9f7f15f 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
@@ -2,13 +2,14 @@ package lcsb.mapviewer.persist.dao.map;
import java.util.List;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.apache.logging.log4j.*;
-import org.springframework.stereotype.Repository;
-
/**
* Data access object for {@link Model} class.
*
@@ -17,97 +18,97 @@ import org.springframework.stereotype.Repository;
*/
@Repository
public class ModelDao extends BaseDao<ModelData> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(ModelDao.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(ModelDao.class);
- /**
- * Default constructor.
- */
- public ModelDao() {
- super(ModelData.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 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;
- }
+ @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;
- }
- }
+ /**
+ * 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());
- }
+ /**
+ * 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());
- }
+ /**
+ * 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());
- }
+ /**
+ * "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());
- }
+ /**
+ * 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 e247e2ae12..1fb5802dc8 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.persist.dao.map;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for {@link Reaction} class.
@@ -13,11 +14,11 @@ import org.springframework.stereotype.Repository;
@Repository
public class ReactionDao extends BaseDao<Reaction> {
- /**
- * Default constructor.
- */
- public ReactionDao() {
- super(Reaction.class);
- }
+ /**
+ * 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 1d97a7c509..09e8415561 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
@@ -2,10 +2,11 @@ package lcsb.mapviewer.persist.dao.map.layout;
import java.util.List;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for {@link ReferenceGenome} objects.
@@ -16,22 +17,22 @@ import org.springframework.stereotype.Repository;
@Repository
public class ReferenceGenomeDao extends BaseDao<ReferenceGenome> {
- /**
- * Default constructor.
- */
- public ReferenceGenomeDao() {
- super(ReferenceGenome.class);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 603763c4af..57b2596140 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.persist.dao.map.layout;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for {@link ReferenceGenomeGeneMapping} objects.
@@ -13,11 +14,11 @@ import org.springframework.stereotype.Repository;
@Repository
public class ReferenceGenomeGeneMappingDao extends BaseDao<ReferenceGenomeGeneMapping> {
- /**
- * Default constructor.
- */
- public ReferenceGenomeGeneMappingDao() {
- super(ReferenceGenomeGeneMapping.class);
- }
+ /**
+ * 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 522503b60b..d3a51d7c5e 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
@@ -2,4 +2,3 @@
* 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 4a4870b438..3ac42df8f3 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
@@ -2,4 +2,3 @@
* 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 b7dabc2922..8f6b494960 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.persist.dao.map.species;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data Access Object class for Alias class.
@@ -13,11 +14,11 @@ import org.springframework.stereotype.Repository;
@Repository
public class ElementDao extends BaseDao<Element> {
- /**
- * Default constructor.
- */
- public ElementDao() {
- super(Element.class);
- }
+ /**
+ * 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 0f52154a77..74d87ba037 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
@@ -2,4 +2,3 @@
* 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 ccb94767c2..367b79f605 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
@@ -1,11 +1,12 @@
package lcsb.mapviewer.persist.dao.map.statistics;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.map.statistics.SearchHistory;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.apache.logging.log4j.*;
-import org.springframework.stereotype.Repository;
-
/**
* Data access object for {@link SearchHistory} class.
*
@@ -14,17 +15,17 @@ import org.springframework.stereotype.Repository;
*/
@Repository
public class SearchHistoryDao extends BaseDao<SearchHistory> {
- /**
- * Default constructor.
- */
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger(SearchHistoryDao.class);
+ /**
+ * Default constructor.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger(SearchHistoryDao.class);
- /**
- * Default constructor.
- */
- public SearchHistoryDao() {
- super(SearchHistory.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 9330947661..c3acfb04c8 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
@@ -2,4 +2,3 @@
* 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 b16509a62e..58ddacd73b 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
@@ -2,4 +2,3 @@
* 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 353d1b08c6..492fa92d29 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
@@ -1,8 +1,9 @@
package lcsb.mapviewer.persist.dao.plugin;
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.model.plugin.Plugin;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object class for {@link Plugin} objects.
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 e4c8acb74f..7d86a2da96 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
@@ -3,12 +3,13 @@ package lcsb.mapviewer.persist.dao.plugin;
import java.util.ArrayList;
import java.util.List;
+import org.springframework.stereotype.Repository;
+
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;
-import org.springframework.stereotype.Repository;
/**
* Data access object class for {@link PluginDataEntry} objects.
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/security/PrivilegeDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/security/PrivilegeDao.java
index 2ec5436193..9c5acdf318 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/security/PrivilegeDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/security/PrivilegeDao.java
@@ -1,12 +1,14 @@
package lcsb.mapviewer.persist.dao.security;
+import java.util.Arrays;
+import java.util.List;
+
+import org.springframework.stereotype.Repository;
+
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.security.Privilege;
import lcsb.mapviewer.model.security.PrivilegeType;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
-
-import java.util.*;
@Repository
public class PrivilegeDao extends BaseDao<Privilege> {
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 9359eba087..4ea490640d 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
@@ -1,10 +1,9 @@
package lcsb.mapviewer.persist.dao.user;
-import java.util.List;
+import org.springframework.stereotype.Repository;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
@Repository
public class UserDao extends BaseDao<User> {
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 5718df5478..62c5cf4723 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
@@ -2,4 +2,3 @@
* 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/ArrowTypeDataMapper.java b/persist/src/main/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapper.java
index 9b6253809a..d01c888be9 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapper.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapper.java
@@ -2,9 +2,7 @@ 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 java.sql.*;
import org.hibernate.HibernateException;
import org.hibernate.engine.spi.SharedSessionContractImplementor;
@@ -12,9 +10,7 @@ import org.hibernate.type.StringType;
import org.hibernate.type.Type;
import org.hibernate.usertype.CompositeUserType;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.*;
/**
* This class allows to put {@link Point2D} objects into hibernate based models.
@@ -45,10 +41,6 @@ public class ArrowTypeDataMapper implements CompositeUserType {
return returnValue;
}
- private String arrowTypeDataToString(final ArrowTypeData atd) {
- return atd.getAngle() + ";" + atd.getLen() + ";" + atd.getArrowType().name() + ";" + atd.getArrowLineType();
- }
-
@Override
public void setPropertyValue(Object component, int property, Object value) {
final ArrowTypeData atd = (ArrowTypeData) component;
@@ -81,21 +73,6 @@ public class ArrowTypeDataMapper implements CompositeUserType {
return x.hashCode();
}
- @Override
- public Object deepCopy(Object value) {
- if (value == null) {
- return null;
- }
- final ArrowTypeData receivedParam = (ArrowTypeData) value;
- final ArrowTypeData point = receivedParam.copy();
- return point;
- }
-
- @Override
- public boolean isMutable() {
- return true;
- }
-
@Override
public Object nullSafeGet(ResultSet rs, String[] names, SharedSessionContractImplementor session, Object owner)
throws HibernateException, SQLException {
@@ -107,14 +84,6 @@ public class ArrowTypeDataMapper implements CompositeUserType {
return atd;
}
- private void assignSerializedProperties(ArrowTypeData atd, final String val) {
- final String[] values = val.split(";");
- atd.setAngle(Double.parseDouble(values[0]));
- atd.setLen(Double.parseDouble(values[1]));
- atd.setArrowType(ArrowType.valueOf(values[2]));
- atd.setArrowLineType(LineType.valueOf(values[3]));
- }
-
@Override
public void nullSafeSet(PreparedStatement st, Object value, int index, SharedSessionContractImplementor session)
throws HibernateException, SQLException {
@@ -126,6 +95,21 @@ public class ArrowTypeDataMapper implements CompositeUserType {
}
}
+ @Override
+ public Object deepCopy(Object value) {
+ if (value == null) {
+ return null;
+ }
+ final ArrowTypeData receivedParam = (ArrowTypeData) value;
+ final ArrowTypeData point = receivedParam.copy();
+ return point;
+ }
+
+ @Override
+ public boolean isMutable() {
+ return true;
+ }
+
@Override
public Serializable disassemble(Object value, SharedSessionContractImplementor session) throws HibernateException {
return (Serializable) value;
@@ -143,4 +127,16 @@ public class ArrowTypeDataMapper implements CompositeUserType {
return this.deepCopy(original);
}
+ private String arrowTypeDataToString(final ArrowTypeData atd) {
+ return atd.getAngle() + ";" + atd.getLen() + ";" + atd.getArrowType().name() + ";" + atd.getArrowLineType();
+ }
+
+ private void assignSerializedProperties(ArrowTypeData atd, final String val) {
+ final String[] values = val.split(";");
+ atd.setAngle(Double.parseDouble(values[0]));
+ atd.setLen(Double.parseDouble(values[1]));
+ atd.setArrowType(ArrowType.valueOf(values[2]));
+ atd.setArrowLineType(LineType.valueOf(values[3]));
+ }
+
}
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 9c1b536705..83ffb5b908 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
@@ -2,9 +2,7 @@ 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 java.sql.*;
import org.hibernate.HibernateException;
import org.hibernate.engine.spi.SharedSessionContractImplementor;
@@ -73,21 +71,6 @@ public class Point2DMapper implements CompositeUserType {
return x.hashCode();
}
- @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 Object nullSafeGet(ResultSet rs, String[] names, SharedSessionContractImplementor session, Object owner)
throws HibernateException, SQLException {
@@ -111,6 +94,21 @@ public class Point2DMapper implements CompositeUserType {
}
}
+ @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, SharedSessionContractImplementor session) throws HibernateException {
return (Serializable) value;
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 1cd2295a41..449e09f70c 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
@@ -2,4 +2,3 @@
* 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/migration/V14_0_0_20190701__bcrypt_passwords.java b/persist/src/main/java/lcsb/mapviewer/persist/migration/V14_0_0_20190701__bcrypt_passwords.java
index 95fc8f9e22..d24de9c4ee 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/migration/V14_0_0_20190701__bcrypt_passwords.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/migration/V14_0_0_20190701__bcrypt_passwords.java
@@ -1,12 +1,12 @@
package lcsb.mapviewer.persist.migration;
+import java.sql.ResultSet;
+import java.sql.Statement;
+
import org.flywaydb.core.api.migration.BaseJavaMigration;
import org.flywaydb.core.api.migration.Context;
import org.springframework.security.crypto.bcrypt.BCrypt;
-import java.sql.ResultSet;
-import java.sql.Statement;
-
public class V14_0_0_20190701__bcrypt_passwords extends BaseJavaMigration {
@Override
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 0f558d88ba..21c502bed1 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/package-info.java
@@ -3,4 +3,3 @@
* stored in database.
*/
package lcsb.mapviewer.persist;
-
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java b/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java
index a8394a73a6..3bee2e142f 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.persist;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.lang.reflect.Constructor;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java b/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java
index e7144712bf..1048c09f89 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java
@@ -10,10 +10,9 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.common.exception.InvalidStateException;
public class DbUtilsTest extends PersistTestFunctions {
- Logger logger = LogManager.getLogger(DbUtilsTest.class);
-
@Autowired
protected DbUtils dbUtils;
+ Logger logger = LogManager.getLogger(DbUtilsTest.class);
@Test
public void testCreateSession() throws Exception {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/InitialStateTest.java b/persist/src/test/java/lcsb/mapviewer/persist/InitialStateTest.java
index 950cbe3777..3897f40df2 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/InitialStateTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/InitialStateTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.persist;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
-import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
index f49eea32e4..12d8772d46 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.persist;
-import java.awt.Color;
+import java.awt.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -34,25 +34,17 @@ public abstract class PersistTestFunctions {
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(PersistTestFunctions.class);
-
- PointTransformation pt = new PointTransformation();
-
public double EPSILON = 1e-6;
-
@Autowired
protected ProjectDao projectDao;
-
@Autowired
protected ModelDao modelDao;
-
@Autowired
protected UserDao userDao;
-
protected int identifierCounter = 0;
-
+ PointTransformation pt = new PointTransformation();
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(PersistTestFunctions.class);
private int zIndex = 0;
protected User createUser() {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java b/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java
index 30dae41a84..2a0b2a0127 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java
@@ -1,29 +1,27 @@
package lcsb.mapviewer.persist;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
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"));
- }
+ @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/ConfigurationDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java
index ab254f8846..e40ed5d5c5 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java
@@ -3,9 +3,7 @@ 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.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.model.user.ConfigurationElementType;
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 774531dd15..68d002731f 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
@@ -6,9 +6,9 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ BigFileEntryDaoTest.class,
- CacheTypeDaoTest.class,
- CacheQueryDaoTest.class,
- UploadedFileEntryDaoTest.class,
+ CacheTypeDaoTest.class,
+ CacheQueryDaoTest.class,
+ UploadedFileEntryDaoTest.class,
})
public class AllCacheDbTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java
index c0bd4dea7e..80a27be126 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.persist.dao.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
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 5cbb5ee9c0..067005709e 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.persist.dao.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
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 77b22f20f1..c29ceff111 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.persist.dao.cache;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
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 619751e748..c483920daa 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
@@ -1,20 +1,14 @@
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.*;
-import java.awt.Color;
+import java.awt.*;
import java.awt.geom.Point2D;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.graphics.*;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class PolylineDataTest extends PersistTestFunctions {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index dc2df4e2a1..4a0e19615c 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.persist.dao.map;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
@@ -24,8 +25,8 @@ public class CommentDaoTest extends PersistTestFunctions {
protected CommentDao commentDao;
User user;
- private Project project;
String projectId = "Some_id";
+ private Project project;
@Before
public void setUp() throws Exception {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
index 54f3d341f9..8948958f37 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
@@ -27,11 +27,10 @@ import lcsb.mapviewer.persist.PersistTestFunctions;
public class LayoutDaoTest extends PersistTestFunctions {
+ final static Logger logger = LogManager.getLogger(LayoutDaoTest.class);
@Autowired
private LayoutDao layoutDao;
- final static Logger logger = LogManager.getLogger(LayoutDaoTest.class);
-
@Before
public void setUp() throws Exception {
}
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 f7983dae4b..07aff13865 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
@@ -24,9 +24,9 @@ public class ModelDaoTest extends PersistTestFunctions {
ModelComparator modelComparator = new ModelComparator();
Logger logger = LogManager.getLogger(ModelDaoTest.class);
- private Project project;
String projectId = "Some_id";
int identifierCounter = 0;
+ private Project project;
@Before
public void setUp() throws Exception {
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 fb3285bb7d..343374f35c 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
@@ -8,8 +8,8 @@ import lcsb.mapviewer.persist.dao.map.layout.alias.AllAliasTests;
@RunWith(Suite.class)
@SuiteClasses({ AllAliasTests.class,
- ReferenceGenomeDaoTest.class,
- ReferenceGenomeGeneMappingDaoTest.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 1145263d3c..97ede00331 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.persist.dao.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
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 fb301563a6..277b2ea1bd 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.persist.dao.map.layout;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
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 d788a1c1e3..5f263b57cb 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
@@ -1,6 +1,6 @@
package lcsb.mapviewer.persist.dao.map.statistics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java
index 571c4dc906..e73250fe61 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java
@@ -17,10 +17,10 @@ public class PluginDaoTest extends PersistTestFunctions {
public void testGetPlugins() {
assertTrue(pluginDao.getAll().size() >= 0);
}
-
+
@Test
public void testAddPlugin() {
- Plugin plugin =new Plugin();
+ Plugin plugin = new Plugin();
plugin.setHash("x");
plugin.setName("Plugin name");
plugin.setVersion("0.0.1");
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java
index e0311262ea..fbcb0795e7 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java
@@ -21,17 +21,17 @@ public class PluginDataEntryDaoTest extends PersistTestFunctions {
@Test
public void testGetByKeyForGlobalParam() {
- Plugin plugin =new Plugin();
+ Plugin plugin = new Plugin();
plugin.setHash("x");
plugin.setName("Plugin name");
plugin.setVersion("0.0.1");
pluginDao.add(plugin);
-
+
PluginDataEntry entry = new PluginDataEntry();
entry.setPlugin(plugin);
entry.setKey("x");
entry.setValue("y");
-
+
pluginDataEntryDao.add(entry);
PluginDataEntry entry2 = pluginDataEntryDao.getByKey(entry.getPlugin(), entry.getKey(), entry.getUser());
@@ -42,23 +42,23 @@ public class PluginDataEntryDaoTest extends PersistTestFunctions {
@Test
public void testGetByKeyForUserParam() {
User user = createUser();
- Plugin plugin =new Plugin();
+ Plugin plugin = new Plugin();
plugin.setHash("x");
plugin.setName("Plugin name");
plugin.setVersion("0.0.1");
pluginDao.add(plugin);
-
+
PluginDataEntry entry = new PluginDataEntry();
entry.setPlugin(plugin);
entry.setUser(user);
entry.setKey("x");
entry.setValue("y");
-
+
pluginDataEntryDao.add(entry);
PluginDataEntry entry2 = pluginDataEntryDao.getByKey(entry.getPlugin(), entry.getKey(), user);
assertEquals(entry, entry2);
-
+
assertNull(pluginDataEntryDao.getByKey(entry.getPlugin(), "blabla", user));
assertNull(pluginDataEntryDao.getByKey(entry.getPlugin(), entry.getKey(), null));
}
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 d1fd99e485..363cb67214 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
@@ -85,7 +85,6 @@ public class UserDaoTest extends PersistTestFunctions {
}
}
-
@Test(expected = PropertyValueException.class)
public void testTryUserWithNullLogin() {
try {
@@ -106,7 +105,7 @@ public class UserDaoTest extends PersistTestFunctions {
user.setLogin(testLogin);
user.setCryptedPassword("");
userDao.add(user);
-
+
User user2 = new User();
user2.setLogin(testLogin);
user2.setCryptedPassword("");
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapperTest.java b/persist/src/test/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapperTest.java
index 8c9b78c29b..1525c38493 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapperTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/mapper/ArrowTypeDataMapperTest.java
@@ -5,14 +5,11 @@ import static org.junit.Assert.assertTrue;
import java.io.Serializable;
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.*;
public class ArrowTypeDataMapperTest {
Logger logger = LogManager.getLogger(ArrowTypeDataMapperTest.class);
@@ -35,7 +32,7 @@ public class ArrowTypeDataMapperTest {
atd2.setArrowLineType(LineType.DASHED);
atd2.setArrowType(ArrowType.BLANK);
atd2.setLen(33.3);
-
+
}
@After
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 252cc6c5d1..83db3ca64d 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/mapper/Point2DMapperTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/mapper/Point2DMapperTest.java
@@ -6,9 +6,7 @@ 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;
+import org.junit.*;
public class Point2DMapperTest {
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 2f9942b3e9..b7be8ff5af 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -1,28 +1,16 @@
package lcsb.mapviewer.api;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-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 java.util.*;
+
+import javax.xml.transform.*;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.io.ClassPathResource;
import org.springframework.core.io.Resource;
@@ -30,32 +18,19 @@ 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.*;
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.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.converter.Converter;
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.*;
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.annotator.AnnotatorConfigParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorParameter;
-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.model.user.annotator.*;
+import lcsb.mapviewer.services.interfaces.*;
import lcsb.mapviewer.services.search.ElementMatcher;
@Transactional
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/ContentNegotiationConfig.java b/rest-api/src/main/java/lcsb/mapviewer/api/ContentNegotiationConfig.java
index 1a23890595..73ba8a2b47 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/ContentNegotiationConfig.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/ContentNegotiationConfig.java
@@ -1,9 +1,7 @@
package lcsb.mapviewer.api;
import org.springframework.context.annotation.Configuration;
-import org.springframework.web.servlet.config.annotation.ContentNegotiationConfigurer;
-import org.springframework.web.servlet.config.annotation.EnableWebMvc;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
+import org.springframework.web.servlet.config.annotation.*;
/**
* This class is a configuration for spring that disables content type
@@ -24,9 +22,9 @@ import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
@Configuration
@EnableWebMvc
public class ContentNegotiationConfig implements WebMvcConfigurer {
- @Override
- public void configureContentNegotiation(final ContentNegotiationConfigurer configurer) {
- // Turn off suffix-based content negotiation
- configurer.favorPathExtension(false);
- }
+ @Override
+ public void configureContentNegotiation(final ContentNegotiationConfigurer configurer) {
+ // Turn off suffix-based content negotiation
+ configurer.favorPathExtension(false);
+ }
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/ElementIdentifierType.java b/rest-api/src/main/java/lcsb/mapviewer/api/ElementIdentifierType.java
index 5bae9785dd..82f8d7a448 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/ElementIdentifierType.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/ElementIdentifierType.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Enum identifying type of {@link ElementIdentifier}.
@@ -25,13 +26,12 @@ public enum ElementIdentifierType {
*/
REACTION("REACTION");
+ private static Logger logger = LogManager.getLogger(ElementIdentifierType.class);
/**
* String used in JavaScript code to identify type.
*/
private String jsName;
- private static Logger logger = LogManager.getLogger(ElementIdentifierType.class);
-
/**
* Constructor initializing enum type.
*
@@ -42,17 +42,9 @@ public enum ElementIdentifierType {
this.jsName = jsName;
}
- /**
- * @return the jsName
- * @see #jsName
- */
- public String getJsName() {
- return jsName;
- }
-
/**
* Returns {@link ElementIdentifierType} by the JavaScript name.
