diff --git a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
index 077b9a4064b56d26b2a368dbd51dfe74bc31acaa..9df1420f0ec98316d275ecea40f8b14f17fda233 100644
--- a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
+++ b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
@@ -4,6 +4,7 @@ import java.awt.Desktop;
import java.io.File;
import java.io.IOException;
+import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
@@ -29,22 +30,22 @@ public class LegendGenerator {
*
*/
private enum LegendObject {
- /**
- * First legend element.
- */
- LEGEND_A("testFiles/legend/legend_5_2.xml", "legend_a.png", 50, 0, 600, 480),
- /**
- * Second legend element.
- */
- LEGEND_B("testFiles/legend/legend_4_3.xml", "legend_b.png", 920, 0, 600, 480),
- /**
- * Third legend element.
- */
- LEGEND_C("testFiles/legend/legend_4_4.xml", "legend_c.png", 500, 0, 600, 480),
+// /**
+// * First legend element.
+// */
+// LEGEND_A("testFiles/legend/legend_5_2.xml", "legend_a.png", 50, 0, 600, 480),
+// /**
+// * Second legend element.
+// */
+// LEGEND_B("testFiles/legend/legend_4_3.xml", "legend_b.png", 920, 0, 600, 480),
+// /**
+// * Third legend element.
+// */
+// LEGEND_C("testFiles/legend/legend_4_4.xml", "legend_c.png", 500, 0, 600, 480),
/**
* Fourth legend element.
*/
- LEGEND_D("testFiles/legend/legend_4_5.xml", "legend_d.png", 500, 0, 600, 480);
+ LEGEND_D("C:/Users/piotr.gawron/Desktop/test.xml", "legend_d.png", 0, 0, 1280, 480);
/**
* File with the legend data in CellDEsigner format.
@@ -157,8 +158,9 @@ public class LegendGenerator {
// and save it to leged.png
String fileName = lo.outputFile;
+ Model copy = new CopyCommand(model).execute();
PngImageGenerator generator = new PngImageGenerator(new Params()
- .scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(model));
+ .scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(2).semanticZoom(true));
generator.saveToFile(fileName);
Desktop.getDesktop().open(new File(fileName));
}
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 a1ab11fc4ad10cb3e8b74f6fb9e6b0196013f9b4..ccec089ae552859c1d2c1d97aabab79ff12d9676 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
@@ -1,6 +1,7 @@
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;
@@ -21,6 +22,8 @@ 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.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -100,25 +103,90 @@ public class RestAnnotationParser extends XmlParser {
* @return note string with structural information about element
*/
public String createAnnotationString(Element element) {
- String symbol = element.getSymbol();
- if (symbol == null) {
- symbol = "";
- }
- String name = element.getFullName();
- if (name == null) {
- name = "";
- }
+ return createAnnotationString(element, false);
+ }
+
+ /**
+ * Creates note string with structural information about element.
