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Commit 0a57f6da authored by Piotr Gawron's avatar Piotr Gawron
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export of center line improved

parent c5e6a5f5
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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!581Resolve "export to sbml layout creates partial lines for operators"
Pipeline #8294 passed
Stage: test
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    converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
    + 2
    − 8
    View file @ 0a57f6da
    ......@@ -191,8 +191,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
    boolean firstReactant = true;
    reactionGlyph.setCurve(new Curve());
    Point2D reactantEndPoint = null;
    for (Reactant reactant : reaction.getReactants()) {
    SpeciesReferenceGlyph reactantGlyph = createNodeGlyph(reactionGlyph, reactant);
    if (firstReactant) {
    ......@@ -200,14 +198,9 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
    for (NodeOperator operator : reaction.getOperators()) {
    if (operator.isReactantOperator()) {
    addOperatorLineToGlyph(reactionGlyph, operator, false);
    if (reactantEndPoint == null) {
    reactantEndPoint = operator.getLine().getEndPoint();
    }
    break;
    }
    }
    if (reactantEndPoint == null) {
    reactantEndPoint = reactant.getLine().getEndPoint();
    }
    } else {
    reactantGlyph.setRole(SpeciesReferenceRole.SIDESUBSTRATE);
    }
    ......@@ -221,6 +214,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
    for (NodeOperator operator : reaction.getOperators()) {
    if (operator.isProductOperator()) {
    addOperatorLineToGlyph(reactionGlyph, operator, false);
    break;
    }
    }
    } else {
    ......
    converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
    + 31
    − 4
    View file @ 0a57f6da
    ......@@ -90,7 +90,6 @@ public class SbmlExporterTest {
    private Model getModelAfterSerializing(Model originalModel) throws Exception {
    String xml = exporter.toXml(originalModel);
    logger.debug(xml);
    ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
    Model result = parser.createModel(new ConverterParams().inputStream(stream));
    // showImage(originalModel);
    ......@@ -635,12 +634,40 @@ public class SbmlExporterTest {
    assertEquals("Notes weren't exported/imported properly", model.getNotes(), deserializedModel.getNotes());
    }
    @Test
    public void testExportImportOfInputOperator() throws Exception {
    Model originalModel = new CellDesignerXmlParser().createModel(new ConverterParams().filename("testFiles/cell_designer_problems/heterodimer_association.xml"));
    Model originalModel = new CellDesignerXmlParser()
    .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/heterodimer_association.xml"));
    Model model = getModelAfterSerializing(originalModel);
    List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
    List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
    ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
    assertEquals(0, comparator.compare(lines1, lines2));
    }
    @Test
    public void testExportImportOfAdvancedInputOperator() throws Exception {
    Model originalModel = new CellDesignerXmlParser().createModel(new ConverterParams()
    .filename("testFiles/cell_designer_problems/heterodimer_association_with_additional_reactant.xml"));
    Model model = getModelAfterSerializing(originalModel);
    Reaction r1 = originalModel.getReactions().iterator().next();
    Reaction r2 = model.getReactions().iterator().next();
    Line2D line1 = r1.getCenterLine();
    Line2D line2 = r2.getCenterLine();
    assertEquals(0, new LineComparator().compare(line1, line2));
    }
    @Test
    public void testExportImportOfOutputOperator() throws Exception {
    Model originalModel = new CellDesignerXmlParser()
    .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/dissociation.xml"));
    Model model = getModelAfterSerializing(originalModel);
    List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
    List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
    List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
    ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
    ......