- *
+ *
* @param jsName
* JavaScript name of the type
* @return {@link ElementIdentifierType} by the JavaScript name
@@ -67,4 +59,12 @@ public enum ElementIdentifierType {
return null;
}
+ /**
+ * @return the jsName
+ * @see #jsName
+ */
+ public String getJsName() {
+ return jsName;
+ }
+
}
\ No newline at end of file
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 5754c1c7d3..d0c05917af 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
@@ -8,31 +8,31 @@ package lcsb.mapviewer.api;
*/
public class ObjectNotFoundException extends QueryException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public ObjectNotFoundException(String message) {
- super(message);
- }
+ /**
+ * 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);
- }
+ /**
+ * 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 11abd5a073..01b2f8dd15 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/QueryException.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/QueryException.java
@@ -8,35 +8,35 @@ package lcsb.mapviewer.api;
*/
public class QueryException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public QueryException(String message) {
- super(message);
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * error message
+ */
+ public QueryException(String message) {
+ super(message);
+ }
public QueryException(Exception e) {
super(e);
}
- /**
- * 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);
- }
+ /**
+ * 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/SpringRestApiConfig.java b/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
index 4be01b64b1..2836562969 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
@@ -1,16 +1,14 @@
package lcsb.mapviewer.api;
-import lcsb.mapviewer.services.SpringServiceConfig;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.*;
import org.springframework.web.servlet.config.annotation.EnableWebMvc;
+import lcsb.mapviewer.services.SpringServiceConfig;
+
@Configuration
@EnableWebMvc
-@Import({SpringServiceConfig.class})
-@ComponentScan(basePackages = {"lcsb.mapviewer.api"})
+@Import({ SpringServiceConfig.class })
+@ComponentScan(basePackages = { "lcsb.mapviewer.api" })
public class SpringRestApiConfig {
}
-
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 177fd53650..2fa57722c1 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
@@ -1,16 +1,9 @@
package lcsb.mapviewer.api.configuration;
-import java.util.ArrayList;
-import java.util.LinkedHashSet;
-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 java.util.*;
-import lcsb.mapviewer.model.security.PrivilegeType;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -32,9 +25,8 @@ 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.ConfigurationElementEditType;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.security.PrivilegeType;
+import lcsb.mapviewer.model.user.*;
import lcsb.mapviewer.model.user.annotator.BioEntityField;
import lcsb.mapviewer.modelutils.map.ClassTreeNode;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -61,7 +53,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getAllValues() {
List<Map<String, Object>> result = new ArrayList<>();
- for (ConfigurationOption option : configurationService.getAllValues()){
+ for (ConfigurationOption option : configurationService.getAllValues()) {
result.add(optionToMap(option));
}
return result;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
index f7287da9c9..6bfd47dbc4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
@@ -4,7 +4,8 @@ import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.SBMLException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -21,48 +22,47 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
@RestController
@RequestMapping(value = "/convert", produces = MediaType.APPLICATION_JSON_VALUE)
public class ConvertController extends BaseController {
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(ConvertController.class);
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(ConvertController.class);
- private ConvertRestImpl convertController;
+ private ConvertRestImpl convertController;
- @Autowired
- public ConvertController(ConvertRestImpl convertController) {
- this.convertController = convertController;
- }
+ @Autowired
+ public ConvertController(ConvertRestImpl convertController) {
+ this.convertController = convertController;
+ }
- @PostMapping(value = "/{fromFormat}:{toFormat}", produces = MediaType.APPLICATION_XML_VALUE)
- public String convertInput(@PathVariable(value = "fromFormat") String fromFormat,
- @PathVariable(value = "toFormat") String toFormat,
- @RequestBody String body)
- throws IOException, QueryException, SBMLException,
- InvalidInputDataExecption, InconsistentModelException, ConverterException
- {
- return convertController.convert(fromFormat, toFormat, body);
- }
+ @PostMapping(value = "/{fromFormat}:{toFormat}", produces = MediaType.APPLICATION_XML_VALUE)
+ public String convertInput(@PathVariable(value = "fromFormat") String fromFormat,
+ @PathVariable(value = "toFormat") String toFormat,
+ @RequestBody String body)
+ throws IOException, QueryException, SBMLException,
+ InvalidInputDataExecption, InconsistentModelException, ConverterException {
+ return convertController.convert(fromFormat, toFormat, body);
+ }
- @PostMapping(value = "/image/{fromFormat}:{toFormat}")
- public @ResponseBody ResponseEntity<byte[]> convertInputToImage(
- @PathVariable(value = "fromFormat") String fromFormat,
- @PathVariable(value = "toFormat") String toFormat,
- @RequestBody String body)
- throws IOException, QueryException, SBMLException, InvalidInputDataExecption, ConverterException, DrawingException
- {
- ByteArrayOutputStream os = convertController.converToImage(fromFormat, toFormat, body);
- return ResponseEntity.ok().contentLength(os.size())
- .contentType(MediaType.APPLICATION_OCTET_STREAM)
- .header("Content-Disposition", "attachment; filename=model" + toFormat )
- .body(os.toByteArray());
- }
+ @PostMapping(value = "/image/{fromFormat}:{toFormat}")
+ public @ResponseBody ResponseEntity<byte[]> convertInputToImage(
+ @PathVariable(value = "fromFormat") String fromFormat,
+ @PathVariable(value = "toFormat") String toFormat,
+ @RequestBody String body)
+ throws IOException, QueryException, SBMLException, InvalidInputDataExecption, ConverterException,
+ DrawingException {
+ ByteArrayOutputStream os = convertController.converToImage(fromFormat, toFormat, body);
+ return ResponseEntity.ok().contentLength(os.size())
+ .contentType(MediaType.APPLICATION_OCTET_STREAM)
+ .header("Content-Disposition", "attachment; filename=model" + toFormat)
+ .body(os.toByteArray());
+ }
- @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
- public Map<String, Object> getInformation() {
- return convertController.getInformation();
- }
+ @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
+ public Map<String, Object> getInformation() {
+ return convertController.getInformation();
+ }
- @RequestMapping(value = "/image/", method = { RequestMethod.GET, RequestMethod.POST })
- public Map<String, Object> getInformationImage() {
- return convertController.getInformationImage();
- }
+ @RequestMapping(value = "/image/", method = { RequestMethod.GET, RequestMethod.POST })
+ public Map<String, Object> getInformationImage() {
+ return convertController.getInformationImage();
+ }
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
index 1824c0bcf4..d763144b87 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
@@ -1,16 +1,10 @@
package lcsb.mapviewer.api.convert;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.LogManager;
@@ -22,13 +16,9 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
+import lcsb.mapviewer.converter.graphics.*;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
@@ -36,156 +26,154 @@ import lcsb.mapviewer.model.map.model.Model;
@Service
public class ConvertRestImpl extends BaseRestImpl {
- private Logger logger = LogManager.getLogger(ConvertRestImpl.class);
-
+ private Logger logger = LogManager.getLogger(ConvertRestImpl.class);
public String convert(String fromFormat, String toFormat, String input)
- throws InvalidInputDataExecption, SBMLException, InconsistentModelException, IOException, ConverterException, QueryException
- {
- ConverterParams params = createConvertParams(input);
- Model model = getModelParserByNameOrClass(fromFormat).createModel(params);
-
- Converter exporter = getModelParserByNameOrClass(toFormat);
- return IOUtils.toString(exporter.model2InputStream(model), StandardCharsets.UTF_8);
+ throws InvalidInputDataExecption, SBMLException, InconsistentModelException, IOException, ConverterException,
+ QueryException {
+ ConverterParams params = createConvertParams(input);
+ Model model = getModelParserByNameOrClass(fromFormat).createModel(params);
+
+ Converter exporter = getModelParserByNameOrClass(toFormat);
+ return IOUtils.toString(exporter.model2InputStream(model), StandardCharsets.UTF_8);
}
-
+
public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, String input,
- Double targetWidth, Double targetHeight)
- throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException, QueryException
- {
- Model model = getModelParserByNameOrClass(fromFormat).createModel(createConvertParams(input));
-
- AbstractImageGenerator generator = getImageGenerator(toFormat, createImageParams(model, targetWidth, targetHeight));
- ByteArrayOutputStream os = new ByteArrayOutputStream();
- generator.saveToOutputStream(os);
- return os;
+ Double targetWidth, Double targetHeight)
+ throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException,
+ QueryException {
+ Model model = getModelParserByNameOrClass(fromFormat).createModel(createConvertParams(input));
+
+ AbstractImageGenerator generator = getImageGenerator(toFormat, createImageParams(model, targetWidth, targetHeight));
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ generator.saveToOutputStream(os);
+ return os;
}
-
+
public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, String input)
- throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException, QueryException
- {
- return converToImage(fromFormat, toFormat, input, 0.0, 0.0);
+ throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException,
+ QueryException {
+ return converToImage(fromFormat, toFormat, input, 0.0, 0.0);
}
-
- public Map<String, Object> getInformation(){
- Map<String, Object> info = new LinkedHashMap<>();
-
-
- List<Object> converters = new ArrayList<>();
- for (Converter converter: getModelConverters()) {
-
- List<String> names = new ArrayList<>();
- names.add(removeWhiteSpaces(converter.getCommonName()));
- names.add(converter.getClass().getCanonicalName());
-
- Map<String, Object> names_item = new LinkedHashMap<>();
- names_item.put("available_names", names);
- converters.add(names_item);
- }
-
- info.put("inputs", converters);
- info.put("outputs", converters);
- return info;
+
+ public Map<String, Object> getInformation() {
+ Map<String, Object> info = new LinkedHashMap<>();
+
+ List<Object> converters = new ArrayList<>();
+ for (Converter converter : getModelConverters()) {
+
+ List<String> names = new ArrayList<>();
+ names.add(removeWhiteSpaces(converter.getCommonName()));
+ names.add(converter.getClass().getCanonicalName());
+
+ Map<String, Object> names_item = new LinkedHashMap<>();
+ names_item.put("available_names", names);
+ converters.add(names_item);
+ }
+
+ info.put("inputs", converters);
+ info.put("outputs", converters);
+ return info;
}
-
- public Map<String, Object> getInformationImage(){
- Map<String, Object> info = getInformation();
-
- List<Object> generators = new ArrayList<>();
- ImageGenerators igs = new ImageGenerators();
- for (Pair<String, Class<? extends AbstractImageGenerator>> generator: igs.getAvailableImageGenerators()) {
-
- List<String> names = new ArrayList<>();
- names.add(igs.getExtension(generator.getRight()));
- names.add(generator.getRight().getCanonicalName());
-
- Map<String, Object> names_item = new LinkedHashMap<>();
- names_item.put("available_names", names);
- generators.add(names_item);
- }
-
- info.remove("outputs");
- info.put("outputs", generators);
- return info;
+
+ public Map<String, Object> getInformationImage() {
+ Map<String, Object> info = getInformation();
+
+ List<Object> generators = new ArrayList<>();
+ ImageGenerators igs = new ImageGenerators();
+ for (Pair<String, Class<? extends AbstractImageGenerator>> generator : igs.getAvailableImageGenerators()) {
+
+ List<String> names = new ArrayList<>();
+ names.add(igs.getExtension(generator.getRight()));
+ names.add(generator.getRight().getCanonicalName());
+
+ Map<String, Object> names_item = new LinkedHashMap<>();
+ names_item.put("available_names", names);
+ generators.add(names_item);
+ }
+
+ info.remove("outputs");
+ info.put("outputs", generators);
+ return info;
}
-
+
private Converter getModelParserByNameOrClass(String id) throws QueryException {
- try {
- return getModelParserByName(id);
- } catch (QueryException e) {
- return getModelParser(id);
- }
+ try {
+ return getModelParserByName(id);
+ } catch (QueryException e) {
+ return getModelParser(id);
+ }
}
-
+
private String removeWhiteSpaces(String str) {
- return str.replace(' ', '_');
+ return str.replace(' ', '_');
}
-
+
private Converter getModelParserByName(String name) throws QueryException {
- for (Converter converter : getModelConverters()) {
- if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
- return converter;
- }
- }
- throw new QueryException("Unknown parser name: " + name);
+ for (Converter converter : getModelConverters()) {
+ if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
+ return converter;
+ }
+ }
+ throw new QueryException("Unknown parser name: " + name);
}
-
- private AbstractImageGenerator getImageGenerator(String extOrClass, AbstractImageGenerator.Params params) throws QueryException
- {
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : new ImageGenerators().getAvailableImageGenerators()) {
-
- try {
- Class<? extends AbstractImageGenerator> clazz = element.getRight();
- Constructor<?> ctor = clazz.getConstructor(AbstractImageGenerator.Params.class);
- AbstractImageGenerator generator = (AbstractImageGenerator) ctor.newInstance(params);
- if (extOrClass.equals(clazz.getCanonicalName()) || extOrClass.equals(generator.getFileExtension())) {
- return generator;
- }
-
- } catch (NoSuchMethodException | java.lang.SecurityException | InstantiationException
- | IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
- logger.error("Creation of image generator class for '" + element.getLeft() + "' failed.");
- throw new QueryException("Issue with obtaining image generator for extension " + extOrClass + ".");
- }
-
- }
-
- throw new QueryException("Image generator for extension " + extOrClass + " not available.");
- }
-
- private AbstractImageGenerator.Params createImageParams(Model model, Double targetWidth, Double targetHeight){
- Double padding = 5.0;
- Double maxDim = 10000.0;
-
- Double w = model.getWidth();
- Double h = model.getHeight();
-
- if (targetHeight == 0) targetHeight = Math.min(h, maxDim);
- if (targetWidth == 0) targetWidth = Math.min(w, maxDim);
-
- Double scale = targetWidth / w;
- if (h * scale > targetHeight) {
- scale = targetHeight / h;
- }
-
- Double wScaled = w*scale;
- Double hScaled = h*scale;
-
- return new AbstractImageGenerator.Params().
- model(model).
- width(wScaled + padding).
- height(hScaled + padding).
- scale(1/scale)
- .x(0);
-
- }
-
-private ConverterParams createConvertParams(String input) {
- ConverterParams params = new ConverterParams();
- InputStream is = new ByteArrayInputStream(input.getBytes());
-
- params.inputStream(is);
-
- return params;
+
+ private AbstractImageGenerator getImageGenerator(String extOrClass, AbstractImageGenerator.Params params)
+ throws QueryException {
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : new ImageGenerators()
+ .getAvailableImageGenerators()) {
+
+ try {
+ Class<? extends AbstractImageGenerator> clazz = element.getRight();
+ Constructor<?> ctor = clazz.getConstructor(AbstractImageGenerator.Params.class);
+ AbstractImageGenerator generator = (AbstractImageGenerator) ctor.newInstance(params);
+ if (extOrClass.equals(clazz.getCanonicalName()) || extOrClass.equals(generator.getFileExtension())) {
+ return generator;
+ }
+
+ } catch (NoSuchMethodException | java.lang.SecurityException | InstantiationException
+ | IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+ logger.error("Creation of image generator class for '" + element.getLeft() + "' failed.");
+ throw new QueryException("Issue with obtaining image generator for extension " + extOrClass + ".");
+ }
+
+ }
+
+ throw new QueryException("Image generator for extension " + extOrClass + " not available.");
+ }
+
+ private AbstractImageGenerator.Params createImageParams(Model model, Double targetWidth, Double targetHeight) {
+ Double padding = 5.0;
+ Double maxDim = 10000.0;
+
+ Double w = model.getWidth();
+ Double h = model.getHeight();
+
+ if (targetHeight == 0)
+ targetHeight = Math.min(h, maxDim);
+ if (targetWidth == 0)
+ targetWidth = Math.min(w, maxDim);
+
+ Double scale = targetWidth / w;
+ if (h * scale > targetHeight) {
+ scale = targetHeight / h;
+ }
+
+ Double wScaled = w * scale;
+ Double hScaled = h * scale;
+
+ return new AbstractImageGenerator.Params().model(model).width(wScaled + padding).height(hScaled + padding)
+ .scale(1 / scale)
+ .x(0);
+
+ }
+
+ private ConverterParams createConvertParams(String input) {
+ ConverterParams params = new ConverterParams();
+ InputStream is = new ByteArrayInputStream(input.getBytes());
+
+ params.inputStream(is);
+
+ return params;
}
}
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 ca66ec9014..fee30ce281 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
@@ -2,7 +2,6 @@ package lcsb.mapviewer.api.files;
import java.util.Map;
-import lcsb.mapviewer.services.interfaces.IUserService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.security.access.prepost.PostAuthorize;
@@ -12,6 +11,7 @@ import org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.services.interfaces.IUserService;
@RestController
@RequestMapping(value = "/files", produces = MediaType.APPLICATION_JSON_VALUE)
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 ca2fa051d2..e3aa38fe52 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
@@ -4,7 +4,6 @@ import java.io.IOException;
import java.util.List;
import java.util.Map;
-import lcsb.mapviewer.api.ObjectNotFoundException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.security.access.prepost.PreAuthorize;
@@ -12,8 +11,7 @@ import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.*;
@RestController
@RequestMapping(value = "/genomics", produces = MediaType.APPLICATION_JSON_VALUE)
@@ -50,11 +48,11 @@ public class ReferenceGenomeController extends BaseController {
@PreAuthorize("hasAuthority('IS_ADMIN')")
@PostMapping(value = "/")
public Map<String, Object> addGenome(@RequestBody MultiValueMap<String, Object> formData)
- throws QueryException, IOException, ReferenceGenomeConnectorException {
+ throws QueryException, IOException, ReferenceGenomeConnectorException {
return referenceGenomeController.addReferenceGenome(formData);
}
- @GetMapping(value = "/" )
+ @GetMapping(value = "/")
public List<Map<String, Object>> getDownloaded() {
return referenceGenomeController.getReferenceGenomes();
}
@@ -82,9 +80,8 @@ public class ReferenceGenomeController extends BaseController {
@DeleteMapping(value = "/{genomeId}/geneMapping/{mappingId}/")
public Map<String, Object> removeGeneMapping(
@PathVariable(value = "genomeId") String genomeId,
- @PathVariable(value = "mappingId") String mappingId
- ) throws IOException, ObjectNotFoundException {
- return referenceGenomeController.removeGeneMapping(genomeId,mappingId);
+ @PathVariable(value = "mappingId") String mappingId) throws IOException, ObjectNotFoundException {
+ return referenceGenomeController.removeGeneMapping(genomeId, mappingId);
}
@PreAuthorize("hasAuthority('IS_ADMIN')")
@@ -92,7 +89,7 @@ public class ReferenceGenomeController extends BaseController {
public Map<String, Object> addGeneMapping(
@PathVariable(value = "genomeId") String genomeId,
@RequestBody MultiValueMap<String, Object> formData)
- throws QueryException, IOException, ReferenceGenomeConnectorException {
+ throws QueryException, IOException, ReferenceGenomeConnectorException {
return referenceGenomeController.addGeneMapping(formData, genomeId);
}
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 9de6bd5bc9..d6271f6d2b 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
@@ -3,15 +3,10 @@ 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.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -19,15 +14,10 @@ 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.ObjectExistsException;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.*;
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.map.layout.*;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
@@ -64,8 +54,7 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
try {
ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
version = version.replaceAll("\\*", "");
- ReferenceGenome genome = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version
- );
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version);
if (genome == null) {
throw new ObjectNotFoundException("Cannot find requested reference genome");
}
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 5fa4891dd9..a308997f26 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
@@ -2,14 +2,15 @@ package lcsb.mapviewer.api.mesh;
import java.util.Map;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.*;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
@RestController
@RequestMapping(value = "/mesh", produces = MediaType.APPLICATION_JSON_VALUE)
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 b6ae5237bc..5988f8cced 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
@@ -1,9 +1,10 @@
package lcsb.mapviewer.api.mesh;
-import java.util.TreeMap;
import java.util.Map;
+import java.util.TreeMap;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/MinervaNetController.java b/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/MinervaNetController.java
index 8077da81e0..798531448e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/MinervaNetController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/MinervaNetController.java
@@ -1,10 +1,9 @@
package lcsb.mapviewer.api.minervanet;
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import java.io.IOException;
+
+import javax.servlet.ServletContext;
+
import org.apache.http.HttpEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
@@ -13,12 +12,17 @@ import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.util.EntityUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.*;
-import javax.servlet.ServletContext;
-import java.io.IOException;
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
@RestController
@RequestMapping("/minervanet")
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/ReportSubmissionException.java b/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/ReportSubmissionException.java
index edf3480c67..d211dd2518 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/ReportSubmissionException.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/minervanet/ReportSubmissionException.java
@@ -22,7 +22,8 @@ public class ReportSubmissionException extends RuntimeException {
super(cause);
}
- protected ReportSubmissionException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
+ protected ReportSubmissionException(String message, Throwable cause, boolean enableSuppression,
+ boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
}
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 0a874b9635..68d9cc937e 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
@@ -3,9 +3,8 @@ package lcsb.mapviewer.api.plugins;
import java.util.List;
import java.util.Map;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.security.access.prepost.PreAuthorize;
@@ -14,6 +13,8 @@ import org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IUserService;
@RestController
@RequestMapping(value = "/plugins", produces = MediaType.APPLICATION_JSON_VALUE)
@@ -67,8 +68,7 @@ public class PluginController extends BaseController {
Authentication authentication,
@PathVariable(value = "hash") String hash,
@PathVariable(value = "key") String key,
- @RequestParam(value = "value", defaultValue = "") String value
- ) throws ObjectNotFoundException {
+ @RequestParam(value = "value", defaultValue = "") String value) throws ObjectNotFoundException {
User user = userService.getUserByLogin(authentication.getName());
return pluginRest.createPluginDataEntry(hash, user, key, value);
}
@@ -77,8 +77,7 @@ public class PluginController extends BaseController {
public Map<String, Object> createPluginDataEntry(
@PathVariable(value = "hash") String hash,
@PathVariable(value = "key") String key,
- @RequestParam(value = "value", defaultValue = "") String value
- ) throws ObjectNotFoundException {
+ @RequestParam(value = "value", defaultValue = "") String value) throws ObjectNotFoundException {
return pluginRest.createPluginDataEntry(hash, null, key, value);
}
@@ -86,8 +85,7 @@ public class PluginController extends BaseController {
public Map<String, Object> getPluginDataEntry(
Authentication authentication,
@PathVariable(value = "hash") String hash,
- @PathVariable(value = "key") String key
- ) throws ObjectNotFoundException {
+ @PathVariable(value = "key") String key) throws ObjectNotFoundException {
User user = userService.getUserByLogin(authentication.getName());
return pluginRest.getPluginDataEntry(hash, user, key);
}
@@ -95,8 +93,7 @@ public class PluginController extends BaseController {
@GetMapping(value = "/{hash}/data/global/{key}")
public Map<String, Object> getPluginDataEntry(
@PathVariable(value = "hash") String hash,
- @PathVariable(value = "key") String key
- ) throws ObjectNotFoundException {
+ @PathVariable(value = "key") String key) throws ObjectNotFoundException {
return pluginRest.getPluginDataEntry(hash, null, key);
}
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 57b0994f20..8a676d07ac 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
@@ -1,10 +1,6 @@
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 java.util.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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 5424d80a2e..00139e1e0f 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
@@ -509,35 +509,6 @@ public class ProjectRestImpl extends BaseRestImpl {
return getProject(projectId);
}
- 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;
- @SuppressWarnings("unused")
- public String level;
- }
-
public Map<String, Object> getLogs(String projectId, String level, String startString, Integer length,
String sortColumn, String sortOrder, String search) throws QueryException {
Project project = getProjectService().getProjectByProjectId(projectId);
@@ -721,4 +692,31 @@ public class ProjectRestImpl extends BaseRestImpl {
}
}
+ 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 Integer id;
+ public String content;
+ @SuppressWarnings("unused")
+ public String level;
+ public LogEntry(int id, String content, String level) {
+ this.id = id;
+ this.content = content;
+ this.level = level;
+ }
+ }
+
}
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 7ab8ad17d0..1490893a5b 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.api.projects.chemicals;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -30,8 +28,7 @@ public class ChemicalController extends BaseController {
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "columns", defaultValue = "") String columns,
@RequestParam(value = "query", defaultValue = "") String query,
- @RequestParam(value = "target", defaultValue = "") String target
- ) throws QueryException {
+ @RequestParam(value = "target", defaultValue = "") String target) throws QueryException {
if (!query.equals("")) {
return chemicalController.getChemicalsByQuery(projectId, columns, query);
} else if (target.contains(":")) {
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 7c11c2a048..f154db8981 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
@@ -2,21 +2,17 @@ package lcsb.mapviewer.api.projects.chemicals;
import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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.*;
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.api.*;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
@@ -81,57 +77,57 @@ public class ChemicalRestImpl extends BaseRestImpl {
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);
- }
+ 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;
switch (column) {
- case "id":
- case "idobject":
- value = chemical.getChemicalId();
- break;
- case "name":
- value = chemical.getChemicalName();
- break;
- case "references":
- List<Map<String, Object>> references = new ArrayList<>();
- references.add(createAnnotation(chemical.getChemicalId()));
- if (chemical.getCasID() != null) {
- references.add(createAnnotation(chemical.getCasID()));
- }
- value = references;
- break;
- case "directevidencereferences":
- value = createAnnotations(chemical.getDirectEvidencePublication());
- break;
- case "description":
- value = description;
- break;
- case "directevidence":
- if (chemical.getDirectEvidence() != null) {
- value = chemical.getDirectEvidence().getValue();
- }
- break;
- case "synonyms":
- value = synonyms;
- break;
- case "targets":
- value = prepareTargets(chemical.getInferenceNetwork(), models);
- break;
- default:
- value = "Unknown column";
- break;
+ case "id":
+ case "idobject":
+ value = chemical.getChemicalId();
+ break;
+ case "name":
+ value = chemical.getChemicalName();
+ break;
+ case "references":
+ List<Map<String, Object>> references = new ArrayList<>();
+ references.add(createAnnotation(chemical.getChemicalId()));
+ if (chemical.getCasID() != null) {
+ references.add(createAnnotation(chemical.getCasID()));
+ }
+ value = references;
+ break;
+ case "directevidencereferences":
+ value = createAnnotations(chemical.getDirectEvidencePublication());
+ break;
+ case "description":
+ value = description;
+ break;
+ case "directevidence":
+ if (chemical.getDirectEvidence() != null) {
+ value = chemical.getDirectEvidence().getValue();
+ }
+ break;
+ case "synonyms":
+ value = synonyms;
+ break;
+ case "targets":
+ value = prepareTargets(chemical.getInferenceNetwork(), models);
+ break;
+ default:
+ value = "Unknown column";
+ break;
}
result.put(string, value);
}
@@ -156,7 +152,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getChemicalsByTarget(String projectId, String targetType,
- String targetId, String columns) throws QueryException {
+ String targetId, String columns) throws QueryException {
Model model = getModelService().getLastModelByProjectId(projectId);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
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 27a107f30d..e1a9f7d38e 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
@@ -21,7 +21,7 @@ import lcsb.mapviewer.model.security.PrivilegeType;
@RestController
@RequestMapping(value = "/projects/{projectId}/comments", produces = MediaType.APPLICATION_JSON_VALUE)
public class CommentController extends BaseController {
-
+
Logger logger = LogManager.getLogger();
private CommentRestImpl commentController;
@@ -41,11 +41,13 @@ public class CommentController extends BaseController {
Authentication authentication,
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "columns", defaultValue = "") String columns,
- @RequestParam(value = "removed", defaultValue = "") String removed
- ) throws QueryException {
- boolean isAdmin = authentication.getAuthorities().contains(new SimpleGrantedAuthority(PrivilegeType.IS_ADMIN.name()));
- boolean isProjectCurator = authentication.getAuthorities().contains(new SimpleGrantedAuthority(PrivilegeType.IS_CURATOR.name()))
- && authentication.getAuthorities().contains(new SimpleGrantedAuthority(PrivilegeType.READ_PROJECT.name() + ":" + projectId));
+ @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
+ boolean isAdmin = authentication.getAuthorities()
+ .contains(new SimpleGrantedAuthority(PrivilegeType.IS_ADMIN.name()));
+ boolean isProjectCurator = authentication.getAuthorities()
+ .contains(new SimpleGrantedAuthority(PrivilegeType.IS_CURATOR.name()))
+ && authentication.getAuthorities()
+ .contains(new SimpleGrantedAuthority(PrivilegeType.READ_PROJECT.name() + ":" + projectId));
List<Map<String, Object>> comments = commentController.getCommentList(
projectId, columns, "", "", removed);
@@ -66,8 +68,7 @@ public class CommentController extends BaseController {
public Map<String, Object> removeComment(
@RequestBody(required = false) String body,
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "commentId") String commentId
- ) throws QueryException, IOException {
+ @PathVariable(value = "commentId") String commentId) throws QueryException, IOException {
Map<String, Object> node = parseBody(body);
String reason = (String) node.get("reason");
return commentController.removeComment(projectId, commentId, reason);
@@ -83,8 +84,7 @@ public class CommentController extends BaseController {
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "columns", defaultValue = "") String columns,
@PathVariable(value = "reactionId") String reactionId,
- @RequestParam(value = "removed", defaultValue = "") String removed
- ) throws QueryException {
+ @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
return commentController.getCommentList(projectId, columns, reactionId,
ElementIdentifierType.REACTION.getJsName(), removed);
}
@@ -99,8 +99,7 @@ public class CommentController extends BaseController {
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "columns", defaultValue = "") String columns,
@PathVariable(value = "elementId") String elementId,
- @RequestParam(value = "removed", defaultValue = "") String removed
- ) throws QueryException {
+ @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
return commentController.getCommentList(