+ *
+ * @param element
+ * element for which notes are created
+ * @param forceFullInfo
+ * when true annotation string will contain information about empty
+ * fields
+ * @return note string with structural information about element
+ */
+ public String createAnnotationString(Element element, boolean forceFullInfo) {
+ Set<MiriamData> data = element.getMiriamData();
StringBuilder sb = new StringBuilder();
- sb.append(NoteField.SYMBOL.getCommonName() + ": " + symbol + "\n");
- sb.append(NoteField.NAME.getCommonName() + ": " + name + "\n");
- // descrfiption will be in the string anyways so we don't need to repeat it
- sb.append(NoteField.DESCRIPTION.getCommonName() + ": \n");
- sb.append(NoteField.PREVIOUS_SYMBOLS.getCommonName() + ": " + StringUtils.join(element.getFormerSymbols(), ", ") + "\n");
- sb.append(NoteField.SYNONYMS.getCommonName() + ": " + StringUtils.join(element.getSynonyms(), ", ") + "\n");
+ sb.append(createEntry(NoteField.SYMBOL, element.getSymbol(), forceFullInfo));
+ sb.append(createEntry(NoteField.NAME, element.getFullName(), forceFullInfo));
+ sb.append(createEntry(NoteField.PREVIOUS_SYMBOLS, element.getFormerSymbols(), forceFullInfo));
+ sb.append(createEntry(NoteField.SYNONYMS, element.getSynonyms(), forceFullInfo));
+ sb.append(createEntry(NoteField.HGNC, filterMiriam(data, MiriamType.HGNC), forceFullInfo));
+ sb.append(createEntry(NoteField.ENTREZ, filterMiriam(data, MiriamType.ENTREZ), forceFullInfo));
+ sb.append(createEntry(NoteField.REFSEQ, filterMiriam(data, MiriamType.REFSEQ), forceFullInfo));
+ sb.append(createEntry(NoteField.REACTOME, filterMiriam(data, MiriamType.REACTOME), forceFullInfo));
+ sb.append(createEntry(NoteField.PUBMED, filterMiriam(data, MiriamType.PUBMED), forceFullInfo));
+ sb.append(createEntry(NoteField.KEGG_GENES, filterMiriam(data, MiriamType.KEGG_GENES), forceFullInfo));
+ sb.append(createEntry(NoteField.PANTHER, filterMiriam(data, MiriamType.PANTHER), forceFullInfo));
+ sb.append(createEntry(NoteField.DESCRIPTION, null, forceFullInfo));
+ sb.append(createEntry(NoteField.ABBREVIATION, element.getAbbreviation(), forceFullInfo));
+ sb.append(createEntry(NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY, element.getSemanticZoomLevelVisibility(), forceFullInfo));
+ sb.append(createEntry(NoteField.CHARGED_FORMULA, element.getFormula(), forceFullInfo));
+ if (element instanceof Species) {
+ sb.append(createEntry(NoteField.CHARGE, ((Species) element).getCharge(), forceFullInfo));
+ }
+
sb.append("\n");
return sb.toString();
}
+ private List<MiriamData> filterMiriam(Collection<MiriamData> miriamDataSet, MiriamType type) {
+ List<MiriamData> result = new ArrayList<>();
+ for (MiriamData miriamData : miriamDataSet) {
+ if (miriamData.getDataType().equals(type)) {
+ result.add(miriamData);
+ }
+ }
+ return result;
+ }
+
+ private String createEntry(NoteField type, Object value, boolean forceFullInfo) {
+ if (value == null) {
+ if (forceFullInfo) {
+ return type.getCommonName() + ": \n";
+ } else {
+ return "";
+ }
+ } else if (value instanceof String) {
+ return type.getCommonName() + ": " + value + "\n";
+ } else if (value instanceof Integer) {
+ return type.getCommonName() + ": " + value + "\n";
+ } else if (value instanceof Collection) {
+ Collection<?> collection = (Collection) value;
+ if (collection.size() > 0 || forceFullInfo) {
+ String result = "";
+ for (Object object : collection) {
+ if (!result.equals("")) {
+ result = result + ", ";
+ }
+ if (object instanceof MiriamData) {
+ result += ((MiriamData) object).getResource();
+ } else {
+ result += object;
+ }
+
+ }
+ return type.getCommonName() + ": " + result + "\n";
+ } else {
+ return "";
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + value.getClass());
+ }
+ }
+
/**
* Returns value for the type of the structurized annotation. Structurized
* annotation is in format:
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 5c51659632457f51772e78fbcb1d2b7546a0222f..80bbf90fe849da95df3d1532716d03bc06b35dd7 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
@@ -7,6 +7,7 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
@@ -26,12 +27,12 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CompartmentXmlParser.class.getName());
+ private static Logger logger = Logger.getLogger(CompartmentXmlParser.class.getName());
/**
* Parser used to retrieve Miriam data for the element.