    converter-sbml/testFiles/cell_designer_problems/dissociation.xml 0 → 100644
    + 204
    − 0
    View file @ 0a57f6da
    <?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:listOfComplexSpeciesAliases/>
    <celldesigner:listOfSpeciesAliases>
    <celldesigner:speciesAlias id="sa1" species="s1">
    <celldesigner:activity>inactive</celldesigner:activity>
    <celldesigner:bounds x="271.0" y="95.0" w="80.0" h="40.0"/>
    <celldesigner:font size="12"/>
    <celldesigner:view state="usual"/>
    <celldesigner:usualView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="80.0" height="40.0"/>
    <celldesigner:singleLine width="1.0"/>
    <celldesigner:paint color="ffccffcc" scheme="Color"/>
    </celldesigner:usualView>
    <celldesigner:briefView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="80.0" height="60.0"/>
    <celldesigner:singleLine width="0.0"/>
    <celldesigner:paint color="3fff0000" scheme="Color"/>
    </celldesigner:briefView>
    <celldesigner:info state="empty" angle="-1.5707963267948966"/>
    </celldesigner:speciesAlias>
    <celldesigner:speciesAlias id="sa2" species="s2">
    <celldesigner:activity>inactive</celldesigner:activity>
    <celldesigner:bounds x="269.0" y="234.0" w="80.0" h="40.0"/>
    <celldesigner:font size="12"/>
    <celldesigner:view state="usual"/>
    <celldesigner:usualView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="80.0" height="40.0"/>
    <celldesigner:singleLine width="1.0"/>
    <celldesigner:paint color="ffccffcc" scheme="Color"/>
    </celldesigner:usualView>
    <celldesigner:briefView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="80.0" height="60.0"/>
    <celldesigner:singleLine width="0.0"/>
    <celldesigner:paint color="3fff0000" scheme="Color"/>
    </celldesigner:briefView>
    <celldesigner:info state="empty" angle="-1.5707963267948966"/>
    </celldesigner:speciesAlias>
    <celldesigner:speciesAlias id="sa3" species="s3">
    <celldesigner:activity>inactive</celldesigner:activity>
    <celldesigner:bounds x="462.0" y="165.0" w="80.0" h="40.0"/>
    <celldesigner:font size="12"/>
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    <celldesigner:singleLine width="1.0"/>
    <celldesigner:paint color="ffccffcc" scheme="Color"/>
    </celldesigner:usualView>
    <celldesigner:briefView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="80.0" height="60.0"/>
    <celldesigner:singleLine width="0.0"/>
    <celldesigner:paint color="3fff0000" scheme="Color"/>
    </celldesigner:briefView>
    <celldesigner:info state="empty" angle="-1.5707963267948966"/>
    </celldesigner:speciesAlias>
    </celldesigner:listOfSpeciesAliases>
    <celldesigner:listOfGroups/>
    <celldesigner:listOfProteins>
    <celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
    <celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
    <celldesigner:protein id="pr3" name="s3" type="GENERIC"/>
    </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="CDMT00004" kind="mole"/>
    </listOfUnits>
    </unitDefinition>
    <unitDefinition metaid="volume" id="volume" name="volume">
    <listOfUnits>
    <unit metaid="CDMT00005" kind="litre"/>
    </listOfUnits>
    </unitDefinition>
    <unitDefinition metaid="area" id="area" name="area">
    <listOfUnits>
    <unit metaid="CDMT00006" kind="metre" exponent="2"/>
    </listOfUnits>
    </unitDefinition>
    <unitDefinition metaid="length" id="length" name="length">
    <listOfUnits>
    <unit metaid="CDMT00007" kind="metre"/>
    </listOfUnits>
    </unitDefinition>
    <unitDefinition metaid="time" id="time" name="time">
    <listOfUnits>
    <unit metaid="CDMT00008" kind="second"/>
    </listOfUnits>
    </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
    <compartment metaid="default" id="default" size="1" units="volume"/>
    </listOfCompartments>
    <listOfSpecies>
    <species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
    <annotation>
    <celldesigner:extension>
    <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
    <celldesigner:speciesIdentity>
    <celldesigner:class>PROTEIN</celldesigner:class>
    <celldesigner:proteinReference>pr1</celldesigner:proteinReference>
    </celldesigner:speciesIdentity>
    </celldesigner:extension>
    </annotation>
    </species>
    <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
    <annotation>
    <celldesigner:extension>
    <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
    <celldesigner:speciesIdentity>
    <celldesigner:class>PROTEIN</celldesigner:class>
    <celldesigner:proteinReference>pr2</celldesigner:proteinReference>
    </celldesigner:speciesIdentity>
    </celldesigner:extension>
    </annotation>
    </species>
    <species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
    <annotation>
    <celldesigner:extension>
    <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
    <celldesigner:speciesIdentity>
    <celldesigner:class>PROTEIN</celldesigner:class>
    <celldesigner:proteinReference>pr3</celldesigner:proteinReference>