projectId, columns, elementId, ElementIdentifierType.ALIAS.getJsName(), removed);
}
@@ -115,8 +114,7 @@ public class CommentController extends BaseController {
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "columns", defaultValue = "") String columns,
@PathVariable(value = "coordinates") String coordinates,
- @RequestParam(value = "removed", defaultValue = "") String removed
- ) throws QueryException {
+ @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
return commentController.getCommentList(projectId, columns, coordinates,
ElementIdentifierType.POINT.getJsName(), removed);
}
@@ -131,8 +129,7 @@ public class CommentController extends BaseController {
@RequestParam(value = "content") String content,
@RequestParam(value = "pinned", defaultValue = "true") String pinned,
@RequestParam(value = "coordinates") String coordinates,
- @PathVariable(value = "modelId") String modelId
- ) throws QueryException {
+ @PathVariable(value = "modelId") String modelId) throws QueryException {
Point2D pointCoordinates = parseCoordinates(coordinates);
return commentController.addComment(projectId, ElementIdentifierType.ALIAS.getJsName(), elementId, name,
email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
@@ -148,8 +145,7 @@ public class CommentController extends BaseController {
@RequestParam(value = "content") String content,
@RequestParam(value = "pinned", defaultValue = "true") String pinned,
@RequestParam(value = "coordinates") String coordinates,
- @PathVariable(value = "modelId") String modelId
- ) throws QueryException {
+ @PathVariable(value = "modelId") String modelId) throws QueryException {
Point2D pointCoordinates = parseCoordinates(coordinates);
return commentController.addComment(projectId, ElementIdentifierType.REACTION.getJsName(), reactionId, name,
email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
@@ -164,8 +160,7 @@ public class CommentController extends BaseController {
@RequestParam(value = "content") String content,
@RequestParam(value = "pinned", defaultValue = "true") String pinned,
@PathVariable(value = "coordinates") String coordinates,
- @PathVariable(value = "modelId") String modelId
- ) throws QueryException {
+ @PathVariable(value = "modelId") String modelId) throws QueryException {
Point2D pointCoordinates = parseCoordinates(coordinates);
return commentController.addComment(projectId, ElementIdentifierType.POINT.getJsName(), coordinates, name,
email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
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 92e263860c..fe9519beb2 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
@@ -1,8 +1,6 @@
package lcsb.mapviewer.api.projects.drugs;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -30,8 +28,7 @@ public class DrugController extends BaseController {
@PathVariable(value = "projectId") String projectId,
@RequestParam(value = "columns", defaultValue = "") String columns,
@RequestParam(value = "query", defaultValue = "") String query,
- @RequestParam(value = "target", defaultValue = "") String target
- ) throws QueryException {
+ @RequestParam(value = "target", defaultValue = "") String target) throws QueryException {
if (!query.equals("")) {
return drugController.getDrugsByQuery(projectId, columns, query);
} else if (target.contains(":")) {
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 6747226e25..420e788f38 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.api.projects.drugs;
import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -10,9 +11,7 @@ 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.api.*;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
@@ -129,7 +128,7 @@ public class DrugRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getDrugsByTarget(String projectId, String targetType, String targetId,
- String columns) throws QueryException {
+ String columns) throws QueryException {
Model model = getModelService().getLastModelByProjectId(projectId);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
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 73e888a601..82250cbc06 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
@@ -2,18 +2,15 @@ package lcsb.mapviewer.api.projects.mirnas;
import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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.annotation.services.*;
+import lcsb.mapviewer.api.*;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
@@ -73,17 +70,17 @@ public class MiRnaRestImpl extends BaseRestImpl {
String column = string.toLowerCase();
Object value;
switch (column) {
- case "id":
- case "idobject":
- case "name":
- value = miRna.getName();
- break;
- case "targets":
- value = prepareTargets(miRna.getTargets(), models);
- break;
- default:
- value = "Unknown column";
- break;
+ case "id":
+ case "idobject":
+ case "name":
+ value = miRna.getName();
+ break;
+ case "targets":
+ value = prepareTargets(miRna.getTargets(), models);
+ break;
+ default:
+ value = "Unknown column";
+ break;
}
result.put(string, value);
}
@@ -103,7 +100,7 @@ public class MiRnaRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getMiRnasByTarget(String projectId, String targetType, String targetId,
- String columns) throws QueryException {
+ String columns) throws QueryException {
Model model = getModelService().getLastModelByProjectId(projectId);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
index b4310eff3f..dabceafea3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -4,9 +4,6 @@ import java.io.IOException;
import java.util.List;
import java.util.Map;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.impl.UserService;
-import lcsb.mapviewer.services.interfaces.IUserService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
@@ -14,15 +11,15 @@ import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.security.core.Authentication;
import org.springframework.web.bind.annotation.*;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.*;
import lcsb.mapviewer.commands.CommandExecutionException;
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.model.user.User;
+import lcsb.mapviewer.services.interfaces.IUserService;
@RestController
@RequestMapping(value = "/projects/{projectId:.+}/models", produces = MediaType.APPLICATION_JSON_VALUE)
@@ -48,8 +45,7 @@ public class ModelController extends BaseController {
@GetMapping(value = "/{modelId:.+}")
public Object getModel(
@PathVariable(value = "modelId") String modelId,
- @PathVariable(value = "projectId") String projectId
- ) throws ObjectNotFoundException {
+ @PathVariable(value = "projectId") String projectId) throws ObjectNotFoundException {
if (modelId.equals("*")) {
return modelController.getModels(projectId);
} else {
@@ -62,8 +58,7 @@ public class ModelController extends BaseController {
public Object updateModel(
@PathVariable(value = "modelId") String modelId,
@PathVariable(value = "projectId") String projectId,
- @RequestBody String body
- ) throws IOException, QueryException {
+ @RequestBody String body) throws IOException, QueryException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "model");
return modelController.updateModel(projectId, modelId, data);
@@ -79,8 +74,8 @@ public class ModelController extends BaseController {
@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 QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString)
+ throws QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
User user = userService.getUserByLogin(authentication.getName());
FileEntry file = modelController.getModelAsImage(
projectId, modelId, handlerClass, backgroundOverlayId, overlayIds, zoomLevel, polygonString, user);
@@ -100,8 +95,8 @@ public class ModelController extends BaseController {
@RequestParam(value = "overlayIds", defaultValue = "") String overlayIds,
@RequestParam(value = "polygonString", defaultValue = "") String polygonString,
@RequestParam(value = "elementIds", defaultValue = "") String elementIds,
- @RequestParam(value = "reactionIds", defaultValue = "") String reactionIds
- ) throws QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ @RequestParam(value = "reactionIds", defaultValue = "") String reactionIds)
+ throws QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
ConverterException, InconsistentModelException {
User user = userService.getUserByLogin(authentication.getName());
FileEntry file = modelController.getModelAsModelFile(
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index 4cc9e73a85..15c1affd90 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -1,20 +1,10 @@
package lcsb.mapviewer.api.projects.models;
-import java.awt.Color;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
+import java.awt.*;
+import java.awt.geom.*;
+import java.io.*;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.LogManager;
@@ -23,16 +13,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-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.api.*;
+import lcsb.mapviewer.commands.*;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.ConverterException;
@@ -43,12 +25,8 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.InconsistentModelException;
-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.ModelData;
-import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.layout.*;
+import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.interfaces.ILayoutService;
@@ -188,8 +166,8 @@ public class ModelRestImpl extends BaseRestImpl {
}
public FileEntry getModelAsModelFile(String projectId, String modelId, String handlerClass,
- String overlayIds, String polygonString, String elementIds,
- String reactionIds, User user)
+ String overlayIds, String polygonString, String elementIds,
+ String reactionIds, User user)
throws QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
ConverterException, InconsistentModelException {
Model originalModel = getModelByModelId(projectId, modelId);
@@ -273,7 +251,8 @@ public class ModelRestImpl extends BaseRestImpl {
}
public FileEntry getModelAsImage(String projectId, String modelId, String handlerClass,
- String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString, User user) throws QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString, User user)
+ throws QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
Project project = getProjectService().getProjectByProjectId(projectId);
Model topModel = getModelService().getLastModelByProjectId(projectId);
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 ffa3eab335..d50410936b 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
@@ -1,9 +1,7 @@
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 java.util.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -14,8 +12,7 @@ import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
@RestController
-@RequestMapping(value = "/projects/{projectId}/models/{modelId}/",
- produces = MediaType.APPLICATION_JSON_VALUE)
+@RequestMapping(value = "/projects/{projectId}/models/{modelId}/", produces = MediaType.APPLICATION_JSON_VALUE)
public class BioEntitiesController extends BaseController {
private BioEntitiesRestImpl bioEntitiesRestImpl;
@@ -34,8 +31,7 @@ public class BioEntitiesController extends BaseController {
@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 {
+ @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch) throws QueryException {
if (!coordinates.trim().isEmpty()) {
if (modelId.equals("*")) {
throw new QueryException("modelId must be defined when searching by coordinates");
@@ -70,7 +66,7 @@ public class BioEntitiesController extends BaseController {
}
@PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
- @RequestMapping(value = "bioEntities/suggestedQueryList", method = {RequestMethod.GET, RequestMethod.POST })
+ @RequestMapping(value = "bioEntities/suggestedQueryList", method = { RequestMethod.GET, RequestMethod.POST })
public String[] getSuggestedQueryList(@PathVariable(value = "projectId") String projectId) {
return bioEntitiesRestImpl.getSuggestedQueryList(projectId);
}
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 be11ccf537..8fbc50e6ae 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
@@ -1,13 +1,10 @@
package lcsb.mapviewer.api.projects.models.bioEntities;
import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -59,7 +56,7 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getElementsByQuery(String projectId, String query,
- Integer maxElements, String perfectMatch) {
+ Integer maxElements, String perfectMatch) {
List<Map<String, Object>> resultMap = new ArrayList<>();
Model model = getModelService().getLastModelByProjectId(projectId);
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 ac752def6e..79dfaf50ef 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
@@ -6,38 +6,34 @@ import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.security.access.prepost.PreAuthorize;
-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 org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
@RestController
-@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements",
- produces = MediaType.APPLICATION_JSON_VALUE)
+@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements", produces = MediaType.APPLICATION_JSON_VALUE)
public class ElementsController extends BaseController {
- private ElementsRestImpl projectController;
+ private ElementsRestImpl projectController;
- @Autowired
- public ElementsController(ElementsRestImpl projectController) {
- this.projectController = projectController;
- }
+ @Autowired
+ public ElementsController(ElementsRestImpl projectController) {
+ this.projectController = projectController;
+ }
- @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
- @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
- 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
- ) throws QueryException {
- return projectController.getElements(projectId, id, columns, modelId, type, includedCompartmentIds, excludedCompartmentIds);
- }
+ @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
+ @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
+ 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)
+ throws QueryException {
+ return projectController.getElements(projectId, id, columns, modelId, 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 756a4dabfd..8baf0a46d5 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
@@ -2,7 +2,8 @@ package lcsb.mapviewer.api.projects.models.bioEntities.elements;
import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -13,23 +14,8 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.Modification
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.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
@Transactional
@Service
@@ -42,7 +28,7 @@ public class ElementsRestImpl extends BaseRestImpl {
private Logger logger = LogManager.getLogger(ElementsRestImpl.class);
public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId,
- String type, String includedCompartmentIds, String excludedCompartmentIds)
+ String type, String includedCompartmentIds, String excludedCompartmentIds)
throws QueryException {
Set<Integer> ids = new LinkedHashSet<>();
if (!id.equals("")) {
@@ -138,98 +124,98 @@ public class ElementsRestImpl extends BaseRestImpl {
String column = string.toLowerCase();
Object value = null;
switch (column) {
- case "id":
- case "idobject":
- value = element.getId();
- break;
- case "modelid":
- value = element.getModelData().getId();
- break;
- case "elementid":
- value = element.getElementId();
- break;
- case "name":
- value = element.getName();
- break;
- case "type":
- value = element.getStringType();
- break;
- case "symbol":
- value = element.getSymbol();
- break;
- case "fullname":
- value = element.getFullName();
- break;
- case "abbreviation":
- value = element.getAbbreviation();
- break;
- case "compartmentid":
- if (element.getCompartment() != null) {
- value = element.getCompartment().getId();
- }
- break;
- case "complexid":
- if (element instanceof Species) {
- if (((Species) element).getComplex() != null) {
- value = ((Species) element).getComplex().getId();
- }
- }
- break;
- case "initialconcentration":
- if (element instanceof Species) {
- value = ((Species) element).getInitialConcentration();
- }
- break;
- case "initialamount":
- if (element instanceof Species) {
- value = ((Species) element).getInitialAmount();
- }
- break;
- case "boundarycondition":
- if (element instanceof Species) {
- value = ((Species) element).isBoundaryCondition();
- }
- break;
- case "constant":
- if (element instanceof Species) {
- value = ((Species) element).isConstant();
- }
- break;
- case "references":
- value = createAnnotations(element.getMiriamData());
- break;
- case "synonyms":
- value = element.getSynonyms();
- break;
- case "formula":
- value = element.getFormula();
- break;
- case "notes":
- value = element.getNotes();
- break;
- case "other":
- value = getOthersForElement(element);
- break;
- case "formersymbols":
- value = element.getFormerSymbols();
- break;
- case "hierarchyvisibilitylevel":
- value = element.getVisibilityLevel();
- break;
- case "transparencylevel":
- value = element.getTransparencyLevel();
- break;
- case "linkedsubmodel":
- if (element.getSubmodel() != null) {
- value = element.getSubmodel().getSubmodel().getId();
+ case "id":
+ case "idobject":
+ value = element.getId();
+ break;
+ case "modelid":
+ value = element.getModelData().getId();
+ break;
+ case "elementid":
+ value = element.getElementId();
+ break;
+ case "name":
+ value = element.getName();
+ break;
+ case "type":
+ value = element.getStringType();
+ break;
+ case "symbol":
+ value = element.getSymbol();
+ break;
+ case "fullname":
+ value = element.getFullName();
+ break;
+ case "abbreviation":
+ value = element.getAbbreviation();
+ break;
+ case "compartmentid":
+ if (element.getCompartment() != null) {
+ value = element.getCompartment().getId();
+ }
+ break;
+ case "complexid":
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() != null) {
+ value = ((Species) element).getComplex().getId();
}
- break;
- case "bounds":
- value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
- break;
- default:
- value = "Unknown column";
- break;
+ }
+ break;
+ case "initialconcentration":
+ if (element instanceof Species) {
+ value = ((Species) element).getInitialConcentration();
+ }
+ break;
+ case "initialamount":
+ if (element instanceof Species) {
+ value = ((Species) element).getInitialAmount();
+ }
+ break;
+ case "boundarycondition":
+ if (element instanceof Species) {
+ value = ((Species) element).isBoundaryCondition();
+ }
+ break;
+ case "constant":
+ if (element instanceof Species) {
+ value = ((Species) element).isConstant();
+ }
+ break;
+ case "references":
+ value = createAnnotations(element.getMiriamData());
+ break;
+ case "synonyms":
+ value = element.getSynonyms();
+ break;
+ case "formula":
+ value = element.getFormula();
+ break;
+ case "notes":
+ value = element.getNotes();
+ break;
+ case "other":
+ value = getOthersForElement(element);
+ break;
+ case "formersymbols":
+ value = element.getFormerSymbols();
+ break;
+ case "hierarchyvisibilitylevel":
+ value = element.getVisibilityLevel();
+ break;
+ case "transparencylevel":
+ value = element.getTransparencyLevel();
+ break;
+ case "linkedsubmodel":
+ if (element.getSubmodel() != null) {
+ value = element.getSubmodel().getSubmodel().getId();
+ }
+ break;
+ case "bounds":
+ value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
+ break;
+ default:
+ value = "Unknown column";
+ break;
}
result.put(string, value);
}
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 38ff797d2b..630088f526 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
@@ -5,11 +5,7 @@ import java.util.Map;
import org.springframework.http.MediaType;
import org.springframework.security.access.prepost.PreAuthorize;
-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 org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
@@ -18,23 +14,22 @@ import lcsb.mapviewer.api.QueryException;
@RequestMapping("/projects/{projectId}/models/{modelId}/bioEntities/reactions")
public class ReactionsController extends BaseController {
- private ReactionsRestImpl reactionController;
-
- public ReactionsController(ReactionsRestImpl reactionController) {
- this.reactionController = reactionController;
- }
-
- @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
- @RequestMapping(value = "/", 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,
- @RequestParam(value = "participantId", defaultValue = "") String participantId
- ) throws QueryException {
- return reactionController.getReactions(projectId, id, columns, modelId, participantId);
- }
+ private ReactionsRestImpl reactionController;
+
+ public ReactionsController(ReactionsRestImpl reactionController) {
+ this.reactionController = reactionController;
+ }
+
+ @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
+ @RequestMapping(value = "/", 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,
+ @RequestParam(value = "participantId", defaultValue = "") String participantId) throws QueryException {
+ return reactionController.getReactions(projectId, id, columns, modelId, 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 d677547b21..19aaf9f02c 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
@@ -6,7 +6,8 @@ import java.util.*;
import javax.xml.transform.TransformerException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -15,17 +16,9 @@ import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.geometry.PointTransformation;
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.kinetics.*;
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.reaction.*;
import lcsb.mapviewer.model.map.species.Element;
@Transactional
@@ -43,7 +36,7 @@ public class ReactionsRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId,
- String participantElementId) throws QueryException {
+ String participantElementId) throws QueryException {
Set<Integer> ids = new LinkedHashSet<>();
if (!id.equals("")) {
for (String str : id.split(",")) {
@@ -97,68 +90,68 @@ public class ReactionsRestImpl extends BaseRestImpl {
String column = string.toLowerCase();
Object value;
switch (column) {
- case "id":
- case "idobject":
- value = reaction.getId();
- break;
- case "modelid":
- value = reaction.getModelData().getId();
- break;
- case "reactionid":
- value = reaction.getIdReaction();
- break;
- case "name":
- value = reaction.getName();
- break;
- case "centerpoint":
- Line2D centerLine = reaction.getLine().getLines().get(reaction.getLine().getLines().size() / 2);
- value = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5);
- break;
- case "products": {
- List<Map<String, Object>> ids = new ArrayList<>();
- for (Product product : reaction.getProducts()) {
- ids.add(createReactionNode(product));
- }
- value = ids;
- break;
+ case "id":
+ case "idobject":
+ value = reaction.getId();
+ break;
+ case "modelid":
+ value = reaction.getModelData().getId();
+ break;
+ case "reactionid":
+ value = reaction.getIdReaction();
+ break;
+ case "name":
+ value = reaction.getName();
+ break;
+ case "centerpoint":
+ Line2D centerLine = reaction.getLine().getLines().get(reaction.getLine().getLines().size() / 2);
+ value = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5);
+ break;
+ case "products": {
+ List<Map<String, Object>> ids = new ArrayList<>();
+ for (Product product : reaction.getProducts()) {
+ ids.add(createReactionNode(product));
}
- case "reactants": {
- List<Map<String, Object>> ids = new ArrayList<>();
- for (Reactant reactant : reaction.getReactants()) {
- ids.add(createReactionNode(reactant));
- }
- value = ids;
- break;
+ value = ids;
+ break;
+ }
+ case "reactants": {
+ List<Map<String, Object>> ids = new ArrayList<>();
+ for (Reactant reactant : reaction.getReactants()) {
+ ids.add(createReactionNode(reactant));
}
- case "modifiers": {
- List<Map<String, Object>> ids = new ArrayList<>();
- for (Modifier modifier : reaction.getModifiers()) {
- ids.add(createReactionNode(modifier));
- }
- value = ids;
- break;
+ value = ids;
+ break;
+ }
+ case "modifiers": {
+ List<Map<String, Object>> ids = new ArrayList<>();
+ for (Modifier modifier : reaction.getModifiers()) {
+ ids.add(createReactionNode(modifier));
}
- case "type":
- value = reaction.getStringType();
- break;
- case "hierarchyvisibilitylevel":
- value = reaction.getVisibilityLevel();
- break;
- case "lines":
- value = getLines(reaction);
- break;
- case "notes":
- value = reaction.getNotes();
- break;
- case "kineticlaw":
- value = kineticsToMap(reaction.getKinetics());
- break;
- case "references":
- value = createAnnotations(reaction.getMiriamData());
- break;
- default:
- value = "Unknown column";
- break;
+ value = ids;
+ break;
+ }
+ case "type":
+ value = reaction.getStringType();
+ break;
+ case "hierarchyvisibilitylevel":
+ value = reaction.getVisibilityLevel();
+ break;
+ case "lines":
+ value = getLines(reaction);
+ break;
+ case "notes":
+ value = reaction.getNotes();
+ break;
+ case "kineticlaw":
+ value = kineticsToMap(reaction.getKinetics());
+ break;
+ case "references":
+ value = createAnnotations(reaction.getMiriamData());
+ break;
+ default:
+ value = "Unknown column";
+ break;
}
result.put(string, value);
}
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 8237c947b8..28fe17044f 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
@@ -27,8 +27,7 @@ public class FunctionsController extends BaseController {
public Map<String, Object> getFunction(
@PathVariable(value = "projectId") String projectId,
@PathVariable(value = "modelId") String modelId,
- @PathVariable(value = "functionId") String functionId
- ) throws QueryException {
+ @PathVariable(value = "functionId") String functionId) throws QueryException {
return functionController.getFunction(projectId, modelId, functionId);
}
@@ -36,8 +35,7 @@ public class FunctionsController extends BaseController {
@GetMapping(value = "/")
public List<Map<String, Object>> getFunctions(
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "modelId") String modelId
- ) throws QueryException {
+ @PathVariable(value = "modelId") String modelId) throws QueryException {
return functionController.getFunctions(projectId, modelId);
}
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 e2dc966ac3..af01f2ecf9 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
@@ -1,18 +1,11 @@
package lcsb.mapviewer.api.projects.models.functions;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
+import java.io.*;
+import java.util.*;
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.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
@@ -20,15 +13,11 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
+import org.w3c.dom.*;
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.api.*;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.model.Model;
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 6c45b34dcf..e9d2aebe0b 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
@@ -12,8 +12,7 @@ import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
@RestController
-@RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters",
- produces = MediaType.APPLICATION_JSON_VALUE)
+@RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters", produces = MediaType.APPLICATION_JSON_VALUE)
public class ParametersController extends BaseController {
private ParametersRestImpl parameterController;
@@ -28,8 +27,7 @@ public class ParametersController extends BaseController {
public Map<String, Object> getParameter(
@PathVariable(value = "projectId") String projectId,
@PathVariable(value = "modelId") String modelId,
- @PathVariable(value = "parameterId") String parameterId
- ) throws QueryException {
+ @PathVariable(value = "parameterId") String parameterId) throws QueryException {
return parameterController.getParameter(projectId, modelId, parameterId);
}
@@ -37,8 +35,7 @@ public class ParametersController extends BaseController {
@GetMapping(value = "/")
public List<Map<String, Object>> getParameters(
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "modelId") String modelId
- ) throws QueryException {
+ @PathVariable(value = "modelId") String modelId) throws QueryException {
return parameterController.getParameters(projectId, modelId);
}
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 337029b853..62ef329cc8 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
@@ -1,19 +1,13 @@
package lcsb.mapviewer.api.projects.models.parameters;
-import java.util.ArrayList;
-import java.util.TreeMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.*;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
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 2bfe2e6093..cbf66d0a60 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
@@ -11,29 +11,27 @@ import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
@RestController
-@RequestMapping(value = "/projects/{projectId}/models/{modelId}/publications",
- produces = MediaType.APPLICATION_JSON_VALUE)
+@RequestMapping(value = "/projects/{projectId}/models/{modelId}/publications", produces = MediaType.APPLICATION_JSON_VALUE)
public class PublicationsController extends BaseController {
- private PublicationsRestImpl projectController;
-
- @Autowired
- public PublicationsController(PublicationsRestImpl projectController) {
- this.projectController = projectController;
- }
-
- @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
- @GetMapping(value = "/")
- public Map<String, Object> getPublications(
- @PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "modelId") String modelId,
- @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 {
- return projectController.getPublications(projectId, modelId, start, length, sortColumn, sortOrder, search);
- }
+ private PublicationsRestImpl projectController;
+
+ @Autowired
+ public PublicationsController(PublicationsRestImpl projectController) {
+ this.projectController = projectController;
+ }
+
+ @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
+ @GetMapping(value = "/")
+ public Map<String, Object> getPublications(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @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 {
+ return projectController.getPublications(projectId, modelId, 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 0cec45bf48..8ba10793a1 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
@@ -1,18 +1,11 @@
package lcsb.mapviewer.api.projects.models.publications;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import java.util.Map.Entry;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -24,9 +17,7 @@ import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.comparator.IntegerComparator;
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.*;
import lcsb.mapviewer.model.map.model.Model;
@Transactional
@@ -65,20 +56,6 @@ public class PublicationsRestImpl extends BaseRestImpl {
return publications;
}
- 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 startString, Integer length,
String sortColumn, String sortOrder, String search) throws QueryException {
@@ -94,8 +71,8 @@ public class PublicationsRestImpl extends BaseRestImpl {
List<Map.Entry<MiriamData, List<BioEntity>>> filteredList = new ArrayList<>();
for (Map.Entry<MiriamData, List<BioEntity>> entry : publications.entrySet()) {
- Set<Model> publicationModels= new LinkedHashSet<>();
- for (BioEntity bioEntity: entry.getValue()) {
+ Set<Model> publicationModels = new LinkedHashSet<>();
+ for (BioEntity bioEntity : entry.getValue()) {
publicationModels.add(bioEntity.getModel());
}
if (isSearchResult(entry.getKey(), search, publicationModels)) {
@@ -282,4 +259,18 @@ public class PublicationsRestImpl extends BaseRestImpl {
}
+ enum SortColumn {
+ PUBMED_ID("pubmedId"),
+ YEAR("year"),
+ JOURNAL("journal"),
+ TITLE("title"),
+ AUTHORS("authors");
+
+ private String commonName;
+
+ SortColumn(String commonName) {
+ this.commonName = commonName;
+ }
+ }
+
}
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 64643ca83c..9b815e03ae 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
@@ -27,8 +27,7 @@ public class UnitsController extends BaseController {
public Map<String, Object> getUnit(
@PathVariable(value = "projectId") String projectId,
@PathVariable(value = "modelId") String modelId,
- @PathVariable(value = "unitId") String unitId
- ) throws QueryException {
+ @PathVariable(value = "unitId") String unitId) throws QueryException {
return unitController.getUnit(projectId, modelId, unitId);
}
@@ -36,8 +35,7 @@ public class UnitsController extends BaseController {
@GetMapping(value = "/")
public List<Map<String, Object>> getUnits(
@PathVariable(value = "projectId") String projectId,
- @PathVariable(value = "modelId") String modelId
- ) throws QueryException {
+ @PathVariable(value = "modelId") String modelId) throws QueryException {
return unitController.getUnits(projectId, modelId);
}
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 5ae03239d7..b276f87957 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
@@ -1,17 +1,13 @@
package lcsb.mapviewer.api.projects.models.units;
-import java.util.ArrayList;
-import java.util.TreeMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.*;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
import lcsb.mapviewer.model.map.model.Model;
@@ -54,7 +50,7 @@ public class UnitsRestImpl extends BaseRestImpl {
}
private Map<String, Object> factorToMap(SbmlUnitTypeFactor factor) {
- Map<String, Object> result = new TreeMap<>();
+ Map<String, Object> result = new TreeMap<>();
result.put("id", factor.getId());
result.put("exponent", factor.getExponent());
result.put("multiplier", factor.getMultiplier());
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 ea8ab18960..fd8a5c6044 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
@@ -42,7 +42,8 @@ public class OverlayController extends BaseController {
@RequestParam(value = "publicOverlay", defaultValue = "false") boolean publicOverlay) {
return overlayRestImp.getOverlayList(projectId).stream()
.filter(overlay -> !publicOverlay || (Boolean) overlay.get("publicOverlay"))
- .filter(overlay -> creator.isEmpty() || (overlay.get("creator") != null && overlay.get("creator").equals(creator)))