*/
- private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+ private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
/**
* Collection of {@link CellDesignerElement cell designer elements} parsed
@@ -39,6 +40,11 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
*/
private CellDesignerElementCollection elements;
+ /**
+ * Xml parser used for processing notes into structurized data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
/**
* Default constructor.
*
@@ -63,6 +69,8 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("annotation")) {
parseAnnotationNode(compartment, node);
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ compartment.setNotes(rap.getNotes(node));
} else {
throw new InvalidXmlSchemaException("Unknown element of Compartment: " + node.getNodeName());
}
@@ -132,8 +140,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
sb.append("size=\"1\" ");
sb.append("units=\"volume\" ");
String parentName = "default";
-
-
+
if (compartment.getCompartment() != null && !(compartment.getCompartment() instanceof PathwayCompartment)) {
parentName = elements.getElementId(compartment.getCompartment());
}
@@ -149,6 +156,15 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
sb.append("</celldesigner:extension>\n");
sb.append(xmlAnnotationParser.dataSetToXmlString(compartment.getMiriamData()));
sb.append("</annotation>\n");
+ sb.append("<notes>");
+ sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ RestAnnotationParser rap = new RestAnnotationParser();
+ sb.append(rap.createAnnotationString(compartment));
+ if (compartment.getNotes() != null) {
+ sb.append(compartment.getNotes());
+ }
+ sb.append("</body></html>");
+ sb.append("</notes>\n");
sb.append("</compartment>\n");
return sb.toString();
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index d61b82e9ce953779a6573159251e049ad34b7598..445722f2721ab372ecf8e31f9188c3822fb3551b 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
@@ -975,4 +975,20 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testCompartmentWithNotes() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/compartment_with_notes.xml"));
+ model.setName(null);
+ assertNotNull(model);
+ String str = parser.toXml(model);
+ Model model2 = parser.createModel(new ConverterParams().inputStream(new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8))));
+ assertEquals(0, new ModelComparator().compare(model, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index f8ab6d2d441325298cd4f0bc6455476c01aca300..6cca1af6e56bd8d559e4375b6f6ca2a69282bba5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -22,6 +22,7 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -286,10 +287,19 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
GenericProtein element = new GenericProtein("id");
element.addFormerSymbol(former1);
element.addFormerSymbol(former2);
- String str = rap.createAnnotationString(element);
+ element.setCharge(1);
+ String str = rap.createAnnotationString(element, true);
+ logger.debug(str);
assertTrue(str.contains(former1));
assertTrue(str.contains(former2));
+ for (NoteField field : NoteField.values()) {
+ if (field.getClazz().isAssignableFrom(element.getClass()) || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
+ assertTrue("Export string doesn't contain info about: " + field.getCommonName(), str.indexOf(field.getCommonName()) >= 0);
+ }
+
+ }
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-CellDesigner/testFiles/compartment_with_notes.xml b/converter-CellDesigner/testFiles/compartment_with_notes.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9dfe7f29eeea19f24a81caa36715b6073863781e
--- /dev/null
+++ b/converter-CellDesigner/testFiles/compartment_with_notes.xml
@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="108.0" y="82.0" w="265.0" h="160.0"/>
+<celldesigner:namePoint x="233.0" y="205.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases/>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>notes
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+</model>
+</sbml>
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 16e997154b53d5419fbf41c379f9d409dd39ac33..4841de9b38bb51a02959f7c75562d910e30384a9 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
@@ -739,7 +739,7 @@ public abstract class AbstractImageGenerator {
// be
// visible.
- if (compartment.getVisibilityLevel() > level) {
+ if (compartment.getVisibilityLevel() > level && params.nested) {
return;
}
@@ -821,7 +821,7 @@ public abstract class AbstractImageGenerator {
// VisibilityLevel is big enough, then it is
// displayed.