    </celldesigner:speciesIdentity>
    </celldesigner:extension>
    </annotation>
    </species>
    </listOfSpecies>
    <listOfReactions>
    <reaction metaid="re1" id="re1" reversible="false">
    <annotation>
    <celldesigner:extension>
    <celldesigner:reactionType>DISSOCIATION</celldesigner:reactionType>
    <celldesigner:baseReactants>
    <celldesigner:baseReactant species="s3" alias="sa3">
    <celldesigner:linkAnchor position="INACTIVE"/>
    </celldesigner:baseReactant>
    </celldesigner:baseReactants>
    <celldesigner:baseProducts>
    <celldesigner:baseProduct species="s2" alias="sa2">
    <celldesigner:linkAnchor position="INACTIVE"/>
    </celldesigner:baseProduct>
    <celldesigner:baseProduct species="s1" alias="sa1">
    <celldesigner:linkAnchor position="INACTIVE"/>
    </celldesigner:baseProduct>
    </celldesigner:baseProducts>
    <celldesigner:connectScheme connectPolicy="direct">
    <celldesigner:listOfLineDirection>
    <celldesigner:lineDirection arm="0" index="0" value="unknown"/>
    <celldesigner:lineDirection arm="1" index="0" value="unknown"/>
    <celldesigner:lineDirection arm="2" index="0" value="unknown"/>
    </celldesigner:listOfLineDirection>
    </celldesigner:connectScheme>
    <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.3278504252688371,0.3231668477649965</celldesigner:editPoints>
    <celldesigner:line width="1.0" color="ff000000"/>
    </celldesigner:extension>
    </annotation>
    <listOfReactants>
    <speciesReference metaid="CDMT00001" species="s3">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa3</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    </listOfReactants>
    <listOfProducts>
    <speciesReference metaid="CDMT00002" species="s2">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa2</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    <speciesReference metaid="CDMT00003" species="s1">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa1</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    </listOfProducts>
    </reaction>
    </listOfReactions>
    </model>
    </sbml>
    converter-sbml/testFiles/cell_designer_problems/heterodimer_association_with_additional_reactant.xml 0 → 100644
    + 253
    − 0
    View file @ 0a57f6da
    <?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:listOfComplexSpeciesAliases/>
    <celldesigner:listOfSpeciesAliases>
    <celldesigner:speciesAlias id="sa1" species="s1">
    <celldesigner:activity>inactive</celldesigner:activity>
    <celldesigner:bounds x="161.0" y="74.0" w="80.0" h="40.0"/>
    <celldesigner:font size="12"/>
    <celldesigner:view state="usual"/>
    <celldesigner:usualView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="80.0" height="40.0"/>
    <celldesigner:singleLine width="1.0"/>
    <celldesigner:paint color="ffccffcc" scheme="Color"/>
    </celldesigner:usualView>
    <celldesigner:briefView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
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    <celldesigner:paint color="3fff0000" scheme="Color"/>
    </celldesigner:briefView>
    <celldesigner:info state="empty" angle="-1.5707963267948966"/>
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    </annotation>
    </species>
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    </celldesigner:listOfLineDirection>
    </celldesigner:connectScheme>
    <celldesigner:line width="1.0" color="ff000000" type="Straight"/>
    </celldesigner:reactantLink>
    </celldesigner:listOfReactantLinks>
    <celldesigner:connectScheme connectPolicy="direct">
    <celldesigner:listOfLineDirection>
    <celldesigner:lineDirection arm="0" index="0" value="unknown"/>
    <celldesigner:lineDirection arm="1" index="0" value="unknown"/>
    <celldesigner:lineDirection arm="2" index="0" value="unknown"/>
    </celldesigner:listOfLineDirection>
    </celldesigner:connectScheme>
    <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.3416972140762462,0.3398093841642229</celldesigner:editPoints>
    <celldesigner:line width="1.0" color="ff000000"/>
    </celldesigner:extension>
    </annotation>
    <listOfReactants>
    <speciesReference metaid="CDMT00009" species="s1">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa1</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    <speciesReference metaid="CDMT00010" species="s2">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa2</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    <speciesReference metaid="CDMT00011" species="s4">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa4</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    </listOfReactants>
    <listOfProducts>
    <speciesReference metaid="CDMT00012" species="s3">
    <annotation>
    <celldesigner:extension>
    <celldesigner:alias>sa3</celldesigner:alias>
    </celldesigner:extension>
    </annotation>
    </speciesReference>
    </listOfProducts>
    </reaction>
    </listOfReactions>
    </model>
    </sbml>
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