+ .filter(
+ overlay -> creator.isEmpty() || (overlay.get("creator") != null && overlay.get("creator").equals(creator)))
.collect(Collectors.toList());
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyController.java b/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyController.java
index eb5e97fce8..ea6dbf812f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyController.java
@@ -2,14 +2,15 @@ package lcsb.mapviewer.api.taxonomy;
import java.util.Map;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.*;
+import lcsb.mapviewer.annotation.services.TaxonomySearchException;
import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
@RestController
@RequestMapping(value = "/taxonomy", produces = MediaType.APPLICATION_JSON_VALUE)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyRestImpl.java
index 9285e330a5..d2290bcfa1 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/taxonomy/TaxonomyRestImpl.java
@@ -3,7 +3,8 @@ package lcsb.mapviewer.api.taxonomy;
import java.util.Map;
import java.util.TreeMap;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
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 69d1187ba0..4ff58ffd83 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
@@ -4,7 +4,6 @@ import java.io.IOException;
import java.util.*;
import java.util.stream.Collectors;
-import lcsb.mapviewer.common.Configuration;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@@ -15,7 +14,7 @@ import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.api.*;
-import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.services.interfaces.IUserService;
@RestController
@@ -23,7 +22,7 @@ import lcsb.mapviewer.services.interfaces.IUserService;
public class UserController extends BaseController {
Logger logger = LogManager.getLogger();
-
+
private IUserService userService;
private UserRestImpl userRest;
@@ -41,7 +40,7 @@ public class UserController extends BaseController {
@GetMapping(value = "/isSessionValid")
@PreAuthorize("isAuthenticated() and authentication.name != '" + Configuration.ANONYMOUS_LOGIN + "'")
public Object isSessionValid(Authentication authentication) {
- Map<String,Object> result = new TreeMap<>();
+ Map<String, Object> result = new TreeMap<>();
result.put("login", authentication.getName());
return result;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 6ad901b578..64a2d48d50 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -2,36 +2,22 @@ package lcsb.mapviewer.api.users;
import java.util.*;
-import lcsb.mapviewer.model.security.PrivilegeType;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.crypto.password.PasswordEncoder;
import org.springframework.stereotype.Service;
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.OperationNotAllowedException;
-import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.*;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
import lcsb.mapviewer.model.security.Privilege;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserClassAnnotators;
-import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
-import lcsb.mapviewer.model.user.UserClassValidAnnotations;
-import lcsb.mapviewer.model.user.UserGuiPreference;
-import lcsb.mapviewer.model.user.annotator.AnnotatorConfigParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import lcsb.mapviewer.model.security.PrivilegeType;
+import lcsb.mapviewer.model.user.*;
+import lcsb.mapviewer.model.user.annotator.*;
@Transactional
@Service
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/BaseControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/BaseControllerTest.java
index 91a4f789eb..25d4046b49 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/BaseControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/BaseControllerTest.java
@@ -6,10 +6,7 @@ import static org.mockito.Mockito.CALLS_REAL_METHODS;
import java.util.Map;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.*;
import org.mockito.Mockito;
public class BaseControllerTest {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
index b8956aa191..77e415ea34 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.api;
import static org.junit.Assert.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.CALLS_REAL_METHODS;
import java.util.List;
import java.util.Map;
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 819a8d1da9..52c60423bf 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.api;
-import static org.mockito.ArgumentMatchers.*;
+import static org.mockito.ArgumentMatchers.anyString;
import java.io.*;
import java.net.URL;
@@ -47,11 +47,9 @@ import lcsb.mapviewer.services.interfaces.*;
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class RestTestFunctions {
+ private static Map<String, Model> models = new HashMap<>();
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
- private Logger logger = LogManager.getLogger(RestTestFunctions.class);
-
public double EPSILON = 1e-6;
@Autowired
@@ -66,6 +64,7 @@ public abstract class RestTestFunctions {
protected String username;
protected String adminToken;
+ private Logger logger = LogManager.getLogger(RestTestFunctions.class);
@Before
public void generalSetUp() {
@@ -142,8 +141,6 @@ public abstract class RestTestFunctions {
return doc;
}
- private static Map<String, Model> models = new HashMap<>();
-
protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
Model result = null;
if (!fromCache) {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/SpringRestApiTestConfig.java b/rest-api/src/test/java/lcsb/mapviewer/api/SpringRestApiTestConfig.java
index ac7262267a..697a1f1860 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/SpringRestApiTestConfig.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/SpringRestApiTestConfig.java
@@ -1,12 +1,11 @@
package lcsb.mapviewer.api;
+import org.springframework.context.annotation.*;
+import org.springframework.security.core.session.SessionRegistryImpl;
+
import lcsb.mapviewer.annotation.SpringAnnotationConfig;
import lcsb.mapviewer.persist.SpringPersistConfig;
import lcsb.mapviewer.services.SpringServiceConfig;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
-import org.springframework.security.core.session.SessionRegistryImpl;
@Configuration
@Import({
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
index 5fb67137f0..84615b6126 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
@@ -19,11 +19,10 @@ import lcsb.mapviewer.model.user.annotator.BioEntityField;
public class ConfigurationRestImplTest extends RestTestFunctions {
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(ConfigurationRestImplTest.class);
-
@Autowired
public ConfigurationRestImpl configurationRestImpl;
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(ConfigurationRestImplTest.class);
@AfterClass
public static void tearDownAfterClass() throws Exception {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
index b94871d6fb..0c69b7ff2f 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
@@ -24,11 +24,10 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
public class ConvertRestImplTest extends RestTestFunctions {
- @SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger(ConvertRestImplTest.class);
-
@Autowired
public ConvertRestImpl convertRestImpl;
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(ConvertRestImplTest.class);
@AfterClass
public static void tearDownAfterClass() throws Exception {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
index c282688096..413ae7eadb 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
@@ -1,20 +1,18 @@
package lcsb.mapviewer.api.files;
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.*;
import java.util.Map;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IUserService;
import org.apache.commons.lang3.ArrayUtils;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+import lcsb.mapviewer.services.interfaces.IUserService;
public class FileRestImplTest extends RestTestFunctions {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
index 3caee1b2fe..feb41d73e4 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.genomics;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import java.util.List;
import java.util.Map;
@@ -14,10 +15,9 @@ import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
public class ReferenceGenomeControllerTest extends RestTestFunctions {
- Logger logger = LogManager.getLogger(ReferenceGenomeControllerTest.class);
-
@Autowired
public ReferenceGenomeRestImpl referenceGenomeRestImpl;
+ Logger logger = LogManager.getLogger(ReferenceGenomeControllerTest.class);
@AfterClass
public static void tearDownAfterClass() throws Exception {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java
index 3faec73672..5cf68a4d88 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java
@@ -5,7 +5,8 @@ import static org.junit.Assert.assertTrue;
import java.util.Map;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
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 1e03f78932..d97c2772b4 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.api.projects;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.times;
import java.util.*;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
index a89809ec7d..476579347e 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.api.projects.chemicals;
-import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.ArgumentMatchers.anyString;
import java.util.ArrayList;
import java.util.Map;
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 56729f273b..a41ef74ff9 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
@@ -1,7 +1,8 @@
package lcsb.mapviewer.api.projects.comments;
-import static org.mockito.ArgumentMatchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.times;
import java.util.ArrayList;
import java.util.List;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
index 94c82b5e78..b1ee837dba 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.api.projects.drugs;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.util.List;
import java.util.Map;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java
index 0cc98a4983..8a1d5e8c6b 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.api.projects.mirnas;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
import java.util.*;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
index e61b549aa1..0c494545f7 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
@@ -1,7 +1,9 @@
package lcsb.mapviewer.api.projects.models;
-import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.ArgumentMatchers.refEq;
import java.util.*;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
index 9483cb1af5..26935e8e93 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
@@ -1,7 +1,8 @@
package lcsb.mapviewer.api.projects.models.bioEntities;
-import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.ArgumentMatchers.anyString;
import java.awt.geom.Point2D;
import java.util.List;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index bf4ffea57d..13e2a706c1 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.api.projects.models.bioEntities.elements;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
+import static org.mockito.ArgumentMatchers.anyString;
import java.util.List;
import java.util.Map;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImplTest.java
index e5ca846db1..39825c8d23 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImplTest.java
@@ -10,9 +10,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
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.model.map.reaction.*;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class ReactionsRestImplTest extends RestTestFunctions {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImplTest.java
index 2d5b428fc7..2b2ca8b6ec 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImplTest.java
@@ -1,10 +1,9 @@
package lcsb.mapviewer.api.projects.models.functions;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
@@ -17,7 +16,7 @@ public class FunctionsRestImplTest extends RestTestFunctions {
FunctionsRestImpl functionRestImpl;
@Test
- public void testExtractLambda() throws Exception{
+ public void testExtractLambda() throws Exception {
String lambda = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<lambda>\n<bvar>\n<ci> x </ci>\n</bvar>\n<bvar>\n<ci> y </ci>\n</bvar>\n<apply>\n<plus/>\n<ci> x </ci>\n<ci> y </ci>\n<cn type=\"integer\"> 2 </cn>\n</apply>\n</lambda>\n\n</math>";
String definition = functionRestImpl.extractLambda(lambda);
assertNotNull(definition);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
index 738a8cbabc..778f7bebe4 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.api.projects.models.publications;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.*;
+import static org.mockito.ArgumentMatchers.anyString;
import java.util.*;
import java.util.Map.Entry;
@@ -104,8 +104,8 @@ public class PublicationsRestImplTest extends RestTestFunctions {
Entry<MiriamData, List<BioEntity>> valid = new Entry<MiriamData, List<BioEntity>>() {
@Override
- public List<BioEntity> setValue(List<BioEntity> value) {
- return null;
+ public MiriamData getKey() {
+ return new MiriamData(MiriamType.PUBMED, "12345");
}
@Override
@@ -114,15 +114,15 @@ public class PublicationsRestImplTest extends RestTestFunctions {
}
@Override
- public MiriamData getKey() {
- return new MiriamData(MiriamType.PUBMED, "12345");
+ public List<BioEntity> setValue(List<BioEntity> value) {
+ return null;
}
};
Entry<MiriamData, List<BioEntity>> invalid = new Entry<MiriamData, List<BioEntity>>() {
@Override
- public List<BioEntity> setValue(List<BioEntity> value) {
- return null;
+ public MiriamData getKey() {
+ return new MiriamData(MiriamType.PUBMED, "");
}
@Override
@@ -131,8 +131,8 @@ public class PublicationsRestImplTest extends RestTestFunctions {
}
@Override
- public MiriamData getKey() {
- return new MiriamData(MiriamType.PUBMED, "");
+ public List<BioEntity> setValue(List<BioEntity> value) {
+ return null;
}
};
for (SortColumn sortColumn : SortColumn.values()) {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java
index 219f1f7fc1..40702e8a56 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.api.projects.overlays;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import java.util.HashMap;
import java.util.Map;
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 6a6d678f9d..45db6982c7 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.users;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import java.io.IOException;
import java.util.*;
diff --git a/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java b/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java
index 4a184fd3e2..e52ae97df7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java
@@ -2,13 +2,13 @@ package lcsb.mapviewer.services;
public class AuthenticationTokenExpireException extends SecurityException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public AuthenticationTokenExpireException(String message) {
- super(message);
- }
+ /**
+ *
+ */
+ 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 a82e8327f9..99d9bd620a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/InvalidTokenException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/InvalidTokenException.java
@@ -2,13 +2,13 @@ package lcsb.mapviewer.services;
public class InvalidTokenException extends SecurityException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public InvalidTokenException(String message) {
- super(message);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public InvalidTokenException(String message) {
+ super(message);
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/SpringServiceConfig.java b/service/src/main/java/lcsb/mapviewer/services/SpringServiceConfig.java
index a096e18f1a..c6adf62708 100644
--- a/service/src/main/java/lcsb/mapviewer/services/SpringServiceConfig.java
+++ b/service/src/main/java/lcsb/mapviewer/services/SpringServiceConfig.java
@@ -1,17 +1,15 @@
package lcsb.mapviewer.services;
-import lcsb.mapviewer.annotation.SpringAnnotationConfig;
-import lcsb.mapviewer.persist.SpringPersistConfig;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.*;
import org.springframework.security.core.session.SessionRegistry;
import org.springframework.security.core.session.SessionRegistryImpl;
+import lcsb.mapviewer.annotation.SpringAnnotationConfig;
+import lcsb.mapviewer.persist.SpringPersistConfig;
+
@Configuration
-@Import({SpringPersistConfig.class, SpringAnnotationConfig.class})
-@ComponentScan(basePackages = {"lcsb.mapviewer.services"})
+@Import({ SpringPersistConfig.class, SpringAnnotationConfig.class })
+@ComponentScan(basePackages = { "lcsb.mapviewer.services" })
public class SpringServiceConfig {
@Bean
diff --git a/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java b/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java
index 53c705b7ba..6db890b9f7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java
@@ -2,13 +2,13 @@ package lcsb.mapviewer.services;
public class UserAccessException extends SecurityException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public UserAccessException(String message) {
- super(message);
- }
+ /**
+ *
+ */
+ 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 71dc451801..3e4268803e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -1,14 +1,12 @@
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 java.util.*;
import javax.mail.MessagingException;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -23,10 +21,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.CommentDao;
-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.interfaces.*;
import lcsb.mapviewer.services.utils.EmailSender;
/**
@@ -74,9 +69,9 @@ public class CommentService implements ICommentService {
@Autowired
public CommentService(CommentDao commentDao,
- IModelService modelService,
- IUserService userService,
- IConfigurationService configurationService) {
+ IModelService modelService,
+ IUserService userService,
+ IConfigurationService configurationService) {
this.commentDao = commentDao;
this.modelService = modelService;
this.userService = userService;
@@ -85,7 +80,7 @@ public class CommentService implements ICommentService {
@Override
public Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
- boolean pinned, Model submodel) {
+ boolean pinned, Model submodel) {
Comment comment = new Comment();
comment.setName(name);
comment.setEmail(email);
@@ -120,6 +115,74 @@ public class CommentService implements ICommentService {
return comment;
}
+ @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 void deleteComment(Comment comment, String reason) {
+ comment.setDeleted(true);
+ comment.setRemoveReason(reason);
+ commentDao.update(comment);
+ }
+
+ @Override
+ public List<Comment> getCommentsByProject(Project 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 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);
+ }
+ }
+
+ @Override
+ public void removeCommentsForModel(ModelData model) {
+ List<Comment> comments = commentDao.getCommentByModel(model, null, null);
+ for (Comment comment : comments) {
+ commentDao.delete(comment);
+ }
+ }
+
+ @Override
+ public Comment getCommentById(String commentId) {
+ int id = -1;
+ try {
+ id = Integer.parseInt(commentId);
+ } catch (NumberFormatException e) {
+ }
+ return commentDao.getById(id);
+ }
+
/**
* This method returns all comments for model agregated by commented elements.
*
@@ -159,38 +222,6 @@ public class CommentService implements ICommentService {
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
@@ -259,14 +290,6 @@ public class CommentService implements ICommentService {
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.
*
@@ -292,32 +315,4 @@ public class CommentService implements ICommentService {
&& !(Math.abs(y1 - y2) > COMMENT_POINT_DISTANCE_EPSILON);
}
- @Override
- public List<Comment> getCommentsByProject(Project 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 reason) {
- comment.setDeleted(true);
- comment.setRemoveReason(reason);
- commentDao.update(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 768f520835..abce6cca70 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ConfigurationService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ConfigurationService.java
@@ -3,10 +3,10 @@ package lcsb.mapviewer.services.impl;
import java.util.ArrayList;
import java.util.List;
-import lcsb.mapviewer.model.security.PrivilegeType;
import org.apache.commons.lang3.EnumUtils;
import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -14,9 +14,8 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.FrameworkVersion;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.user.ConfigurationElementEditType;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.security.PrivilegeType;
+import lcsb.mapviewer.model.user.*;
import lcsb.mapviewer.persist.dao.ConfigurationDao;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
@@ -119,16 +118,6 @@ public class ConfigurationService implements IConfigurationService {
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) {
@@ -142,13 +131,17 @@ public class ConfigurationService implements IConfigurationService {
}
@Override
- public String getSystemGitVersion(String baseDir) {
- return lcsb.mapviewer.common.Configuration.getSystemBuildVersion(baseDir);
+ public Long getMemoryUsage() {
+ Runtime runtime = Runtime.getRuntime();
+
+ return (runtime.totalMemory() - runtime.freeMemory()) / MEGABYTE_SIZE;
}
@Override
- public String getSystemBuild(String baseDir) {
- return lcsb.mapviewer.common.Configuration.getSystemBuild(baseDir);
+ public Long getMaxMemory() {
+ Runtime runtime = Runtime.getRuntime();
+
+ return runtime.maxMemory() / MEGABYTE_SIZE;
}
@Override
@@ -157,17 +150,23 @@ public class ConfigurationService implements IConfigurationService {
}
@Override
- public Long getMemoryUsage() {
- Runtime runtime = Runtime.getRuntime();
-
- return (runtime.totalMemory() - runtime.freeMemory()) / MEGABYTE_SIZE;
+ public String getSystemBuild(String baseDir) {
+ return lcsb.mapviewer.common.Configuration.getSystemBuild(baseDir);
}
@Override
- public Long getMaxMemory() {
- Runtime runtime = Runtime.getRuntime();
+ public String getSystemGitVersion(String baseDir) {
+ return lcsb.mapviewer.common.Configuration.getSystemBuildVersion(baseDir);
+ }
- return runtime.maxMemory() / MEGABYTE_SIZE;
+ @Override
+ public ConfigurationOption getValue(ConfigurationElementType type) {
+ ConfigurationOption configuration = configurationDao.getByType(type);
+ if (configuration == null) {
+ getConfigurationValue(type);
+ configuration = configurationDao.getByType(type);
+ }
+ return configuration;
}
@Override
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoder.java b/service/src/main/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoder.java
index 5e170d0197..1b36d9175e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoder.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoder.java
@@ -16,42 +16,42 @@ import org.springframework.security.crypto.password.PasswordEncoder;
*/
public class CustomMd5PasswordEncoder implements PasswordEncoder {
- @Override
- public String encode(CharSequence password) {
+ /**
+ * 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;
+ }
- 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 String encode(CharSequence password) {
- @Override
- public boolean matches(CharSequence arg0, String arg1) {
- return encode(arg0).equals(arg1);
- }
+ 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;
+ }
- /**
- * 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;
- }
+ @Override
+ public boolean matches(CharSequence arg0, String arg1) {
+ return encode(arg0).equals(arg1);
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java b/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java
index fe9cd97e3a..8519510c35 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/FileService.java
@@ -1,12 +1,13 @@
package lcsb.mapviewer.services.impl;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
-import lcsb.mapviewer.services.interfaces.IFileService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+import lcsb.mapviewer.services.interfaces.IFileService;
+
@Transactional
@Service
public class FileService implements IFileService {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 0cf9d42a3b..83cc8fe1e6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -1,29 +1,22 @@
package lcsb.mapviewer.services.impl;
-import java.awt.Color;
+import java.awt.*;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
+import java.util.*;
import java.util.Comparator;
import java.util.List;
-import java.util.Map;
import javax.mail.MessagingException;
import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.commands.*;
+import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.MapGenerator;
@@ -33,14 +26,7 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.DataOverlayImageLayer;
-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.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.LayoutStatus;
+import lcsb.mapviewer.model.map.layout.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -48,9 +34,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.map.LayoutDao;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.interfaces.*;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
@@ -65,8 +49,8 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
@Service
public class LayoutService implements ILayoutService {
- private static final Comparator<? super Pair<? extends BioEntity, ColorSchema>> ELEMENT_PAIR_COMPARATOR =
- Comparator.comparingInt(o -> o.getLeft().getId());
+ private static final Comparator<? super Pair<? extends BioEntity, ColorSchema>> ELEMENT_PAIR_COMPARATOR = Comparator
+ .comparingInt(o -> o.getLeft().getId());
/**
* Default class logger.
@@ -101,9 +85,9 @@ public class LayoutService implements ILayoutService {
@Autowired
public LayoutService(LayoutDao layoutDao,
- IUserService userService,
- IConfigurationService configurationService,
- DbUtils dbUtils) {
+ IUserService userService,
+ IConfigurationService configurationService,
+ DbUtils dbUtils) {
this.layoutDao = layoutDao;
this.userService = userService;
this.configurationService = configurationService;
@@ -164,6 +148,65 @@ public class LayoutService implements ILayoutService {
layoutDao.update(layout);
}
+ @Override
+ public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
+ if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && params.getColorSchemaType() != null) {
+ parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, params.getColorSchemaType().name());
+ }
+ final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(), parameters);
+
+ // check if we can color our model using this schema,
+ // if not then exception will be thrown and passed up
+ try {
+ Model model = params.getProject().getModels().iterator().next().getModel();
+ Model copy = new CopyCommand(model).execute();
+ new ColorModelCommand(copy, schemas, userService.getColorExtractorForUser(params.getUser())).execute();
+ } catch (CommandExecutionException e) {
+ throw new InvalidColorSchemaException(e);
+ }
+
+ layoutDao.flush();
+
+ Layout topLayout = new Layout(params.getName(), false);
+ topLayout.setColorSchemaType(params.getColorSchemaType());
+ if (params.getUser() == null) {
+ topLayout.setPublicLayout(true);
+ } else {
+ topLayout.setPublicLayout(false);
+ }
+ topLayout.setGoogleLicenseConsent(params.isGoogleLicenseConsent());
+ topLayout.setStatus(LayoutStatus.OK);
+ topLayout.setProgress(0.0);
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
+ fileEntry.setOriginalFileName(params.getLayoutFileName());
+ fileEntry.setLength(fileEntry.getFileContent().length);
+ fileEntry.setOwner(params.getUser());
+ topLayout.setInputData(fileEntry);
+ topLayout.setDescription(params.getDescription());
+ topLayout.setProject(params.getProject());
+ topLayout.setCreator(params.getUser());
+ layoutDao.add(topLayout);
+
+ Thread sendEmailThread = new Thread(() -> {
+ try {
+ // open transaction for this thread
+ dbUtils.createSessionForCurrentThread();
+ sendSuccessfullGenerationEmail(params, schemas);
+ } catch (MessagingException e) {
+ logger.error("Problem with sending email", e);
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ });
+
+ logger.info("Data overlay " + topLayout.getId() + " created successfully");
+ sendEmailThread.start();
+ return topLayout;
+ }
+
@Override
public Layout createLayoutWithImages(final CreateLayoutParams params)
throws IOException, InvalidColorSchemaException, CommandExecutionException {
@@ -304,62 +347,134 @@ public class LayoutService implements ILayoutService {
}
@Override
- public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
- ColorSchemaReader reader = new ColorSchemaReader();
- Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
- if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && params.getColorSchemaType() != null) {
- parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, params.getColorSchemaType().name());
+ public List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId) {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ List<Pair<Element, ColorSchema>> result = new ArrayList<>();
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Element) {
+ result.add(new Pair<>((Element) entry.getKey(), entry.getValue()));
+ }
+ }
+ result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
+ return result;
+ } catch (InvalidColorSchemaException | IOException e) {
+ throw new InvalidStateException(e);
}
- final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(), parameters);
+ }
- // check if we can color our model using this schema,
- // if not then exception will be thrown and passed up
+ @Override
+ public List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId) {
try {
- Model model = params.getProject().getModels().iterator().next().getModel();
- Model copy = new CopyCommand(model).execute();
- new ColorModelCommand(copy, schemas, userService.getColorExtractorForUser(params.getUser())).execute();
- } catch (CommandExecutionException e) {
- throw new InvalidColorSchemaException(e);
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ List<Pair<Reaction, ColorSchema>> result = new ArrayList<>();
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Reaction) {
+ result.add(new Pair<>((Reaction) entry.getKey(), entry.getValue()));
+ }
+ }
+ result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
+ return result;
+ } catch (InvalidColorSchemaException | IOException e) {
+ throw new InvalidStateException(e);
}
+ }
- layoutDao.flush();
+ @Override
+ public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId) {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+ return command.getModifiedElements();
+ } catch (InvalidColorSchemaException | IOException e) {
+ throw new InvalidStateException(e);
+ }
+ }
- Layout topLayout = new Layout(params.getName(), false);
- topLayout.setColorSchemaType(params.getColorSchemaType());
- if (params.getUser() == null) {
- topLayout.setPublicLayout(true);
- } else {
- topLayout.setPublicLayout(false);
+ @Override
+ public Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId) {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Element) {
+ Element alias = (Element) entry.getKey();
+ if (id.equals(alias.getId())) {
+ return new Pair<>(alias, entry.getValue());
+ }
+ }
+ }
+ return null;
+ } catch (InvalidColorSchemaException | IOException e) {
+ throw new InvalidStateException(e);
}
- topLayout.setGoogleLicenseConsent(params.isGoogleLicenseConsent());
- topLayout.setStatus(LayoutStatus.OK);
- topLayout.setProgress(0.0);
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
- fileEntry.setOriginalFileName(params.getLayoutFileName());
- fileEntry.setLength(fileEntry.getFileContent().length);
- fileEntry.setOwner(params.getUser());
- topLayout.setInputData(fileEntry);
- topLayout.setDescription(params.getDescription());
- topLayout.setProject(params.getProject());
- topLayout.setCreator(params.getUser());
- layoutDao.add(topLayout);
+ }
- Thread sendEmailThread = new Thread(() -> {
- try {
- // open transaction for this thread
- dbUtils.createSessionForCurrentThread();
- sendSuccessfullGenerationEmail(params, schemas);
- } catch (MessagingException e) {
- logger.error("Problem with sending email", e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
+ @Override
+ public Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId) {
+ try {
+ Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
+ // colors here are not important
+ ColorModelCommand command = new ColorModelCommand(model, schemas,
+ new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
+
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Reaction) {
+ Reaction alias = (Reaction) entry.getKey();
+ if (id.equals(alias.getId())) {
+ return new Pair<>(alias, entry.getValue());
+ }
+ }
}
- });
+ return null;
+ } catch (InvalidColorSchemaException | IOException e) {
+ throw new InvalidStateException(e);
+ }
+ }
- logger.info("Data overlay " + topLayout.getId() + " created successfully");
- sendEmailThread.start();
- return topLayout;
+ @Override
+ public EmailSender getEmailSender() {
+ if (emailSender == null) {
+ emailSender = new EmailSender(configurationService);
+ }
+ return emailSender;
+ }
+
+ @Override
+ public void setEmailSender(EmailSender emailSender) {
+ this.emailSender = emailSender;
+ }
+
+ @Override
+ public List<Layout> getLayoutsByProject(Project project) {
+ List<Layout> result = new ArrayList<>();
+ if (project == null) {
+ return result;
+ }
+ List<Layout> overlays = layoutDao.getLayoutsByProject(project);
+ result.addAll(overlays);
+ result.sort(Layout.ID_COMPARATOR);
+ return result;
+ }
+
+ @Override
+ public Layout getLayoutById(int overlayId) {
+ return layoutDao.getById(overlayId);
+ }
+
+ public void setLayoutDao(LayoutDao layoutDao) {
+ this.layoutDao = layoutDao;
}
/**
@@ -541,125 +656,125 @@ public class LayoutService implements ILayoutService {
return sb.toString();
}
- /**
- * Returns String representing data of {@link GenericColorSchema} that should
- * appear in a given {@link ColorSchemaColumn}.