- if (species.getVisibilityLevel() > level) {
+ if (species.getVisibilityLevel() > level && params.nested) {
return;
}
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 0f3fbea1f767125d5922bbed62ae53ee300e4999..18ddccbf22573d7029c07b0229f6f48059ca165c 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
@@ -173,11 +173,9 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
} else if (!isAnyReactantVisible(((Reaction) bioEntity).getReactants(), params)) {
result = false;
}
-
} else {
throw new InvalidArgumentException("Unknown class type: " + bioEntity.getClass());
}
-
return result;
}
return true;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index ef0849c07a451034cc2d772aec92e15753b47703..b9388ab2b7cda60cdf0849a52b72dc4dc8feb366 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -384,7 +384,7 @@ public class OverviewParser {
try {
oml.setxCoord(Double.valueOf(coord.split(",")[0]));
oml.setyCoord(Double.valueOf(coord.split(",")[1]));
- } catch (NumberFormatException e) {
+ } catch (NumberFormatException | ArrayIndexOutOfBoundsException e) {
throw new InvalidCoordinatesFile("Problem with parsing coordinates in file \"" + COORDINATES_FILENAME + "\". Problematic text: \"" + coord + "\"", e);
}
try {
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 30148865590f3bd8c3275ded92f250b0e09a7537..5ea871caf6bef7f802521ec6556f9b5c83da107a 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -176,6 +176,7 @@ public class CopyCommand extends NewModelCommand {
if (alias instanceof Compartment) {
Compartment copy = ((Compartment) alias).copy();
copy.getElements().clear();
+ copy.setCompartment(null);
result.addElement(copy);
}
@@ -184,21 +185,25 @@ public class CopyCommand extends NewModelCommand {
for (Element alias : model.getElements()) {
if (alias instanceof Species) {
Species copy = ((Species) alias).copy();
- Compartment ca = copy.getCompartment();
copy.setCompartment(null);
-
- // the trick is that in addAlias also some connections are added, so
- // lets clear info about parents
-
result.addElement(copy);
- if (ca != null) {
- ca = result.getElementByElementId(ca.getElementId());
- copy.setCompartment(ca);
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
}
+
} else if (alias instanceof Compartment) {
- // we already added compartment alias
- continue;
+
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ Compartment copy = result.getElementByElementId(alias.getElementId());
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
+ }
} else {
throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 6b2c37080b2fecc6408d3fe18389a3cd5cbb87f7..cc78f07b6e85b9845474a31b1d1373231e774cb7 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -1,8 +1,12 @@
package lcsb.mapviewer.commands;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
@@ -14,8 +18,11 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -23,9 +30,12 @@ import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class CopyCommandTest extends CommandTestFunctions {
@@ -311,4 +321,57 @@ public class CopyCommandTest extends CommandTestFunctions {
}
}
+ @Test
+ public void testCopyModelReaction() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Compartment c1 = new SquareCompartment("c1");
+ Compartment c2 = new SquareCompartment("c2");
+ c1.setSemanticZoomLevelVisibility("2");
+ c2.setSemanticZoomLevelVisibility("3");
+
+ model.addElement(c1);
+ model.addElement(c2);
+
+ GenericProtein s1 = new GenericProtein("s1");
+ s1.setCompartment(c1);
+ model.addElement(s1);
+
+ GenericProtein s2 = new GenericProtein("s2");
+ s2.setCompartment(c2);
+ model.addElement(s2);
+
+ StateTransitionReaction reaction = new StateTransitionReaction();
+ Reactant reactant = new Reactant(s1);
+ reactant.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10)));
+ reaction.addReactant(reactant);
+ Product product = new Product(s2);
+ product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
+ reaction.addProduct(product);
+ reaction.setSemanticZoomLevelVisibility("4");
+
+ model.addReaction(reaction);
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ Model model2 = new CopyCommand(model).execute();
+ Reaction reaction2 = model2.getReactions().iterator().next();
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
+ assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
+
+ assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
+ assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index 38a1265d1d95e5fab8495462665e6b87e592e897..1feda50e2c6575eb81fc83ab3f6554a4b0ba5adb 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
@@ -95,7 +95,6 @@ public class ReactionComparator implements Comparator<Reaction> {
return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
}
-
if (stringComparator.compare(arg0.getIdReaction(), arg1.getIdReaction()) != 0) {
logger.debug("IdReaction different: " + arg0.getIdReaction() + ", " + arg1.getIdReaction());
return stringComparator.compare(arg0.getIdReaction(), arg1.getIdReaction());
@@ -131,6 +130,11 @@ public class ReactionComparator implements Comparator<Reaction> {
logger.debug("GeneProteinReaction different: " + arg0.getGeneProteinReaction() + ", " + arg1.getGeneProteinReaction());
return stringComparator.compare(arg0.getGeneProteinReaction(), arg1.getGeneProteinReaction());
}
+ if (stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility()) != 0) {
+ logger.debug(
+ "SemanticZoomLevelVisibility different: \"" + arg0.getSemanticZoomLevelVisibility() + "\", \"" + arg1.getSemanticZoomLevelVisibility() + "\"");
+ return stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility());
+ }
IntegerComparator integerComparator = new IntegerComparator();
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 386c2995adde11c9d6870a8b9b243c87ee696007..8cfbc8cc39b3c7dd6745a6ba03ecc18fafd6e91a 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
@@ -301,6 +301,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
addMiriamData(original.getMiriamData());
this.abbreviation = original.getAbbreviation();
this.formula = original.getFormula();
+ setSemanticZoomLevelVisibility(original.getSemanticZoomLevelVisibility());
}
/**
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 5f57312dad2b67e5de11b5bd2a194c3bee34190a..4d6d35a87a27c1d514e467737f9eafa1d3ecd7ae 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
@@ -84,8 +84,9 @@ public class ElementComparator implements Comparator<Element> {
}
/**
- * This method compares only the fields that are defined in {@link Element} class in
- * inheritence tree. By the design it is called by subclass comparator.
+ * This method compares only the fields that are defined in {@link Element}
+ * class in inheritence tree. By the design it is called by subclass
+ * comparator.
*
* @param arg0
* first object to compare
@@ -188,6 +189,12 @@ public class ElementComparator implements Comparator<Element> {
return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
}
+ if (stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility()) != 0) {
+ logger.debug(
+ "SemanticZoomLevelVisibility different: \"" + arg0.getSemanticZoomLevelVisibility() + "\", \"" + arg1.getSemanticZoomLevelVisibility() + "\"");
+ return stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility());
+ }
+
StringSetComparator stringSetComparator = new StringSetComparator();
StringListComparator stringListComparator = new StringListComparator();
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 237aee82abc42b6d8ce6711067084fcf8006b1b2..62875191ca8a99293cb0a87b49e0f4069b891554 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
@@ -168,7 +168,6 @@ public abstract class Species extends Element {
homodimer = original.getHomodimer();
positionToCompartment = original.getPositionToCompartment();
hypothetical = original.getHypothetical();
- setSemanticZoomLevelVisibility(original.getSemanticZoomLevelVisibility());
// don't copy reaction nodes
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index 7ea08b523f44e85ed38eec4b8868694849b6e19e..a7d39db9e7bcbecef1e5d9226d0d35b3c53118c1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -37,9 +37,9 @@ import lcsb.mapviewer.model.map.species.Species;
public class ReactionTest extends ModelTestFunctions {
- Logger logger = Logger.getLogger(ReactantTest.class);
+ Logger logger = Logger.getLogger(ReactantTest.class);
- private Species species;
+ private Species species;
@Before
public void setUp() throws Exception {
@@ -171,11 +171,7 @@ public class ReactionTest extends ModelTestFunctions {
try {
Reaction reaction1 = new Reaction();
- try {
- assertNull(reaction1.getStringType());
- fail("Exception expected");
- } catch (NotImplementedException e) {
- }
+ assertNotNull(reaction1.getStringType());
assertNull(reaction1.getReactionRect());
int id = 61;