- *
- * @param schema
- * object for which data will be returned
- * @param column
- * column for which data should be returned
- * @return {@link String} representing data of {@link GenericColorSchema} that
- * should appear in a given {@link ColorSchemaColumn}
- */
- protected String prepareTableCellForGenericSchema(GenericColorSchema schema, ColorSchemaColumn column) {
- StringBuilder sb = new StringBuilder();
- if (column.equals(ColorSchemaColumn.COLOR)) {
- if (schema.getColor() != null) {
- sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.NAME)) {
- sb.append(schema.getName() + "\t");
- } else if (column.equals(ColorSchemaColumn.MAP_NAME)) {
- sb.append(schema.getModelName() + "\t");
- } else if (column.equals(ColorSchemaColumn.VALUE)) {
- sb.append(schema.getValue() + "\t");
- } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
- for (String str : schema.getCompartments()) {
- sb.append(str + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.TYPE)) {
- for (Class<? extends Element> str : schema.getTypes()) {
- sb.append(str.getSimpleName() + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
- for (MiriamData md : schema.getMiriamData()) {
- sb.append(md.getDataType().getCommonName() + ": " + md.getResource() + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
- sb.append(schema.getElementId() + "\t");
- } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
- sb.append(schema.getLineWidth() + "\t");
- } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
- sb.append(schema.getReverseReaction() + "\t");
- } else if (column.equals(ColorSchemaColumn.POSITION)) {
- sb.append(schema.getReverseReaction() + "\t");
- } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
- sb.append(schema.getDescription() + "\t");
- } else {
- throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
- }
- return sb.toString();
+ /**
+ * Returns String representing data of {@link GenericColorSchema} that should
+ * appear in a given {@link ColorSchemaColumn}.
+ *
+ * @param schema
+ * object for which data will be returned
+ * @param column
+ * column for which data should be returned
+ * @return {@link String} representing data of {@link GenericColorSchema} that
+ * should appear in a given {@link ColorSchemaColumn}
+ */
+ protected String prepareTableCellForGenericSchema(GenericColorSchema schema, ColorSchemaColumn column) {
+ StringBuilder sb = new StringBuilder();
+ if (column.equals(ColorSchemaColumn.COLOR)) {
+ if (schema.getColor() != null) {
+ sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.NAME)) {
+ sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.MAP_NAME)) {
+ sb.append(schema.getModelName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.VALUE)) {
+ sb.append(schema.getValue() + "\t");
+ } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
+ for (String str : schema.getCompartments()) {
+ sb.append(str + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.TYPE)) {
+ for (Class<? extends Element> str : schema.getTypes()) {
+ sb.append(str.getSimpleName() + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
+ for (MiriamData md : schema.getMiriamData()) {
+ sb.append(md.getDataType().getCommonName() + ": " + md.getResource() + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
+ sb.append(schema.getElementId() + "\t");
+ } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
+ sb.append(schema.getLineWidth() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
+ sb.append(schema.getReverseReaction() + "\t");
+ } else if (column.equals(ColorSchemaColumn.POSITION)) {
+ sb.append(schema.getReverseReaction() + "\t");
+ } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
+ sb.append(schema.getDescription() + "\t");
+ } else {
+ throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
}
+ return sb.toString();
+ }
- /**
- * Returns String representing data of {@link GeneVariationColorSchema} that
- * should appear in a given {@link ColorSchemaColumn}.
- *
- * @param schema
- * object for which data will be returned
- * @param column
- * column for which data should be returned
- * @return {@link String} representing data of {@link GeneVariationColorSchema}
- * that should appear in a given {@link ColorSchemaColumn}
- */
- protected String prepareTableCellForGeneVariationSchema(GeneVariationColorSchema schema, ColorSchemaColumn column) {
- StringBuilder sb = new StringBuilder();
- if (column.equals(ColorSchemaColumn.COLOR)) {
- if (schema.getColor() != null) {
- sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.NAME)) {
- sb.append(schema.getName() + "\t");
- } else if (column.equals(ColorSchemaColumn.MAP_NAME)) {
- sb.append(schema.getModelName() + "\t");
- } else if (column.equals(ColorSchemaColumn.VALUE)) {
- sb.append(schema.getValue() + "\t");
- } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
- for (String str : schema.getCompartments()) {
- sb.append(str + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.TYPE)) {
- for (Class<? extends Element> str : schema.getTypes()) {
- sb.append(str.getSimpleName() + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
- for (MiriamData md : schema.getMiriamData()) {
- sb.append(md.getDataType().getCommonName() + ": " + md.getResource() + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
- sb.append(schema.getElementId() + "\t");
- } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
- sb.append(schema.getLineWidth() + "\t");
- } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
- sb.append(schema.getReverseReaction() + "\t");
- } else if (column.equals(ColorSchemaColumn.POSITION)) {
- sb.append(schema.getGeneVariations().get(0).getPosition() + "\t");
- } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
- sb.append(schema.getDescription() + "\t");
- } else if (column.equals(ColorSchemaColumn.ORIGINAL_DNA)) {
- sb.append(schema.getGeneVariations().get(0).getOriginalDna() + "\t");
- } else if (column.equals(ColorSchemaColumn.ALTERNATIVE_DNA)) {
- sb.append(schema.getGeneVariations().get(0).getModifiedDna() + "\t");
- } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_TYPE)) {
- sb.append(schema.getGeneVariations().get(0).getReferenceGenomeType() + "\t");
- } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_VERSION)) {
- sb.append(schema.getGeneVariations().get(0).getReferenceGenomeVersion() + "\t");
- } else if (column.equals(ColorSchemaColumn.CONTIG)) {
- sb.append(schema.getGeneVariations().get(0).getContig() + "\t");
- } else {
- throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
- }
- return sb.toString();
+ /**
+ * Returns String representing data of {@link GeneVariationColorSchema} that
+ * should appear in a given {@link ColorSchemaColumn}.
+ *
+ * @param schema
+ * object for which data will be returned
+ * @param column
+ * column for which data should be returned
+ * @return {@link String} representing data of {@link GeneVariationColorSchema}
+ * that should appear in a given {@link ColorSchemaColumn}
+ */
+ protected String prepareTableCellForGeneVariationSchema(GeneVariationColorSchema schema, ColorSchemaColumn column) {
+ StringBuilder sb = new StringBuilder();
+ if (column.equals(ColorSchemaColumn.COLOR)) {
+ if (schema.getColor() != null) {
+ sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.NAME)) {
+ sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.MAP_NAME)) {
+ sb.append(schema.getModelName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.VALUE)) {
+ sb.append(schema.getValue() + "\t");
+ } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
+ for (String str : schema.getCompartments()) {
+ sb.append(str + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.TYPE)) {
+ for (Class<? extends Element> str : schema.getTypes()) {
+ sb.append(str.getSimpleName() + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
+ for (MiriamData md : schema.getMiriamData()) {
+ sb.append(md.getDataType().getCommonName() + ": " + md.getResource() + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
+ sb.append(schema.getElementId() + "\t");
+ } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
+ sb.append(schema.getLineWidth() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
+ sb.append(schema.getReverseReaction() + "\t");
+ } else if (column.equals(ColorSchemaColumn.POSITION)) {
+ sb.append(schema.getGeneVariations().get(0).getPosition() + "\t");
+ } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
+ sb.append(schema.getDescription() + "\t");
+ } else if (column.equals(ColorSchemaColumn.ORIGINAL_DNA)) {
+ sb.append(schema.getGeneVariations().get(0).getOriginalDna() + "\t");
+ } else if (column.equals(ColorSchemaColumn.ALTERNATIVE_DNA)) {
+ sb.append(schema.getGeneVariations().get(0).getModifiedDna() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_TYPE)) {
+ sb.append(schema.getGeneVariations().get(0).getReferenceGenomeType() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_VERSION)) {
+ sb.append(schema.getGeneVariations().get(0).getReferenceGenomeVersion() + "\t");
+ } else if (column.equals(ColorSchemaColumn.CONTIG)) {
+ sb.append(schema.getGeneVariations().get(0).getContig() + "\t");
+ } else {
+ throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
}
+ return sb.toString();
+ }
/**
* Returns byte array containing data from original input file that was used to
@@ -684,141 +799,10 @@ public class LayoutService implements ILayoutService {
}
}
- @Override
- public List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId) {
- try {
- Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
- List<Pair<Element, ColorSchema>> result = new ArrayList<>();
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Element) {
- result.add(new Pair<>((Element) entry.getKey(), entry.getValue()));
- }
- }
- result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
- return result;
- } catch (InvalidColorSchemaException | IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
private Collection<ColorSchema> createColorSchemaCollection(int overlayId)
throws IOException, InvalidColorSchemaException {
ColorSchemaReader reader = new ColorSchemaReader();
Layout overlay = getLayoutById(overlayId);
return reader.readColorSchema(getInputDataForLayout(overlayId), overlay.getColorSchemaType());
}
-
- @Override
- public List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId) {
- try {
- Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
- List<Pair<Reaction, ColorSchema>> result = new ArrayList<>();
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Reaction) {
- result.add(new Pair<>((Reaction) entry.getKey(), entry.getValue()));
- }
- }
- result.sort(LayoutService.ELEMENT_PAIR_COMPARATOR);
- return result;
- } catch (InvalidColorSchemaException | IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId) {
- try {
- Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
- return command.getModifiedElements();
- } catch (InvalidColorSchemaException | IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public EmailSender getEmailSender() {
- if (emailSender == null) {
- emailSender = new EmailSender(configurationService);
- }
- return emailSender;
- }
-
- @Override
- public void setEmailSender(EmailSender emailSender) {
- this.emailSender = emailSender;
- }
-
- @Override
- public List<Layout> getLayoutsByProject(Project project) {
- List<Layout> result = new ArrayList<>();
- if (project == null) {
- return result;
- }
- List<Layout> overlays = layoutDao.getLayoutsByProject(project);
- result.addAll(overlays);
- result.sort(Layout.ID_COMPARATOR);
- return result;
- }
-
- @Override
- public Layout getLayoutById(int overlayId) {
- return layoutDao.getById(overlayId);
- }
-
- @Override
- public Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId) {
- try {
- Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
-
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Element) {
- Element alias = (Element) entry.getKey();
- if (id.equals(alias.getId())) {
- return new Pair<>(alias, entry.getValue());
- }
- }
- }
- return null;
- } catch (InvalidColorSchemaException | IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId) {
- try {
- Collection<ColorSchema> schemas = createColorSchemaCollection(layoutId);
- // colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas,
- new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
-
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Reaction) {
- Reaction alias = (Reaction) entry.getKey();
- if (id.equals(alias.getId())) {
- return new Pair<>(alias, entry.getValue());
- }
- }
- }
- return null;
- } catch (InvalidColorSchemaException | IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- public void setLayoutDao(LayoutDao layoutDao) {
- this.layoutDao = layoutDao;
- }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java
index 88046b8928..f89a7f1ad5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java
@@ -4,21 +4,13 @@ import java.security.GeneralSecurityException;
import java.util.ArrayList;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import com.unboundid.ldap.sdk.Attribute;
-import com.unboundid.ldap.sdk.BindResult;
-import com.unboundid.ldap.sdk.Filter;
-import com.unboundid.ldap.sdk.LDAPConnection;
-import com.unboundid.ldap.sdk.LDAPException;
-import com.unboundid.ldap.sdk.ResultCode;
-import com.unboundid.ldap.sdk.SearchResult;
-import com.unboundid.ldap.sdk.SearchResultEntry;
-import com.unboundid.ldap.sdk.SearchScope;
-import com.unboundid.ldap.sdk.SimpleBindRequest;
+import com.unboundid.ldap.sdk.*;
import com.unboundid.util.ssl.SSLUtil;
import com.unboundid.util.ssl.TrustAllTrustManager;
@@ -202,6 +194,25 @@ public class LdapService implements ILdapService {
}
}
+ @Override
+ public boolean isValidConfiguration() {
+ try {
+ String baseDn = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_BASE_DN);
+ if (baseDn == null || baseDn.trim().isEmpty()) {
+ return false;
+ }
+ LDAPConnection connection = getConnection();
+ if (connection != null) {
+ connection.close();
+ return true;
+ }
+ return false;
+ } catch (Exception e) {
+ logger.error(e, e);
+ return false;
+ }
+ }
+
private Filter createObjectClassFilter() throws LDAPException {
String objectClass = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS);
@@ -234,23 +245,4 @@ public class LdapService implements ILdapService {
public void setConfigurationService(IConfigurationService configurationService) {
this.configurationService = configurationService;
}
-
- @Override
- public boolean isValidConfiguration() {
- try {
- String baseDn = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_BASE_DN);
- if (baseDn == null || baseDn.trim().isEmpty()) {
- return false;
- }
- LDAPConnection connection = getConnection();
- if (connection != null) {
- connection.close();
- return true;
- }
- return false;
- } catch (Exception e) {
- logger.error(e, e);
- return false;
- }
- }
}
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 d4562371c1..fa4ba2a636 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java
@@ -1,14 +1,14 @@
package lcsb.mapviewer.services.impl;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
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.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
/**
* Implementation of service responsible for accessing miriam registry.
*
@@ -19,42 +19,42 @@ import org.springframework.transaction.annotation.Transactional;
@Service
public class MiriamService implements IMiriamService {
- /**
- * Object accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
- * registry</a>.
- */
- private MiriamConnector miriamConnector;
-
- @Autowired
- public MiriamService(MiriamConnector miriamConnector) {
- this.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);
- }
+ /**
+ * Object accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
+ * registry</a>.
+ */
+ private MiriamConnector miriamConnector;
+
+ @Autowired
+ public MiriamService(MiriamConnector miriamConnector) {
+ this.miriamConnector = miriamConnector;
+ }
+
+ @Override
+ public String getUrlForMiriamData(MiriamData md) {
+ return miriamConnector.getUrlString(md);
+ }
+
+ @Override
+ public MiriamType getTypeForUri(String uri) {
+ return MiriamType.getTypeByUri(uri);
+ }
+
+ /**
+ * @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;
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 46ef85f5d0..953f5f404e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.services.impl;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -12,19 +9,13 @@ import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.annotation.services.*;
import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.common.IProgressUpdater;
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.ModelData;
-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.model.*;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.persist.dao.ProjectDao;
@@ -42,21 +33,18 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Service
public class ModelService implements IModelService {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.getLogger(ModelService.class);
-
/**
* List of cached models.
*/
private static Map<String, Model> models = new HashMap<String, Model>();
-
/**
* List of models that are currently being loaded from database.
*/
private static Set<String> modelsInLoadStage = new HashSet<>();
-
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.getLogger(ModelService.class);
/**
* Service that manages and gives access to user information.
*/
@@ -74,7 +62,6 @@ public class ModelService implements IModelService {
*/
private PubmedParser backend;
-
/**
* Connector used for accessing data from miriam registry.
*/
@@ -82,10 +69,10 @@ public class ModelService implements IModelService {
@Autowired
public ModelService(IUserService userService,
- ModelDao modelDao,
- ProjectDao projectDao,
- PubmedParser backend,
- MiriamConnector miriamConnector) {
+ ModelDao modelDao,
+ ProjectDao projectDao,
+ PubmedParser backend,
+ MiriamConnector miriamConnector) {
this.userService = userService;
this.modelDao = modelDao;
this.projectDao = projectDao;
@@ -240,6 +227,29 @@ public class ModelService implements IModelService {
models.remove(projectId);
}
+ @Override
+ public void updateModel(ModelData model) {
+ Project project = model.getProject();
+ if (project == null) {
+ for (SubmodelConnection sc : model.getParentModels()) {
+ if (sc instanceof ModelSubmodelConnection) {
+ project = ((ModelSubmodelConnection) sc).getParentModel().getModel().getProject();
+ if (project != null) {
+ break;
+ }
+ }
+ }
+ }
+
+ Model topCachedData = getLastModelByProjectId(project.getProjectId());
+ Model cachedData = topCachedData.getSubmodelById(model.getId());
+ cachedData.setDefaultCenterX(model.getDefaultCenterX());
+ cachedData.setDefaultCenterY(model.getDefaultCenterY());
+ cachedData.setDefaultZoomLevel(model.getDefaultZoomLevel());
+ modelDao.update(model);
+
+ }
+
/**
* @return the userService
* @see #userService
@@ -274,27 +284,4 @@ public class ModelService implements IModelService {
this.projectDao = projectDao;
}
- @Override
- public void updateModel(ModelData model) {
- Project project = model.getProject();
- if (project == null) {
- for (SubmodelConnection sc : model.getParentModels()) {
- if (sc instanceof ModelSubmodelConnection) {
- project = ((ModelSubmodelConnection) sc).getParentModel().getModel().getProject();
- if (project != null) {
- break;
- }
- }
- }
- }
-
- Model topCachedData = getLastModelByProjectId(project.getProjectId());
- Model cachedData = topCachedData.getSubmodelById(model.getId());
- cachedData.setDefaultCenterX(model.getDefaultCenterX());
- cachedData.setDefaultCenterY(model.getDefaultCenterY());
- cachedData.setDefaultZoomLevel(model.getDefaultZoomLevel());
- modelDao.update(model);
-
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/PrivilegeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/PrivilegeService.java
index 4b2c3b6e29..51ee7b264b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/PrivilegeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/PrivilegeService.java
@@ -1,12 +1,13 @@
package lcsb.mapviewer.services.impl;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
import lcsb.mapviewer.model.security.Privilege;
import lcsb.mapviewer.model.security.PrivilegeType;
import lcsb.mapviewer.persist.dao.security.PrivilegeDao;
import lcsb.mapviewer.services.interfaces.IPrivilegeService;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
@Transactional
@Service
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 6e092f2b1b..fbe11c351d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -309,11 +309,273 @@ public class ProjectService implements IProjectService {
}
+ @Override
+ public void addProject(Project project) {
+ projectDao.add(project);
+
+ }
+
+ @Override
+ public void createProject(final CreateProjectParams params) throws SecurityException {
+ // 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 = createProjectFromParams(params);
+ projectDao.add(project);
+ if (params.isAsync()) {
+ projectDao.commit();
+ }
+ waitForInitialData.countDown();
+ double[] outOfMemoryBuffer;
+ MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
+ try {
+ 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;
+ }
+
+ UploadedFileEntry file = params.getProjectFile();
+ project.setInputData(file);
+
+ createModel(params, project);
+ Model originalModel = project.getModels().iterator().next().getModel();
+ 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();
+ }
+
+ createImages(project, params);
+
+ for (Layout layout : project.getLayouts()) {
+ for (DataOverlayImageLayer imageLayer : layout.getDataOverlayImageLayers()) {
+ String[] tmp = imageLayer.getDirectory().split("[\\\\/]");
+ imageLayer.setDirectory(tmp[tmp.length - 1]);
+ }
+ }
+
+ projectDao.update(project);
+
+ if (params.isAnalyzeAnnotations()) {
+ analyzeAnnotations(originalModel, params);
+ }
+ MinervaLoggerAppender.unregisterLogEventStorage(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);
+ }
+ }
+
+ logger.info("Project " + project.getProjectId() + " created successfully.");
+ } 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();
+ }
+ MinervaLoggerAppender.unregisterLogEventStorage(appender);
+ }
+ }
+
+ });
+ if (params.isAsync()) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+
+ try {
+ waitForInitialData.await();
+ } catch (InterruptedException e1) {
+ logger.error(e1, e1);
+ }
+
+ }
+
+ @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));
+ List<AnnotatorData> annotators = annotationSchema.getAnnotatorsForClass(clazz);
+ if (annotators == null) {
+ annotators = new ArrayList<>();
+ }
+ TreeNode root = new DefaultTreeNode(new AnnotatedObjectTreeRow(top, modelAnnotator.getAvailableAnnotators(clazz),
+ modelAnnotator.getAnnotatorsFromCommonNames(annotators),
+ 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));
+ annotators = annotationSchema.getAnnotatorsForClass(clazz);
+ if (annotators == null) {
+ annotators = new ArrayList<>();
+ }
+ AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(node, modelAnnotator.getAvailableAnnotators(clazz),
+ modelAnnotator.getAnnotatorsFromCommonNames(annotators),
+ 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;
+
+ }
+
+ @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();
+ queue.addAll(node.getChildren());
+ 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 void updateProject(Project project) {
+ projectDao.update(project);
+ }
+
+ /**
+ * 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.getClassAnnotators().size() == 0) {
+ for (UserClassAnnotators uca : modelAnnotator.createDefaultAnnotatorSchema().getClassAnnotators()) {
+ annotationSchema.addClassAnnotator(uca);
+ }
+ }
+ }
+ if (annotationSchema == null) {
+ annotationSchema = modelAnnotator.createDefaultAnnotatorSchema();
+
+ 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.getDefaultAnnotators(element.getClazz())));
+ annotationSchema.addClassValidAnnotations(
+ new UserClassValidAnnotations(element.getClazz(), validMiriam.get(element.getClazz())));
+ annotationSchema.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(element.getClazz(), requiredMiriam.get(element.getClazz())));
+ nodes.addAll(element.getChildren());
+ }
+ if (user != null) {
+ User dbUser = userDao.getById(user.getId());
+ dbUser.setAnnotationSchema(annotationSchema);
+ userDao.update(dbUser);
+ }
+ }
+ return annotationSchema;
+ }
+
/**
* 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
+ *
+ * @param originalProject
* project that was being removed
* @param exception
*/
@@ -343,15 +605,9 @@ public class ProjectService implements IProjectService {
reportInSeparateThread.start();
}
- @Override
- public void addProject(Project project) {
- projectDao.add(project);
-
- }
-
/**
* This method creates set of images for the model layouts.
- *
+ *
* @param project
* project for which we create layout images
* @param params
@@ -607,120 +863,6 @@ public class ProjectService implements IProjectService {
}
}
- @Override
- public void createProject(final CreateProjectParams params) throws SecurityException {
- // 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 = createProjectFromParams(params);
- projectDao.add(project);
- if (params.isAsync()) {
- projectDao.commit();
- }
- waitForInitialData.countDown();
- double[] outOfMemoryBuffer;
- MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
- try {
- 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;
- }
-
- UploadedFileEntry file = params.getProjectFile();
- project.setInputData(file);
-
- createModel(params, project);
- Model originalModel = project.getModels().iterator().next().getModel();
- 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();
- }
-
- createImages(project, params);
-
- for (Layout layout : project.getLayouts()) {
- for (DataOverlayImageLayer imageLayer : layout.getDataOverlayImageLayers()) {
- String[] tmp = imageLayer.getDirectory().split("[\\\\/]");
- imageLayer.setDirectory(tmp[tmp.length - 1]);
- }
- }
-
- projectDao.update(project);
-
- if (params.isAnalyzeAnnotations()) {
- analyzeAnnotations(originalModel, params);
- }
- MinervaLoggerAppender.unregisterLogEventStorage(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);
- }
- }
-
- logger.info("Project " + project.getProjectId() + " created successfully.");
- } 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();
- }
- MinervaLoggerAppender.unregisterLogEventStorage(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.
*
@@ -742,15 +884,16 @@ public class ProjectService implements IProjectService {
updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MIRIAM, progress, params);
}
});
-
+
logger.warn("Cache of chemicals data is disabled");
-// chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
-// @Override
-// public void setProgress(double progress) {
-// updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, 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
@@ -835,142 +978,6 @@ public class ProjectService implements IProjectService {
emailSender.sendEmail("MapViewer notification", "Map " + projectId + " was successfully removed.<br/>", 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));
- List<AnnotatorData> annotators = annotationSchema.getAnnotatorsForClass(clazz);
- if (annotators == null) {
- annotators = new ArrayList<>();
- }
- TreeNode root = new DefaultTreeNode(new AnnotatedObjectTreeRow(top, modelAnnotator.getAvailableAnnotators(clazz),
- modelAnnotator.getAnnotatorsFromCommonNames(annotators),
- 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));
- annotators = annotationSchema.getAnnotatorsForClass(clazz);
- if (annotators == null) {
- annotators = new ArrayList<>();
- }
- AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(node, modelAnnotator.getAvailableAnnotators(clazz),
- modelAnnotator.getAnnotatorsFromCommonNames(annotators),
- 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.getClassAnnotators().size() == 0) {
- for (UserClassAnnotators uca : modelAnnotator.createDefaultAnnotatorSchema().getClassAnnotators()) {
- annotationSchema.addClassAnnotator(uca);
- }
- }
- }
- if (annotationSchema == null) {
- annotationSchema = modelAnnotator.createDefaultAnnotatorSchema();
-
- 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.getDefaultAnnotators(element.getClazz())));
- annotationSchema.addClassValidAnnotations(
- new UserClassValidAnnotations(element.getClazz(), validMiriam.get(element.getClazz())));
- annotationSchema.addClassRequiredAnnotations(
- new UserClassRequiredAnnotations(element.getClazz(), requiredMiriam.get(element.getClazz())));
- nodes.addAll(element.getChildren());
- }
- 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();
- queue.addAll(node.getChildren());
- 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);
- }
-
/**
* Sends email about unsuccessful project creation.
*
@@ -1007,11 +1014,6 @@ public class ProjectService implements IProjectService {
originalModel.getProject().getNotifyEmail());
}
- @Override
- public void updateProject(Project project) {
- projectDao.update(project);
- }
-
/**
* This method handles situation when sever db error appeared during uploading
* of the project into database.
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 ae6e57598d..681630525a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -4,21 +4,17 @@ import java.io.IOException;
import java.net.URISyntaxException;
import java.util.List;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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.annotation.services.genome.*;
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.model.map.layout.*;
import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
@@ -52,7 +48,7 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
@Autowired
public ReferenceGenomeService(UcscReferenceGenomeConnector ucscReferenceGenomeConnector,
- ReferenceGenomeDao referenceGenomeDao) {
+ ReferenceGenomeDao referenceGenomeDao) {
this.ucscReferenceGenomeConnector = ucscReferenceGenomeConnector;
this.referenceGenomeDao = referenceGenomeDao;
}
@@ -73,23 +69,6 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
}, 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 {
@@ -155,4 +134,21 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
return referenceGenomeDao.getById(id);
}
+ /**
+ * 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);
+ }
+ }
+
}
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 044b165d4d..01b683784a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchHistoryService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchHistoryService.java
@@ -1,14 +1,14 @@
package lcsb.mapviewer.services.impl;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
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.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
/**
* Implementation of the service that manages search history.
*
@@ -19,39 +19,39 @@ import org.springframework.transaction.annotation.Transactional;
@Service
public class SearchHistoryService implements ISearchHistoryService {
- /**
- * Data access object for search history entries.
- */
- private SearchHistoryDao searchHistoryDao;
-
- @Autowired
- public SearchHistoryService(SearchHistoryDao searchHistoryDao) {
- this.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;
- }
+ /**
+ * Data access object for search history entries.
+ */
+ private SearchHistoryDao searchHistoryDao;
+
+ @Autowired
+ public SearchHistoryService(SearchHistoryDao searchHistoryDao) {
+ this.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 9a215f67bf..28efbadb1c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -1,44 +1,21 @@
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.logging.log4j.*;
+import java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
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.common.exception.*;
+import lcsb.mapviewer.model.map.*;
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.species.*;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
@@ -109,6 +86,12 @@ public class SearchService implements ISearchService {
* subcomplex".
*/
private Map<String, Class<? extends Element>> speciesSearchReversePrefix = new HashMap<>();
+ /**
+ * 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>>>();
/**
* Default constructor that set list of prefixes used in the search queries.
@@ -128,7 +111,7 @@ public class SearchService implements ISearchService {
addSearchPrefix("unknown", Unknown.class);
}
- /**
+ /**
* Adds search prefix for an element class.
*
* @param prefix
@@ -139,66 +122,6 @@ public class SearchService implements ISearchService {
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;
- }
};
/**
@@ -389,6 +312,80 @@ public class SearchService implements ISearchService {
return result;
}
+ @Override
+ public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch) {
+ return searchByQuery(model, query, limit, perfectMatch, 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;
+ }
+
+ @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;
+ }
+
+ @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 elements that are annotated with the given miriam data.
*
@@ -442,138 +439,6 @@ public class SearchService implements ISearchService {
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;
-
- /**
- * 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);
- }
-
- /**
- * 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);
- }
-
- @Override
- public int compareTo(DistanceToObject arg0) {
- if (arg0.getDistance() < getDistance()) {
- return 1;
- } else if (arg0.getDistance() > getDistance()) {
- return -1;
- } else {
- if (arg0.getReference().getZ() > getReference().getZ()) {
- return 1;
- } else if (arg0.getReference().getZ() < getReference().getZ()) {
- 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;
- }
-
- }
-
- /**
- * 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.
@@ -618,30 +483,6 @@ public class SearchService implements ISearchService {
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.
*
@@ -695,9 +536,144 @@ public class SearchService implements ISearchService {
this.searchHistoryService = searchHistoryService;
}
- @Override
- public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch) {
- return searchByQuery(model, query, limit, perfectMatch, null);
+/**
+ * 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;
+ }
+ }
+
+ /**
+ * 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;
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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);
+ }
+
+ @Override
+ public int compareTo(DistanceToObject arg0) {
+ if (arg0.getDistance() < getDistance()) {
+ return 1;
+ } else if (arg0.getDistance() > getDistance()) {
+ return -1;
+ } else {
+ if (arg0.getReference().getZ() > getReference().getZ()) {
+ return 1;
+ } else if (arg0.getReference().getZ() < getReference().getZ()) {
+ 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;
+ }
+
}
}
\ No newline at end of file
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 793e35eb32..6d060e5578 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -1,13 +1,11 @@
package lcsb.mapviewer.services.impl;
-import java.awt.Color;
+import java.awt.*;
import java.util.*;
+import java.util.List;
-import lcsb.mapviewer.model.security.*;
-import lcsb.mapviewer.model.user.ConfigurationElementTypeGroup;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.services.interfaces.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -16,9 +14,12 @@ import com.unboundid.ldap.sdk.LDAPException;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.geometry.ColorParser;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.security.Privilege;
+import lcsb.mapviewer.model.security.PrivilegeType;
+import lcsb.mapviewer.model.user.*;
+import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.services.interfaces.*;
@Transactional
@Service
@@ -33,10 +34,10 @@ public class UserService implements IUserService {
@Autowired
public UserService(UserDao userDao,
- ILdapService ldapService,
- IConfigurationService configurationService,
- IPrivilegeService privilegeService,
- ProjectDao projectDao) {
+ ILdapService ldapService,
+ IConfigurationService configurationService,
+ IPrivilegeService privilegeService,
+ ProjectDao projectDao) {
this.userDao = userDao;
this.ldapService = ldapService;
this.configurationService = configurationService;
@@ -54,6 +55,7 @@ public class UserService implements IUserService {
public void updateUser(User user) {
userDao.update(user);
}
+
@Override
public void deleteUser(User user) {
String login = user.getLogin();
@@ -62,13 +64,13 @@ public class UserService implements IUserService {
}
@Override
- public List<User> getUsers() {
- return userDao.getAll();
+ public User getUserByLogin(String login) {
+ return userDao.getUserByLogin(login);
}
@Override
- public User getUserByLogin(String login) {
- return userDao.getUserByLogin(login);
+ public List<User> getUsers() {
+ return userDao.getAll();
}
@Override
@@ -167,21 +169,21 @@ public class UserService implements IUserService {
private void grantPrivilegesForDefaultConfigurationElementType(User user, ConfigurationElementType type) {
switch (type) {
- case DEFAULT_CAN_CREATE_OVERLAYS:
- grantUserPrivilege(user, PrivilegeType.CAN_CREATE_OVERLAYS);
- break;
- case DEFAULT_READ_PROJECT:
- grantUserPrivilege(user, PrivilegeType.READ_PROJECT, "*");
- projectDao.getAll()
- .forEach(project -> grantUserPrivilege(user, PrivilegeType.READ_PROJECT, project.getProjectId()));
- break;
- case DEFAULT_WRITE_PROJECT:
- grantUserPrivilege(user, PrivilegeType.WRITE_PROJECT, "*");
- projectDao.getAll()
- .forEach(project -> grantUserPrivilege(user, PrivilegeType.WRITE_PROJECT, project.getProjectId()));
- break;
- default:
- throw new IllegalArgumentException("The configuration element type '+" + type + "' is not handled.");
+ case DEFAULT_CAN_CREATE_OVERLAYS:
+ grantUserPrivilege(user, PrivilegeType.CAN_CREATE_OVERLAYS);
+ break;
+ case DEFAULT_READ_PROJECT:
+ grantUserPrivilege(user, PrivilegeType.READ_PROJECT, "*");
+ projectDao.getAll()
+ .forEach(project -> grantUserPrivilege(user, PrivilegeType.READ_PROJECT, project.getProjectId()));
+ break;
+ case DEFAULT_WRITE_PROJECT:
+ grantUserPrivilege(user, PrivilegeType.WRITE_PROJECT, "*");
+ projectDao.getAll()
+ .forEach(project -> grantUserPrivilege(user, PrivilegeType.WRITE_PROJECT, project.getProjectId()));
+ break;
+ default:
+ throw new IllegalArgumentException("The configuration element type '+" + type + "' is not handled.");
}
}
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 8579684cb4..4e24366aa9 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
@@ -3,4 +3,3 @@
* layer.
*/
package lcsb.mapviewer.services.impl;
-
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 4aaea5fcfc..0e97cb5383 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -1,19 +1,13 @@
package lcsb.mapviewer.services.interfaces;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
import java.util.List;
import java.util.Map;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.ColorSchemaType;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -29,6 +23,129 @@ import lcsb.mapviewer.services.utils.EmailSender;
*/
public interface ILayoutService {
+ /**
+ * 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);
+
+ /**
+ * 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
+ */
+ 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 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}
+ */
+ List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId);
+
+ /**
+ * 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}
+ */
+ List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId);
+
+ /**
+ * 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}
+ */
+ Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId);
+
+ Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId);
+
+ Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId);
+
+ /**
+ * 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 project
+ * project where the layouts lay on
+ * @return list of custom layouts
+ */
+ List<Layout> getLayoutsByProject(Project project);
+
+ Layout getLayoutById(int overlayId);
+
+ void setLayoutDao(LayoutDao layoutDao);
+
/**
* Parameters used for creation of the layout.
*
@@ -94,7 +211,7 @@ public interface ILayoutService {
*/
private boolean async = false;
- private boolean googleLicenseConsent = false;
+ private boolean googleLicenseConsent = false;
/**
* Type of the uploaded file.
@@ -233,7 +350,7 @@ public interface ILayoutService {
* @see #googleLicenseConsent
*/
public boolean isGoogleLicenseConsent() {
- return googleLicenseConsent;
+ return googleLicenseConsent;
}
/**
@@ -243,8 +360,8 @@ public interface ILayoutService {
* @return {@link CreateLayoutParams} object
*/
public CreateLayoutParams googleLicenseConsent(boolean googleLicenseConsent) {
- this.googleLicenseConsent = googleLicenseConsent;
- return this;
+ this.googleLicenseConsent = googleLicenseConsent;
+ return this;
}
/**
@@ -305,131 +422,4 @@ public interface ILayoutService {
}
}
- /**
- * 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);
-
- /**
- * 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
- */
- 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 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}
- */
- List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId)
- ;
-
- /**
- * 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}
- */
- List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId)
- ;
-
- /**
- * 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}
- */
- Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId);
-
- Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId)
- ;
-
- Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId)
- ;
-
- /**
- * 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 project
- * project where the layouts lay on
- * @return list of custom layouts
- */
- List<Layout> getLayoutsByProject(Project project);
-
- Layout getLayoutById(int overlayId);
-
- void setLayoutDao(LayoutDao layoutDao);
-
}
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 b0fca3a3e3..0226315db0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IMiriamService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IMiriamService.java
@@ -11,22 +11,22 @@ import lcsb.mapviewer.model.map.MiriamType;
*/
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 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);
+ /**
+ * 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/IReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
index 8fa4c19294..645259bc3d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -6,9 +6,7 @@ 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;
+import lcsb.mapviewer.model.map.layout.*;
/**
* Service used to maintain reference genome data.
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 2770c7a866..1293790e22 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchHistoryService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchHistoryService.java
@@ -9,17 +9,17 @@ import lcsb.mapviewer.model.map.statistics.SearchType;
*
*/
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);
+ /**
+ * 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/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
index acc8f8a377..4c9d37fd6f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
@@ -19,9 +19,11 @@ public interface IUserService {
List<User> getUsers();
void grantUserPrivilege(User user, PrivilegeType type);
+
void grantUserPrivilege(User user, PrivilegeType type, String objectId);
void revokeUserPrivilege(User user, PrivilegeType type);
+
void revokeUserPrivilege(User user, PrivilegeType type, String objectId);
void grantDefaultPrivileges(User user);
@@ -29,19 +31,26 @@ public interface IUserService {
void grantPrivilegeToAllUsersWithDefaultAccess(PrivilegeType type, String objectId);
/**
- * When an object is deleted we have to manually remove the access rights to it for every user to avoid pollution.
- * Hibernate delete cascading does not work here, because security is completely decoupled from the business logic.
- * @param privilegeType The concerned privilege domain.
- * @param objectId The objectId for which to remove all access rights.
+ * When an object is deleted we have to manually remove the access rights to it
+ * for every user to avoid pollution. Hibernate delete cascading does not work
+ * here, because security is completely decoupled from the business logic.
+ *
+ * @param privilegeType
+ * The concerned privilege domain.
+ * @param objectId
+ * The objectId for which to remove all access rights.
*
*/
void revokeObjectDomainPrivilegesForAllUsers(PrivilegeType privilegeType, String objectId);
/**
- * Returns {@link ColorExtractor} that transform overlay values into colors for given user.
+ * Returns {@link ColorExtractor} that transform overlay values into colors for
+ * given user.
*
- * @param user {@link User} for which {@link ColorExtractor} will be obtained
- * @return {@link ColorExtractor} that transform overlay values into colors for given user
+ * @param user
+ * {@link User} for which {@link ColorExtractor} will be obtained
+ * @return {@link ColorExtractor} that transform overlay values into colors for
+ * given user
*/
ColorExtractor getColorExtractorForUser(User user);
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 adb9ff9cd6..510e41349e 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
@@ -3,4 +3,3 @@
* 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 684fee0850..a64a8b2a28 100644
--- a/service/src/main/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRow.java
+++ b/service/src/main/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRow.java
@@ -1,12 +1,10 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.model.map.MiriamType;
@@ -22,277 +20,278 @@ import lcsb.mapviewer.modelutils.map.ClassTreeNode;
*/
public class AnnotatedObjectTreeRow implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final transient Logger logger = LogManager.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<>();
-
- /**
- * List of annotators that will be used for annotating {@link #clazz}.
- */
- private List<AnnotatorData> usedAnnotators = new ArrayList<>();
-
- /**
- * 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)) {
- AnnotatorData annotatorData = new AnnotatorData(elementAnnotator.getClass());
- this.usedAnnotators.add(annotatorData);
- } 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<AnnotatorData> getUsedAnnotators() {
- return usedAnnotators;
- }
-
- /**
- * @param usedAnnotators
- * the usedAnnotators to set
- * @see #usedAnnotators
- */
- public void setUsedAnnotators(List<AnnotatorData> 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;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final transient Logger logger = LogManager.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<>();
+
+ /**
+ * List of annotators that will be used for annotating {@link #clazz}.
+ */
+ private List<AnnotatorData> usedAnnotators = new ArrayList<>();
+
+ /**
+ * 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)) {
+ AnnotatorData annotatorData = new AnnotatorData(elementAnnotator.getClass());
+ this.usedAnnotators.add(annotatorData);
+ } 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<AnnotatorData> getUsedAnnotators() {
+ return usedAnnotators;
+ }
+
+ /**
+ * @param usedAnnotators
+ * the usedAnnotators to set
+ * @see #usedAnnotators
+ */
+ public void setUsedAnnotators(List<AnnotatorData> 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/package-info.java b/service/src/main/java/lcsb/mapviewer/services/overlay/package-info.java
index e11e591303..eea494a6f6 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
@@ -4,4 +4,3 @@
*
*/
package lcsb.mapviewer.services.overlay;
-
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/DbSearchService.java b/service/src/main/java/lcsb/mapviewer/services/search/DbSearchService.java
index bf41828482..b0e73954d8 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/DbSearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/DbSearchService.java
@@ -17,31 +17,31 @@ import lcsb.mapviewer.model.map.MiriamType;
@Transactional
public abstract class DbSearchService {
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- protected void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (MiriamType.PUBMED.equals(miriamData.getDataType())) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
+ /**
+ * Service accessing
+ * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ protected void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
+ Set<MiriamData> result = new HashSet<>();
+ result.addAll(targettingStructure.getSources());
+ for (Target target : targettingStructure.getTargets()) {
+ result.addAll(target.getGenes());
+ result.addAll(target.getReferences());
+
+ }
+
+ for (MiriamData miriamData : result) {
+ if (MiriamType.PUBMED.equals(miriamData.getDataType())) {
+ try {
+ pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
+ } catch (NumberFormatException | PubmedSearchException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
+
+ }
}
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 6754f40b15..ceabbcb8e5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -1,22 +1,14 @@
package lcsb.mapviewer.services.search;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.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;
+import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.species.*;
public class ElementMatcher {
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 ff5f7e3562..31ad2b47e3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/IDbSearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/IDbSearchService.java
@@ -18,39 +18,39 @@ import lcsb.mapviewer.model.map.species.Element;
*/
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 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);
+ /**
+ * 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);
+ /**
+ * 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 89c40a2b70..47e2e5e881 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
@@ -1,18 +1,10 @@
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.*;
import java.util.Map.Entry;
-import java.util.Set;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -24,14 +16,9 @@ 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.*;
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.species.*;
import lcsb.mapviewer.services.search.DbSearchCriteria;
import lcsb.mapviewer.services.search.DbSearchService;
@@ -234,22 +221,6 @@ public class ChemicalService extends DbSearchService implements IChemicalService
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;
@@ -291,4 +262,20 @@ public class ChemicalService extends DbSearchService implements IChemicalService
}
}
+ /**
+ * @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);
+ }
+
}
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 2f7d3146cd..9ea2461a03 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
@@ -1,34 +1,23 @@
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 java.util.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
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.*;
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.*;
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.species.*;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.DbSearchCriteria;
@@ -72,9 +61,9 @@ public class DrugService extends DbSearchService implements IDrugService {
@Autowired
public DrugService(DrugbankHTMLParser drugBankParser,
- ChEMBLParser chEMBLParser,
- HgncAnnotator hgncAnnotator,
- ISearchHistoryService searchHistoryService) {
+ ChEMBLParser chEMBLParser,
+ HgncAnnotator hgncAnnotator,
+ ISearchHistoryService searchHistoryService) {
this.drugBankParser = drugBankParser;
this.chEMBLParser = chEMBLParser;
this.hgncAnnotator = hgncAnnotator;
@@ -275,51 +264,6 @@ public class DrugService extends DbSearchService implements IDrugService {
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...");
@@ -366,6 +310,51 @@ public class DrugService extends DbSearchService implements IDrugService {
}
}
+ /**
+ * @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 List<String> getSuggestedQueryList(Project project, MiriamData organism) throws DrugSearchException {
Set<String> resultSet = new HashSet<>();
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 23fcc7bcc0..d01d469cb6 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
@@ -1,11 +1,6 @@
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 java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -19,14 +14,9 @@ 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.*;
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.species.*;
import lcsb.mapviewer.services.search.DbSearchCriteria;
import lcsb.mapviewer.services.search.DbSearchService;
@@ -127,36 +117,6 @@ public class MiRNAService extends DbSearchService implements IMiRNAService {
return mirnaList;
}
- /**
- * Removes targets for unknown organisms from the mirna.
- *
- * @param mirna
- * mirna from which we want to remove targets
- * @param organisms
- * organisms that should be kept
- */
- private void removeUnknownOrganisms(MiRNA mirna, List<MiriamData> organisms) {
- if (organisms.size() > 0) {
- List<Target> toRemove = new ArrayList<Target>();
- for (Target target : mirna.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);
- }
- }
- mirna.getTargets().removeAll(toRemove);
- }
- }
-
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
logger.debug("Caching mirna queries...");
@@ -200,4 +160,34 @@ public class MiRNAService extends DbSearchService implements IMiRNAService {
}
}
+ /**
+ * Removes targets for unknown organisms from the mirna.
+ *
+ * @param mirna
+ * mirna from which we want to remove targets
+ * @param organisms
+ * organisms that should be kept
+ */
+ private void removeUnknownOrganisms(MiRNA mirna, List<MiriamData> organisms) {
+ if (organisms.size() > 0) {
+ List<Target> toRemove = new ArrayList<Target>();
+ for (Target target : mirna.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);
+ }
+ }
+ mirna.getTargets().removeAll(toRemove);
+ }
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index a22f84b61d..72200ad594 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -1,28 +1,17 @@
package lcsb.mapviewer.services.utils;
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.awt.*;
+import java.io.*;
import java.lang.reflect.Field;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
+import java.util.*;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.ColorParser;
@@ -30,13 +19,7 @@ import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
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.ColorSchemaType;
-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.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.layout.*;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
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 ff71b1b57e..fd1be2766a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -1,16 +1,8 @@
package lcsb.mapviewer.services.utils;
import java.io.IOException;
-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 java.util.*;
-import lcsb.mapviewer.model.user.User;
import org.primefaces.model.TreeNode;
import lcsb.mapviewer.converter.Converter;
@@ -19,6 +11,7 @@ import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.MapCanvasType;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.annotator.AnnotatorData;
import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
@@ -457,7 +450,8 @@ public class CreateProjectParams {
while (!queue.isEmpty()) {
TreeNode node = queue.poll();
- map.put(((AnnotatedObjectTreeRow) node.getData()).getClazz(), ((AnnotatedObjectTreeRow) node.getData()).getUsedAnnotators());
+ map.put(((AnnotatedObjectTreeRow) node.getData()).getClazz(),
+ ((AnnotatedObjectTreeRow) node.getData()).getUsedAnnotators());
for (TreeNode node2 : node.getChildren()) {
queue.add(node2);
@@ -653,15 +647,15 @@ public class CreateProjectParams {
return this;
}
+ public User getUser() {
+ return user;
+ }
+
public CreateProjectParams setUser(User user) {
this.user = user;
return this;
}
- public User getUser() {
- return user;
- }
-
public CreateProjectParams semanticZoomContainsMultipleLayouts(boolean semanticZoomContainsMultipleLayouts) {
this.semanticZoomContainsMultipleLayouts = semanticZoomContainsMultipleLayouts;
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 8d0b6f9d76..d23ee6dbbd 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
@@ -1,30 +1,16 @@
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.io.*;
+import java.util.*;
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.logging.log4j.*;
+import javax.activation.*;
+import javax.mail.*;
+import javax.mail.internet.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import com.sun.mail.smtp.SMTPTransport;
@@ -40,7 +26,7 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
*
*/
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.
@@ -171,9 +157,9 @@ public class EmailSender {
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.setProperty("mail.smtp.user", login);
+ // props.setProperty("mail.smtp.password", password);
+ // props.setProperty("mail.smtp.auth", "true");
props.put("mail.smtps.quitwait", "false");
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 6a8506ada0..e4cff15a5f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/InvalidPrivilegeException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/InvalidPrivilegeException.java
@@ -7,18 +7,18 @@ package lcsb.mapviewer.services.utils;
*
*/
public class InvalidPrivilegeException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Public constructor with message that should be reported.
- *
- * @param string
- * message
- */
- public InvalidPrivilegeException(String string) {
- super(string);
- }
+ /**
+ * 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 fe163d7dea..b19b6fdf2c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ReferenceGenomeExistsException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ReferenceGenomeExistsException.java
@@ -9,18 +9,18 @@ import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorExcepti
*
*/
public class ReferenceGenomeExistsException extends ReferenceGenomeConnectorException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Public constructor with message that should be reported.
- *
- * @param string
- * message
- */
- public ReferenceGenomeExistsException(String string) {
- super(string);
- }
+ /**
+ * 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 b3224f71f4..832b390e4d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
@@ -1,12 +1,10 @@
package lcsb.mapviewer.services.utils;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import java.util.Map.Entry;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.species.Element;
@@ -20,159 +18,159 @@ import lcsb.mapviewer.model.map.species.Element;
*/
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 = LogManager.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;
- }
+ /**
+ * 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 = LogManager.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 32dd39567f..60a14f170c 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
@@ -8,104 +8,104 @@ package lcsb.mapviewer.services.utils.data;
*
*/
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),
- /**
- * Clean visualization (with colors reset to black and white).
- */
- CLEAN("Empty", "_empty", null, false);
+ /**
+ * 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),
+ /**
+ * Clean visualization (with colors reset to black and white).
+ */
+ CLEAN("Empty", "_empty", null, false);
- /**
- * Title of the layout.
- */
- private String title;
+ /**
+ * Title of the layout.
+ */
+ private String title;
- /**
- * Suffix used for the directory name during image generation.
- */
- private String directorySuffix;
+ /**
+ * Suffix used for the directory name during image generation.
+ */
+ private String directorySuffix;
- /**
- * File with the color values for the layout.
- */
- private String coloringFile;
+ /**
+ * File with the color values for the layout.
+ */
+ private String coloringFile;
- /**
- * Should visualization be hierarchical or simple.
- */
- private boolean nested;
+ /**
+ * 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;
- }
+ /**
+ * 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 title
+ * @see #title
+ */
+ public String getTitle() {
+ return title;
+ }
- /**
- * @return the directorySuffix
- * @see #directorySuffix
- */
- public String getDirectorySuffix() {
- return directorySuffix;
- }
+ /**
+ * @return the directorySuffix
+ * @see #directorySuffix
+ */
+ public String getDirectorySuffix() {
+ return directorySuffix;
+ }
- /**
- * @return the coloringFile
- * @see #coloringFile
- */
- public String getColoringFile() {
- return coloringFile;
- }
+ /**
+ * @return the coloringFile
+ * @see #coloringFile
+ */
+ public String getColoringFile() {
+ return coloringFile;
+ }
- /**
- * @return the nested
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
+ /**
+ * @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 3d73e12531..f199d482eb 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
@@ -3,9 +3,7 @@ package lcsb.mapviewer.services.utils.data;
import java.util.HashSet;
import java.util.Set;
-import lcsb.mapviewer.model.map.layout.ColorSchemaType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.layout.*;
/**
* This enum defines which columns are available for defining
@@ -19,14 +17,14 @@ public enum ColorSchemaColumn {
/**
* Name of the element.
*/
- NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
+ NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC }),
GENE_NAME("name", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Name of the map.
*/
- MAP_NAME("model_name",new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ MAP_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Value that will be transformed into new color.
@@ -43,7 +41,7 @@ public enum ColorSchemaColumn {
/**
* Class type of the element.
*/
- TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
+ TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* New element/reaction color.
@@ -53,7 +51,7 @@ public enum ColorSchemaColumn {
/**
* Identifier of the element.
*/
- IDENTIFIER("references",new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ IDENTIFIER("references", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Element identifier.
@@ -124,14 +122,24 @@ public enum ColorSchemaColumn {
*/
AMINO_ACID_CHANGE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT });
+ /**
+ * Human readable title used in input file.
+ */
+ private String deprecatedColumnName;
+ /**
+ * Set of types where column is allowed.
+ */
+ private Set<ColorSchemaType> types = new HashSet<>();
+
/**
* Constructor that creates enum entry with deprecated column name.
- *
+ *
* @param deprecatedColumnName
* {@link #deprecatedColumnName}
* @param types
* list of {@link ColorSchemaType types} where this column is allowed
- * @deprecated As of release 12.3, replaced by {@link #ColorSchemaColumn(ColorSchemaType[])}
+ * @deprecated As of release 12.3, replaced by
+ * {@link #ColorSchemaColumn(ColorSchemaType[])}
*/
@Deprecated
ColorSchemaColumn(String deprecatedColumnName, ColorSchemaType[] types) {
@@ -143,7 +151,7 @@ public enum ColorSchemaColumn {
/**
* Default constructor that creates enum entry.
- *
+ *
* @param deprecatedColumnName
* {@link #deprecatedColumnName}
* @param types
@@ -155,16 +163,6 @@ public enum ColorSchemaColumn {
}
}
- /**
- * Human readable title used in input file.
- */
- private String deprecatedColumnName;
-
- /**
- * Set of types where column is allowed.
- */
- private Set<ColorSchemaType> types = new HashSet<>();
-
/**
*
* @return {@link #deprecatedColumnName}
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 a5e48ef710..6fe578558e 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
@@ -11,104 +11,103 @@ import lcsb.mapviewer.model.map.species.Species;
*/
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;
- }
+ /**
+ * 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);
+
+ /**
+ * Human readable title.
+ */
+ private String title;
+ /**
+ * Class for which this column should be accessible.
+ */
+ private Class<?> clazz;
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ * @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 1578fe18a2..46b5ef01c2 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
@@ -7,40 +7,40 @@ package lcsb.mapviewer.services.utils.data;
*
*/
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");
+ /**
+ * Tab separated file.
+ */
+ TAB_SEPARATED("Tab separated"),
- /**
- * Default constructor.
- *
- * @param title
- * {@link #title}
- */
- ExportFileType(final String title) {
- this.title = title;
- }
+ /**
+ * Simnple interaction format used by
+ * <a href="http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats"
+ * >Cytoscape</a>.
+ */
- /**
- * Human readable name of the format.
- */
- private String title;
+ SIF("SIF");
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Human readable name of the format.
+ */
+ private String title;
+
+ /**
+ * Default constructor.
+ *
+ * @param title
+ * {@link #title}
+ */
+ ExportFileType(final String title) {
+ this.title = 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 7f4ef6a31e..cf3e217301 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
@@ -3,4 +3,3 @@
* {@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 7f289e56f9..07edbd0ffa 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
@@ -2,4 +2,3 @@
* 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/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index 0696927d2e..2abcca3597 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
@@ -40,19 +40,14 @@ import lcsb.mapviewer.services.search.drug.IDrugService;
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class ServiceTestFunctions {
+ private static Map<String, Model> models = new HashMap<String, Model>();
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
- private Logger logger = LogManager.getLogger(ServiceTestFunctions.class);
-
+ public double EPSILON = 1e-6;
@Autowired
protected DrugbankHTMLParser drugBankHTMLParser;
-
@Autowired
protected ModelAnnotator modelAnnotator;
-
- public double EPSILON = 1e-6;
-
@Autowired
protected IConfigurationService configurationService;
@@ -100,7 +95,7 @@ public abstract class ServiceTestFunctions {
@Autowired
protected DbUtils dbUtils;
-
+ private Logger logger = LogManager.getLogger(ServiceTestFunctions.class);
private MinervaLoggerAppender appender;
@Before
@@ -148,8 +143,6 @@ public abstract class ServiceTestFunctions {
return user;
}
- 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);
diff --git a/service/src/test/java/lcsb/mapviewer/services/SpringServiceTestConfig.java b/service/src/test/java/lcsb/mapviewer/services/SpringServiceTestConfig.java
index d0d08b0389..5cfc7f9519 100644
--- a/service/src/test/java/lcsb/mapviewer/services/SpringServiceTestConfig.java
+++ b/service/src/test/java/lcsb/mapviewer/services/SpringServiceTestConfig.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.services;
+import org.springframework.context.annotation.*;
+import org.springframework.security.core.session.SessionRegistryImpl;
+
import lcsb.mapviewer.annotation.SpringAnnotationConfig;
import lcsb.mapviewer.persist.SpringPersistConfig;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
-import org.springframework.security.core.session.SessionRegistryImpl;
@Configuration
-@Import({SpringServiceConfig.class, SpringPersistConfig.class, SpringAnnotationConfig.class})
+@Import({ SpringServiceConfig.class, SpringPersistConfig.class, SpringAnnotationConfig.class })
public class SpringServiceTestConfig {
@Bean
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoderTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoderTest.java
index 427d3ccbf1..9043fd0825 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CustomMd5PasswordEncoderTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.services.impl;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
import org.junit.*;
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 c7a4866c06..bf15027fdc 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 +1,14 @@
package lcsb.mapviewer.services.impl;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.*;
public class FailServiceMock implements IExternalService {
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Test service", "unknown");
- status.setStatus(ExternalServiceStatusType.DOWN);
- return status;
- }
+ @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/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index 731e4ad090..91b413664d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -2,10 +2,11 @@ package lcsb.mapviewer.services.impl;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.*;
+import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.LogManager;
@@ -47,10 +48,8 @@ public class LayoutServiceTest extends ServiceTestFunctions {
@Autowired
ILayoutService layoutService;
-
- private User user, user2;
-
ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+ private User user, user2;
@Before
public void setUp() throws Exception {
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 e26c4c69e1..d7db97d58f 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 +1,14 @@
package lcsb.mapviewer.services.impl;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.*;
public class OkServiceMock implements IExternalService {
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Test service", "unknown");
- status.setStatus(ExternalServiceStatusType.OK);
- return status;
- }
+ @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/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 6e87809a64..c35bee8b1a 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -44,16 +44,14 @@ import lcsb.mapviewer.services.utils.data.BuildInLayout;
@Rollback(true)
public class ProjectServiceTest extends ServiceTestFunctions {
- private Logger logger = LogManager.getLogger(ProjectServiceTest.class);
- private ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
private final String tmpResultDir = "tmp/";
- private String projectId = "Some_id";
-
@Autowired
ElementDao aliasDao;
-
@Autowired
LayoutDao layoutDao;
+ private Logger logger = LogManager.getLogger(ProjectServiceTest.class);
+ private ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
+ private String projectId = "Some_id";
@Before
public void setUp() throws Exception {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/DbSearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/DbSearchServiceTest.java
index 018bf80c98..2a839d2f22 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/DbSearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/DbSearchServiceTest.java
@@ -4,7 +4,6 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.services.search.DbSearchService;
public class DbSearchServiceTest {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java b/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
index 1b31f49b77..a43c78fd3e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
@@ -3,20 +3,13 @@ package lcsb.mapviewer.services.search;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.junit.*;
+import lcsb.mapviewer.annotation.data.*;
import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.services.ServiceTestFunctions;
public class ElementMatcherTest extends ServiceTestFunctions {
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 8a9f7a18f8..1bd6e92b05 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.services.search.mirna;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -19,10 +20,9 @@ import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.DbSearchCriteria;
public class MiRNAServiceTest extends ServiceTestFunctions {
- Logger logger = LogManager.getLogger(MiRNAServiceTest.class);
-
@Autowired
protected IMiRNAService miRNAService;
+ Logger logger = LogManager.getLogger(MiRNAServiceTest.class);
@Before
public void setUp() throws Exception {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 55fc71dbc6..4592e44bb3 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -2,10 +2,11 @@ package lcsb.mapviewer.services.utils;
import static org.junit.Assert.*;
-import java.awt.Color;
+import java.awt.*;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.*;
+import java.util.List;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.apache.logging.log4j.LogManager;
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CORSFilter.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CORSFilter.java
index 60f694b6ac..3a0341a4c0 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CORSFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CORSFilter.java
@@ -2,16 +2,12 @@ package lcsb.mapviewer.web.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.*;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CacheFilter.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CacheFilter.java
index 72733addc6..5baef1dcef 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CacheFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CacheFilter.java
@@ -2,15 +2,11 @@ package lcsb.mapviewer.web.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.*;
import javax.servlet.http.HttpServletResponse;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This filter disables caching for API queries.
@@ -33,7 +29,7 @@ public class CacheFilter implements Filter {
public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain)
throws IOException, ServletException {
HttpServletResponse response = (HttpServletResponse) res;
- //caching on Safari
+ // caching on Safari
response.addHeader("Vary", "*");
// generic cache prevent mechanism
response.addHeader("Cache-Control", "no-cache, no-store, must-revalidate");
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomFilter.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomFilter.java
index 04d2957a90..7f2a4282a0 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomFilter.java
@@ -2,16 +2,12 @@ package lcsb.mapviewer.web.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.*;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class should be used only for debug purpose. It wrapps
@@ -23,29 +19,30 @@ import org.apache.logging.log4j.*;
*
*/
public class CustomFilter implements Filter {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.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() {
- }
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.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/web/bean/utils/CustomHttpServletResponseWrapper.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomHttpServletResponseWrapper.java
index f3eef2d300..5cfabaf067 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomHttpServletResponseWrapper.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomHttpServletResponseWrapper.java
@@ -5,11 +5,10 @@ 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 javax.servlet.http.*;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class should be used only for debugging. It's a wrapper to standard JSF
@@ -24,225 +23,225 @@ import org.apache.logging.log4j.*;
*/
public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper {
- /**
- * Default class logger.
- */
- private Logger logger = LogManager.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);
-
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = LogManager.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 void addCookie(Cookie cookie) {
+ logger.debug("addCookie");
+ this.addCookie(cookie);
+ } @Override
+ public PrintWriter getWriter() throws IOException {
+ logger.debug("getWriter");
+ return this.getWriter();
+ }
+
+ @Override
+ public boolean containsHeader(String name) {
+ logger.debug("containsHeader");
+ return this.containsHeader(name);
+ } @Override
+ public ServletOutputStream getOutputStream() throws IOException {
+ logger.debug("getOutputStream");
+ logger.debug(new Exception(), new Exception());
+ return this.getOutputStream();
+ }
+
+ @Override
+ public String encodeURL(String url) {
+ logger.debug("encodeURL");
+ return this.encodeURL(url);
+ } @Override
+ public String getCharacterEncoding() {
+ logger.debug("getCharacterEncoding");
+ return this.getCharacterEncoding();
+ }
+
+ @Override
+ public String encodeRedirectURL(String url) {
+ logger.debug("encodeRedirectURL");
+ return this.encodeRedirectURL(url);
+ } @Override
+ public String getContentType() {
+ logger.debug("getContentType");
+ return this.getContentType();
+ }
+
+ @Override
+ public String encodeUrl(String url) {
+ logger.debug("encodeUrl");
+ return this.encodeUrl(url);
+ } @Override
+ public void setCharacterEncoding(String charset) {
+ logger.debug("setCharacterEncoding");
+ this.setCharacterEncoding(charset);
+ }
+
+ @Override
+ public String encodeRedirectUrl(String url) {
+ logger.debug("encodeRedirectUrl");
+ return this.encodeRedirectUrl(url);
+ } @Override
+ public void setContentLength(int len) {
+ logger.debug("setContentLength");
+ this.setContentLength(len);
+ }
+
+ @Override
+ public void sendError(int sc, String msg) throws IOException {
+ logger.debug("sendError");
+ this.sendError(sc);
+
+ } @Override
+ public void setContentType(String type) {
+ logger.debug("setContentType: " + type);
+ logger.debug(new Exception(), new Exception());
+ this.setContentType(type);
+ }
+
+ @Override
+ public void sendError(int sc) throws IOException {
+ logger.debug("sendError");
+ this.sendError(sc);
+
+ } @Override
+ public void setBufferSize(int size) {
+ logger.debug("setBufferSize");
+ this.setBufferSize(size);
+ }
+
+ @Override
+ public void sendRedirect(String location) throws IOException {
+ logger.debug("sendRedirect");
+ this.sendRedirect(location);
+
+ } @Override
+ public int getBufferSize() {
+ logger.debug("getBufferSize");
+ return this.getBufferSize();
+ }
+
+ @Override
+ public void setDateHeader(String name, long date) {
+ logger.debug("setDateHeader");
+ this.setDateHeader(name, date);
+
+ } @Override
+ public void flushBuffer() throws IOException {
+ logger.debug("flushBuffer");
+ this.flushBuffer();
+ }
+
+ @Override
+ public void addDateHeader(String name, long date) {
+ logger.debug("addDateHeader");
+ this.addDateHeader(name, date);
+
+ } @Override
+ public void resetBuffer() {
+ logger.debug("resetBuffer");
+ this.resetBuffer();
+ }
+
+ @Override
+ public void setHeader(String name, String value) {
+ logger.debug("setHeader");
+ this.setHeader(name, value);
+
+ } @Override
+ public boolean isCommitted() {
+ logger.debug("isCommitted");
+ return this.isCommitted();
+ }
+
+ @Override
+ public void addHeader(String name, String value) {
+ logger.debug("addHeader: " + name + " - " + value);
+ this.addHeader(name, value);
+
+ } @Override
+ public void reset() {
+ logger.debug("reset");
+ this.reset();
+ }
+
+ @Override
+ public void setIntHeader(String name, int value) {
+ logger.debug("setIntHeader");
+ this.setIntHeader(name, value);
+
+ } @Override
+ public void setLocale(Locale loc) {
+ logger.debug("setLocale");
+ this.setLocale(loc);
+ }
+
+ @Override
+ public void addIntHeader(String name, int value) {
+ logger.debug("addIntHeader");
+ this.addIntHeader(name, value);
+
+ } @Override
+ public Locale getLocale() {
+ logger.debug("getLocale");
+ return this.getLocale();
+ }
+
+ @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);
+
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
- @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/web/bean/utils/StartupBean.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
index da4d1a3e28..5bb3cdf4d3 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
@@ -18,9 +18,7 @@ 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.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
+import lcsb.mapviewer.services.interfaces.*;
/**
* Bean where init script of the application is placed. The method in this bean
@@ -38,9 +36,9 @@ public class StartupBean {
@Autowired
public StartupBean(IProjectService projectService,
- IConfigurationService configurationService,
- IReferenceGenomeService referenceGenomeService,
- ServletContext servletContext) {
+ IConfigurationService configurationService,
+ IReferenceGenomeService referenceGenomeService,
+ ServletContext servletContext) {
this.projectService = projectService;
this.configurationService = configurationService;
this.referenceGenomeService = referenceGenomeService;
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/VersionResourceHandler.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/VersionResourceHandler.java
index e308a998f4..a647539a8e 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/VersionResourceHandler.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/VersionResourceHandler.java
@@ -3,10 +3,7 @@ package lcsb.mapviewer.web.bean.utils;
import java.io.File;
import java.io.IOException;
-import javax.faces.application.Resource;
-import javax.faces.application.ResourceHandler;
-import javax.faces.application.ResourceHandlerWrapper;
-import javax.faces.application.ResourceWrapper;
+import javax.faces.application.*;
import javax.faces.context.FacesContext;
import org.apache.logging.log4j.LogManager;
@@ -23,16 +20,14 @@ import lcsb.mapviewer.services.impl.ConfigurationService;
*
*/
public class VersionResourceHandler extends ResourceHandlerWrapper {
- /**
- * Default class logger.
- */
- private final Logger logger = LogManager.getLogger(VersionResourceHandler.class);
-
/**
* GIT version of the system.
*/
private static String version = null;
-
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger(VersionResourceHandler.class);
/**
* Resource for which we generate modified url.
*/
@@ -48,6 +43,11 @@ public class VersionResourceHandler extends ResourceHandlerWrapper {
this.wrapped = wrapped;
}
+ @Override
+ public ResourceHandler getWrapped() {
+ return wrapped;
+ }
+
@Override
public Resource createResource(String resourceName) {
return createResource(resourceName, null, null);
@@ -69,13 +69,13 @@ public class VersionResourceHandler extends ResourceHandlerWrapper {
return new ResourceWrapper() {
@Override
- public String getRequestPath() {
- return super.getRequestPath() + "&m_version=" + getVersion();
+ public Resource getWrapped() {
+ return resource;
}
@Override
- public Resource getWrapped() {
- return resource;
+ public String getRequestPath() {
+ return super.getRequestPath() + "&m_version=" + getVersion();
}
@Override
@@ -84,22 +84,17 @@ public class VersionResourceHandler extends ResourceHandlerWrapper {
}
@Override
- public String getResourceName() {
- return getWrapped().getResourceName();
+ public String getLibraryName() {
+ return getWrapped().getLibraryName();
}
@Override
- public String getLibraryName() {
- return getWrapped().getLibraryName();
+ public String getResourceName() {
+ return getWrapped().getResourceName();
}
};
}
- @Override
- public ResourceHandler getWrapped() {
- return wrapped;
- }
-
/**
* This method returns git version of the framework.
*
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/XFrameFilter.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/XFrameFilter.java
index 7cafab8000..518b5ff2c8 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/XFrameFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/XFrameFilter.java
@@ -1,12 +1,14 @@
package lcsb.mapviewer.web.bean.utils;
-import lcsb.mapviewer.common.Configuration;
-import org.apache.commons.validator.routines.UrlValidator;
+import java.io.IOException;
+import java.util.List;
import javax.servlet.*;
import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
-import java.util.List;
+
+import org.apache.commons.validator.routines.UrlValidator;
+
+import lcsb.mapviewer.common.Configuration;
public class XFrameFilter implements Filter {
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/package-info.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/package-info.java
index bcb4a4511e..45bcaea616 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/package-info.java
@@ -2,4 +2,3 @@
* Provides util classes used by the web interface.
*/
package lcsb.mapviewer.web.bean.utils;
-
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationFailureHandlerImpl.java b/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationFailureHandlerImpl.java
index 704d2557c3..9bfe246f61 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationFailureHandlerImpl.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationFailureHandlerImpl.java
@@ -1,14 +1,15 @@
package lcsb.mapviewer.web.config;
-import org.springframework.http.HttpStatus;
-import org.springframework.security.core.AuthenticationException;
-import org.springframework.security.web.authentication.AuthenticationFailureHandler;
-import org.springframework.stereotype.Component;
+import java.io.IOException;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.security.core.AuthenticationException;
+import org.springframework.security.web.authentication.AuthenticationFailureHandler;
+import org.springframework.stereotype.Component;
@Component
public class AuthenticationFailureHandlerImpl implements AuthenticationFailureHandler {
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationSuccessHandlerImpl.java b/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationSuccessHandlerImpl.java
index ec526d7ab6..d6935a0a1a 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationSuccessHandlerImpl.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/AuthenticationSuccessHandlerImpl.java
@@ -8,15 +8,15 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.security.core.Authentication;
import org.springframework.security.web.authentication.AuthenticationSuccessHandler;
import org.springframework.stereotype.Component;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.interfaces.IUserService;
@@ -60,7 +60,7 @@ public class AuthenticationSuccessHandlerImpl implements AuthenticationSuccessHa
result.put("login", user.getLogin());
String json = new ObjectMapper().writeValueAsString(result);
-
+
response.setContentType("application/json");
response.getWriter().print(json);
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/LdapAuthenticationProvider.java b/web/src/main/java/lcsb/mapviewer/web/config/LdapAuthenticationProvider.java
index bc96862d2a..a40ff673bb 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/LdapAuthenticationProvider.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/LdapAuthenticationProvider.java
@@ -43,8 +43,8 @@ public class LdapAuthenticationProvider implements AuthenticationProvider {
throw new BadCredentialsException("Invalid username.");
}
User existingUser = userService.getUserByLogin(username);
-
- if (existingUser!=null) {
+
+ if (existingUser != null) {
if (!existingUser.isConnectedToLdap()) {
throw new BadCredentialsException("User cannot authenticate over LDAP");
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/LocalAuthenticationProvider.java b/web/src/main/java/lcsb/mapviewer/web/config/LocalAuthenticationProvider.java
index 1b36d74097..746fd716b0 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/LocalAuthenticationProvider.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/LocalAuthenticationProvider.java
@@ -1,12 +1,11 @@
package lcsb.mapviewer.web.config;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IUserService;
+import javax.annotation.PostConstruct;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.annotation.Order;
import org.springframework.security.authentication.AuthenticationProvider;
import org.springframework.security.authentication.BadCredentialsException;
-import org.springframework.security.authentication.InternalAuthenticationServiceException;
import org.springframework.security.authentication.dao.DaoAuthenticationProvider;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.AuthenticationException;
@@ -15,7 +14,8 @@ import org.springframework.security.core.userdetails.UsernameNotFoundException;
import org.springframework.security.crypto.password.PasswordEncoder;
import org.springframework.stereotype.Service;
-import javax.annotation.PostConstruct;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IUserService;
@Order(1)
@Service
@@ -29,8 +29,8 @@ public class LocalAuthenticationProvider implements AuthenticationProvider {
@Autowired
public LocalAuthenticationProvider(UserDetailsService userDetailsService,
- PasswordEncoder passwordEncoder,
- IUserService userService) {
+ PasswordEncoder passwordEncoder,
+ IUserService userService) {
this.userDetailsService = userDetailsService;
this.passwordEncoder = passwordEncoder;
this.userService = userService;
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/LogoutSuccessHandlerImpl.java b/web/src/main/java/lcsb/mapviewer/web/config/LogoutSuccessHandlerImpl.java
index 147cd68d16..f44111018b 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/LogoutSuccessHandlerImpl.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/LogoutSuccessHandlerImpl.java
@@ -1,13 +1,14 @@
package lcsb.mapviewer.web.config;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.web.authentication.logout.LogoutSuccessHandler;
-import org.springframework.stereotype.Service;
+import java.io.IOException;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
+
+import org.springframework.security.core.Authentication;
+import org.springframework.security.web.authentication.logout.LogoutSuccessHandler;
+import org.springframework.stereotype.Service;
@Service
public class LogoutSuccessHandlerImpl implements LogoutSuccessHandler {
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/RefreshAuthoritiesInterceptor.java b/web/src/main/java/lcsb/mapviewer/web/config/RefreshAuthoritiesInterceptor.java
index 2d73217101..bdb0699e99 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/RefreshAuthoritiesInterceptor.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/RefreshAuthoritiesInterceptor.java
@@ -1,5 +1,8 @@
package lcsb.mapviewer.web.config;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
import org.springframework.security.core.Authentication;
@@ -9,17 +12,16 @@ import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.servlet.HandlerInterceptor;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
/**
- * This class intercepts a request (before the authorization step) to refresh the current authentication object in case
- * the authorities have been updated since the last request.
+ * This class intercepts a request (before the authorization step) to refresh
+ * the current authentication object in case the authorities have been updated
+ * since the last request.
*
- * Performance note:
- * This code has an impact on performance due to the repeated DB requests, but is much simpler and therefor safer.
- * If performance becomes an issue, user sessions must be updated manually when authorities change. This also requires
- * being able to directly access and modify an arbitrary user session from the current request session.
+ * Performance note: This code has an impact on performance due to the repeated
+ * DB requests, but is much simpler and therefor safer. If performance becomes
+ * an issue, user sessions must be updated manually when authorities change.
+ * This also requires being able to directly access and modify an arbitrary user
+ * session from the current request session.
*/
@Transactional
@Service
@@ -41,8 +43,7 @@ public class RefreshAuthoritiesInterceptor implements HandlerInterceptor {
Authentication newAuth = new UsernamePasswordAuthenticationToken(
auth.getPrincipal(),
auth.getCredentials(),
- userDetailsService.loadUserByUsername(auth.getName()).getAuthorities()
- );
+ userDetailsService.loadUserByUsername(auth.getName()).getAuthorities());
SecurityContextHolder.getContext().setAuthentication(newAuth);
return true;
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/SpringSecurityConfig.java b/web/src/main/java/lcsb/mapviewer/web/config/SpringSecurityConfig.java
index ff4a033e83..d269c94d9f 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/SpringSecurityConfig.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/SpringSecurityConfig.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.web.config;
-import javax.transaction.Transactional;
+import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.*;
@@ -19,11 +19,9 @@ import lcsb.mapviewer.api.SpringRestApiConfig;
import lcsb.mapviewer.services.SpringServiceConfig;
import lcsb.mapviewer.web.bean.utils.*;
-import java.util.List;
-
@Configuration
@ComponentScan(basePackages = { "lcsb.mapviewer.web.config" })
-@Import({SpringRestApiConfig.class, SpringServiceConfig.class})
+@Import({ SpringRestApiConfig.class, SpringServiceConfig.class })
@EnableWebSecurity
public class SpringSecurityConfig extends WebSecurityConfigurerAdapter {
@@ -34,9 +32,9 @@ public class SpringSecurityConfig extends WebSecurityConfigurerAdapter {
@Autowired
SpringSecurityConfig(AuthenticationSuccessHandler successHandler,
- AuthenticationFailureHandler failureHandler,
- LogoutSuccessHandler logoutSuccessHandler,
- List<AuthenticationProvider> authenticationProviders) {
+ AuthenticationFailureHandler failureHandler,
+ LogoutSuccessHandler logoutSuccessHandler,
+ List<AuthenticationProvider> authenticationProviders) {
super(false);
this.successHandler = successHandler;
this.failureHandler = failureHandler;
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java b/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java
index 8a5e92ff18..139b2ad949 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java
@@ -1,22 +1,20 @@
package lcsb.mapviewer.web.config;
-import lcsb.mapviewer.api.SpringRestApiConfig;
+import java.util.List;
+
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.*;
import org.springframework.web.servlet.HandlerInterceptor;
import org.springframework.web.servlet.ViewResolver;
import org.springframework.web.servlet.config.annotation.*;
import org.springframework.web.servlet.view.InternalResourceViewResolver;
-import java.util.List;
+import lcsb.mapviewer.api.SpringRestApiConfig;
@Configuration
@EnableWebMvc
@Import(SpringRestApiConfig.class)
-@ComponentScan(basePackages = {"lcsb.mapviewer.web"})
+@ComponentScan(basePackages = { "lcsb.mapviewer.web" })
public class SpringWebConfig implements WebMvcConfigurer {
private List<HandlerInterceptor> interceptors;
@@ -35,10 +33,8 @@ public class SpringWebConfig implements WebMvcConfigurer {
}
@Override
- public void addViewControllers(ViewControllerRegistry registry) {
- registry
- .addViewController("/")
- .setViewName("index");
+ public void addInterceptors(InterceptorRegistry registry) {
+ interceptors.forEach(registry::addInterceptor);
}
@Override
@@ -54,8 +50,10 @@ public class SpringWebConfig implements WebMvcConfigurer {
}
@Override
- public void addInterceptors(InterceptorRegistry registry) {
- interceptors.forEach(registry::addInterceptor);
+ public void addViewControllers(ViewControllerRegistry registry) {
+ registry
+ .addViewController("/")
+ .setViewName("index");
}
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/UserDetailsServiceImpl.java b/web/src/main/java/lcsb/mapviewer/web/config/UserDetailsServiceImpl.java
index b5c1763048..1d5898de91 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/UserDetailsServiceImpl.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/UserDetailsServiceImpl.java
@@ -5,13 +5,13 @@ import java.util.stream.Collectors;
import javax.transaction.Transactional;
-import lcsb.mapviewer.common.Configuration;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.GrantedAuthority;
import org.springframework.security.core.authority.SimpleGrantedAuthority;
import org.springframework.security.core.userdetails.*;
import org.springframework.stereotype.Service;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.user.UserDao;
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java b/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java
index 945ce43bb8..4833b9fa77 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java
@@ -34,15 +34,6 @@ public class WebAppInitializer extends AbstractAnnotationConfigDispatcherServlet
return new Class[] {};
}
- @Override
- protected String[] getServletMappings() {
- return new String[] { "/", "/api/*" };
- }
-
- @Override
- protected Filter[] getServletFilters() {
- return new Filter[]{new XFrameFilter()};
- }
@Override
public void onStartup(ServletContext container) throws ServletException {
assert container.setInitParameter("com.sun.faces.enableMissingResourceLibraryDetection", "true");
@@ -76,4 +67,14 @@ public class WebAppInitializer extends AbstractAnnotationConfigDispatcherServlet
super.onStartup(container);
}
+
+ @Override
+ protected String[] getServletMappings() {
+ return new String[] { "/", "/api/*" };
+ }
+
+ @Override
+ protected Filter[] getServletFilters() {
+ return new Filter[] { new XFrameFilter() };
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/converter/MiriamTypeConverter.java b/web/src/main/java/lcsb/mapviewer/web/converter/MiriamTypeConverter.java
index 6e2ec9290c..a5bd60c1c5 100644
--- a/web/src/main/java/lcsb/mapviewer/web/converter/MiriamTypeConverter.java
+++ b/web/src/main/java/lcsb/mapviewer/web/converter/MiriamTypeConverter.java
@@ -1,16 +1,15 @@
package lcsb.mapviewer.web.converter;
-import java.util.Map;
+import java.util.*;
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.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* Converter used for {@link lcsb.mapviewer.model.map.MiriamType} in primefaces
@@ -22,38 +21,37 @@ import org.apache.logging.log4j.*;
@FacesConverter(value = "miriamTypeConverter")
public class MiriamTypeConverter implements Converter {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = LogManager.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;
- }
+ /**
+ * Map between custom uuid and MiriamType object.
+ */
+ private static Map<Object, String> entities = new WeakHashMap<Object, String>();
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger(MiriamTypeConverter.class);
+
+ @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;
+ }
+
+ @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);
+ }
+ }
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/converter/package-info.java b/web/src/main/java/lcsb/mapviewer/web/converter/package-info.java
index 9459987d0d..00e738795f 100644
--- a/web/src/main/java/lcsb/mapviewer/web/converter/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/web/converter/package-info.java
@@ -3,4 +3,3 @@
* by primefaces.
*/
package lcsb.mapviewer.web.converter;
-
diff --git a/web/src/main/java/lcsb/mapviewer/web/events/Event.java b/web/src/main/java/lcsb/mapviewer/web/events/Event.java
index 3ad3a4efcf..84ca1302b6 100644
--- a/web/src/main/java/lcsb/mapviewer/web/events/Event.java
+++ b/web/src/main/java/lcsb/mapviewer/web/events/Event.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.web.events;
-
/**
* Abstract event object that might be handled by {@link Listener} class.
*
diff --git a/web/src/main/java/lcsb/mapviewer/web/events/Listener.java b/web/src/main/java/lcsb/mapviewer/web/events/Listener.java
index e80dec2722..56de800f0d 100644
--- a/web/src/main/java/lcsb/mapviewer/web/events/Listener.java
+++ b/web/src/main/java/lcsb/mapviewer/web/events/Listener.java
@@ -10,51 +10,51 @@ import java.io.Serializable;
* @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;
- }
+
+ /**
+ *
+ */
+ 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/web/events/ObjectAddedEvent.java b/web/src/main/java/lcsb/mapviewer/web/events/ObjectAddedEvent.java
index d1724d278c..57437881ce 100644
--- a/web/src/main/java/lcsb/mapviewer/web/events/ObjectAddedEvent.java
+++ b/web/src/main/java/lcsb/mapviewer/web/events/ObjectAddedEvent.java
@@ -9,32 +9,32 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*
*/
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");
- }
+ /**
+ * Object that was removed.
+ */
+ private Object object;
- this.object = object;
- }
+ /**
+ * Default constructor.
+ *
+ * @param object
+ * {@link #object}
+ */
+ public ObjectAddedEvent(Object object) {
+ if (object == null) {
+ throw new InvalidArgumentException("object cannot be null");
+ }
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return object;
- }
+ this.object = object;
+ }
+
+ /**
+ * @return the object
+ * @see #object
+ */
+ public Object getObject() {
+ return object;
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/events/ObjectModifiedEvent.java b/web/src/main/java/lcsb/mapviewer/web/events/ObjectModifiedEvent.java
index 7738d88194..f35620dcb4 100644
--- a/web/src/main/java/lcsb/mapviewer/web/events/ObjectModifiedEvent.java
+++ b/web/src/main/java/lcsb/mapviewer/web/events/ObjectModifiedEvent.java
@@ -9,31 +9,31 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*
*/
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;
- }
+ /**
+ * Object that was modified.
+ */
+ private Object object;
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return 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/web/events/ObjectRemovedEvent.java b/web/src/main/java/lcsb/mapviewer/web/events/ObjectRemovedEvent.java
index 5e88eddac7..34abd352a6 100644
--- a/web/src/main/java/lcsb/mapviewer/web/events/ObjectRemovedEvent.java
+++ b/web/src/main/java/lcsb/mapviewer/web/events/ObjectRemovedEvent.java
@@ -9,32 +9,32 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*
*/
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");
- }
+ /**
+ * Object that was removed.
+ */
+ private Object object;
- this.object = object;
- }
+ /**
+ * Default constructor.
+ *
+ * @param object
+ * {@link #object}
+ */
+ public ObjectRemovedEvent(Object object) {
+ if (object == null) {
+ throw new InvalidArgumentException("object cannot be null");
+ }
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return object;
- }
+ this.object = object;
+ }
+
+ /**
+ * @return the object
+ * @see #object
+ */
+ public Object getObject() {
+ return object;
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/events/package-info.java b/web/src/main/java/lcsb/mapviewer/web/events/package-info.java
index 9060b696b6..58b4c326f8 100644
--- a/web/src/main/java/lcsb/mapviewer/web/events/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/web/events/package-info.java
@@ -2,4 +2,3 @@
* Provides events and listeners functionality.
*/
package lcsb.mapviewer.web.events;
-
diff --git a/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
index d01180bf97..959d2fee3b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -24,11 +24,9 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
@Rollback
public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
+ Logger logger = LogManager.getLogger();
@Autowired
IConfigurationService configurationService;
diff --git a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
index 824e80cae2..1fb757ca94 100644
--- a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.web;
import static org.junit.Assert.*;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.awt.geom.Point2D;
import java.util.Arrays;
@@ -40,19 +40,14 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Rollback
public class CommentControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_PROJECT = "test_project";
-
private static final String TEST_USER_PASSWORD = "test_user_pass";
private static final String TEST_USER_LOGIN = "test_user";
-
private static final String TEST_CURATOR_PASSWORD = "test_curator_pass";
private static final String TEST_CURATOR_LOGIN = "test_curator";
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
+ Logger logger = LogManager.getLogger();
private ModelData map;
private Reaction reaction;
private Element element;
diff --git a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTestWithoutTransaction.java
index ab5abd5463..5a3005d701 100644
--- a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTestWithoutTransaction.java
+++ b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTestWithoutTransaction.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -16,10 +16,9 @@ import org.springframework.test.web.servlet.RequestBuilder;
@Rollback
public class CommentControllerIntegrationTestWithoutTransaction extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String BUILT_IN_TEST_ADMIN_PASSWORD = "admin";
private static final String BUILT_IN_TEST_ADMIN_LOGIN = "admin";
+ Logger logger = LogManager.getLogger();
@Before
public void setup() {
diff --git a/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java
index a8dac431a5..66afc4bc0c 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ConfigurationControllerIntegrationTest.java
@@ -1,8 +1,10 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.patch;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.HashMap;
import java.util.Map;
@@ -31,16 +33,11 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Transactional
@Rollback
public class ConfigurationControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_USER_PASSWORD = "test_pass";
-
private static final String TEST_USER_LOGIN = "test_user";
-
private static final String TEST_ADMIN_PASSWORD = "test_admin_pass";
-
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
+ Logger logger = LogManager.getLogger();
@Autowired
private IUserService userService;
diff --git a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
index 4044855a7d..df0d467a51 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
import java.awt.geom.Point2D;
import java.util.Arrays;
@@ -49,33 +49,23 @@ abstract public class ControllerIntegrationTest {
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
+ protected MockMvc mockMvc;
@Autowired
private WebApplicationContext context;
-
@Autowired
private Filter springSecurityFilterChain;
-
@Autowired
private IUserService userService;
-
@Autowired
private ProjectDao projectDao;
-
@Autowired
private UserDao userDao;
-
@Autowired
private PasswordEncoder passwordEncoder;
-
@Autowired
private UploadedFileEntryDao fileDao;
-
@Autowired
private DbUtils dbUtils;
-
- protected MockMvc mockMvc;
-
private MinervaLoggerAppender appender;
private ExecutorService executorService;
diff --git a/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java
index eaf02a4fc2..c4ed2e324c 100644
--- a/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -24,11 +24,9 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
@Rollback
public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
+ Logger logger = LogManager.getLogger();
@Autowired
IConfigurationService configurationService;
diff --git a/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java b/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java
index 36bcefe396..440278e5ac 100644
--- a/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java
+++ b/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
import java.net.URI;
@@ -25,15 +26,12 @@ import org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandl
@RunWith(SpringJUnit4ClassRunner.class)
public class EndPointsInputValidationTests extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static String[] testValues = { " ", "-1", "0", "empty", "admin", "1.00,2.00", "17.00", "1" };
private static List<HttpStatus> validResponses = Arrays.asList(HttpStatus.OK, HttpStatus.BAD_REQUEST,
HttpStatus.NOT_FOUND, HttpStatus.FORBIDDEN);
-
@Autowired
public RequestMappingHandlerMapping requestMappingHandlerMapping;
-
+ Logger logger = LogManager.getLogger();
@Autowired
ServletContext container;
diff --git a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
index 63fe2306d3..9259b5ba64 100644
--- a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.junit.Assert.assertNotNull;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.Arrays;
diff --git a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTestWithoutTransaction.java
index a90953356c..9d32a6cf18 100644
--- a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTestWithoutTransaction.java
+++ b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTestWithoutTransaction.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.Arrays;
diff --git a/web/src/test/java/lcsb/mapviewer/web/LdapServiceTestConfiguration.java b/web/src/test/java/lcsb/mapviewer/web/LdapServiceTestConfiguration.java
index b111ecbd63..71dbe40e6a 100644
--- a/web/src/test/java/lcsb/mapviewer/web/LdapServiceTestConfiguration.java
+++ b/web/src/test/java/lcsb/mapviewer/web/LdapServiceTestConfiguration.java
@@ -21,15 +21,13 @@ import lcsb.mapviewer.services.interfaces.ILdapService;
@Profile("ldapTest")
@Configuration
public class LdapServiceTestConfiguration {
- @Autowired
- IConfigurationService configurationService;
-
- Logger logger = LogManager.getLogger();
-
static String TEST_LOGIN = "john.doe.test";
static String TEST_PASSWD = "test_passwd";
static String LDAP_FILE_CONTENT = "./src/test/resources/ldap/john-doe-test-example.ldif";
static String TEST_INVALID_PASSWD = "incorrect password";
+ @Autowired
+ IConfigurationService configurationService;
+ Logger logger = LogManager.getLogger();
@Bean
@Primary
diff --git a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
index f61eb579ee..a3aef6a207 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java
index c71986efe6..92b63aad17 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -24,11 +24,9 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
@Rollback
public class MiRnaControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
+ Logger logger = LogManager.getLogger();
@Autowired
IConfigurationService configurationService;
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 5c8360d268..f0dfd1ee1f 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.Arrays;
@@ -40,19 +40,14 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Rollback
public class OverlayControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_PROJECT = "test_project";
-
private static final String TEST_USER_PASSWORD = "test_user_pass";
private static final String TEST_USER_LOGIN = "test_user";
-
private static final String TEST_CURATOR_PASSWORD = "test_curator_pass";
private static final String TEST_CURATOR_LOGIN = "test_curator";
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
+ Logger logger = LogManager.getLogger();
@Autowired
private LayoutDao layoutDao;
@@ -147,9 +142,10 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
- RequestBuilder request = get("/projects/" + TEST_PROJECT + "/overlays/?publicOverlay=false&creator="+TEST_ADMIN_LOGIN)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .session(session);
+ RequestBuilder request = get(
+ "/projects/" + TEST_PROJECT + "/overlays/?publicOverlay=false&creator=" + TEST_ADMIN_LOGIN)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .session(session);
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -1025,8 +1021,8 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
RequestBuilder request = get(
"/projects/" + TEST_PROJECT + "/overlays/" + overlay.getId() + ":downloadSource/")
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .session(session);
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .session(session);
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful());
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTestWithoutTransaction.java
index 2f27f12472..ace9df7f86 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTestWithoutTransaction.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTestWithoutTransaction.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -21,15 +21,12 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
@Rollback
public class OverlayControllerIntegrationTestWithoutTransaction extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String BUILD_IN_TEST_ADMIN_PASSWORD = "admin";
private static final String BUILD_IN_TEST_ADMIN_LOGIN = "admin";
-
- private String defaultProjectId;
-
+ Logger logger = LogManager.getLogger();
@Autowired
IConfigurationService configurationService;
+ private String defaultProjectId;
@Before
public void setup() throws Exception {
diff --git a/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
index e6c8580c56..83ec743993 100644
--- a/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.junit.Assert.assertEquals;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.Arrays;
@@ -11,9 +12,7 @@ import org.apache.http.message.BasicNameValuePair;
import org.apache.http.util.EntityUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.junit.*;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -37,12 +36,9 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Rollback
public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_USER_PASSWORD = "test_pass";
-
private static final String TEST_USER_LOGIN = "test_user";
-
+ Logger logger = LogManager.getLogger();
@Autowired
private PluginDao pluginDao;
@@ -192,9 +188,10 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
Plugin plugin = createPlugin();
- RequestBuilder request = post("/plugins/" + plugin.getHash() + "/data/users/" + Configuration.ANONYMOUS_LOGIN + "/key/")
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .content(body);
+ RequestBuilder request = post(
+ "/plugins/" + plugin.getHash() + "/data/users/" + Configuration.ANONYMOUS_LOGIN + "/key/")
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body);
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful());
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
index 3909060911..04b24c6fe6 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.web;
import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.patch;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -32,15 +33,11 @@ import lcsb.mapviewer.services.interfaces.IUserService;
public class ProjectControllerIntegrationTest extends ControllerIntegrationTest {
private static final String TEST_PROJECT = "test_project";
-
- Logger logger = LogManager.getLogger();
-
private static final String CURATOR_PASSWORD = "test_pass";
private static final String CURATOR_LOGIN = "test_user";
-
private static final String ADMIN_PASSWORD = "admin_pass";
private static final String ADMIN_LOGIN = "admin_user";
-
+ Logger logger = LogManager.getLogger();
@Autowired
private IUserService userService;
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java
index 02dd41778a..607a27e11b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.web;
import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.nio.file.Files;
import java.nio.file.Paths;
@@ -37,18 +38,13 @@ import lcsb.mapviewer.services.interfaces.IUserService;
public class ProjectControllerIntegrationTestForAsyncCalls extends ControllerIntegrationTest {
private static final String TEST_PROJECT = "test_project";
-
- Logger logger = LogManager.getLogger();
-
private static final String CURATOR_PASSWORD = "curator_pass";
private static final String CURATOR_LOGIN = "test_curator";
-
private static final String ADMIN_PASSWORD = "admin_pass";
private static final String ADMIN_LOGIN = "admin_user";
-
private static final String USER_PASSWORD = "user_pass";
private static final String USER_LOGIN = "test_user";
-
+ Logger logger = LogManager.getLogger();
@Autowired
private ProjectDao projectDao;
diff --git a/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java
index 9fdec3d038..5b8340d0d4 100644
--- a/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.web;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/web/src/test/java/lcsb/mapviewer/web/ReactionControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ReactionControllerIntegrationTest.java
index 3d79f671c6..d40c300b85 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ReactionControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ReactionControllerIntegrationTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.junit.Assert.assertTrue;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/web/src/test/java/lcsb/mapviewer/web/SpringSecurityGeneralIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/SpringSecurityGeneralIntegrationTest.java
index 42b7f776f4..744ba7ab53 100644
--- a/web/src/test/java/lcsb/mapviewer/web/SpringSecurityGeneralIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/SpringSecurityGeneralIntegrationTest.java
@@ -1,8 +1,9 @@
package lcsb.mapviewer.web;
import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import javax.servlet.http.HttpSession;
@@ -39,7 +40,7 @@ public class SpringSecurityGeneralIntegrationTest extends ControllerIntegrationT
@Autowired
IConfigurationService configurationService;
-
+
@Before
public void setup() {
createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
diff --git a/web/src/test/java/lcsb/mapviewer/web/SpringSecurityLdapIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/SpringSecurityLdapIntegrationTest.java
index 81a009f6f3..61303def63 100644
--- a/web/src/test/java/lcsb/mapviewer/web/SpringSecurityLdapIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/SpringSecurityLdapIntegrationTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.web;
import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -38,8 +38,6 @@ public class SpringSecurityLdapIntegrationTest extends ControllerIntegrationTest
@Autowired
private IUserService userService;
-
-
@Before
public void setUp() throws LDAPException {
}
@@ -48,7 +46,6 @@ public class SpringSecurityLdapIntegrationTest extends ControllerIntegrationTest
public void tearDown() {
}
-
@Test
public void testInvalidLoginFromLdap() throws Exception {
int count = userService.getUsers().size();
@@ -103,7 +100,7 @@ public class SpringSecurityLdapIntegrationTest extends ControllerIntegrationTest
assertEquals("LDAP login is case insensitive and no new user should be added for different cases",
count + 1, userService.getUsers().size());
}
-
+
@Test
public void testLocalAccountShouldntAuthenticateFromLdap() throws Exception {
createUser(LdapServiceTestConfiguration.TEST_LOGIN, LOCAL_PASSWORD);
diff --git a/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java
index abc8b0655e..e1a58f0e02 100644
--- a/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/TaxonomiesControllerIntegrationTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.junit.Assert.assertTrue;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -39,7 +39,7 @@ public class TaxonomiesControllerIntegrationTest extends ControllerIntegrationTe
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
-
+
int taxonomies = new JsonParser()
.parse(response)
.getAsJsonArray().size();
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
index 5748478576..b646785583 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -19,17 +19,15 @@ import org.springframework.transaction.annotation.Transactional;
import com.google.gson.JsonParser;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.user.User;
@RunWith(SpringJUnit4ClassRunner.class)
@Transactional
@Rollback
public class UserControllerAnonymousIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
+ Logger logger = LogManager.getLogger();
@Before
public void setup() {
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
index aa8068f456..5ea6eb81ca 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.web;
import static org.junit.Assert.*;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.*;
@@ -38,16 +38,12 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Rollback
public class UserControllerIntegrationTest extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_USER_PASSWORD = "test_pass";
private static final String TEST_USER_LOGIN = "test_user";
-
private static final String TEST_ADMIN_PASSWORD = "test_admin";
private static final String TEST_ADMIN_LOGIN = "test_admin";
-
private static final String TEST_PROJECT = "test_project";
-
+ Logger logger = LogManager.getLogger();
private User user;
private User admin;
@@ -301,8 +297,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("name", "FirstName"),
- new BasicNameValuePair("password", "FirstName")
- )));
+ new BasicNameValuePair("password", "FirstName"))));
RequestBuilder grantRequest = post("/users/" + testLogin)
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
@@ -321,8 +316,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
- new BasicNameValuePair("name", "FirstName")
- )));
+ new BasicNameValuePair("name", "FirstName"))));
RequestBuilder grantRequest = post("/users/" + testLogin)
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java
index ba88a60563..2b70d963ed 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTestWithoutTransaction.java
@@ -1,10 +1,9 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.*;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-import java.util.*;
+import java.util.Arrays;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.message.BasicNameValuePair;
@@ -20,31 +19,18 @@ import org.springframework.mock.web.MockHttpSession;
import org.springframework.test.annotation.Rollback;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
-import org.springframework.transaction.annotation.Transactional;
-import com.google.gson.*;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.security.Privilege;
-import lcsb.mapviewer.model.security.PrivilegeType;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.IUserService;
@RunWith(SpringJUnit4ClassRunner.class)
@Rollback
public class UserControllerIntegrationTestWithoutTransaction extends ControllerIntegrationTest {
- Logger logger = LogManager.getLogger();
-
private static final String TEST_USER_PASSWORD = "test_pass";
private static final String TEST_USER_LOGIN = "test_user";
-
private static final String ADMIN_PASSWORD = "admin";
private static final String ADMIN_LOGIN = "admin";
-
+ Logger logger = LogManager.getLogger();
@Autowired
private IUserService userService;
--
GitLab