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Commit 54cf87c4 authored by Piotr Gawron's avatar Piotr Gawron
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parsing of colors in boolean gate reaction added

parent 7a8ac224
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1 merge request!897Resolve "boolean reaction colouring not working"
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converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+ 33
− 0
View file @ 54cf87c4
...@@ -409,6 +409,9 @@ public class ReactionFromXml { ...@@ -409,6 +409,9 @@ public class ReactionFromXml {
} }
applyStylingToLine(line, result.getLine()); applyStylingToLine(line, result.getLine());
if (booleanLogicGateType!=null) {
assignColorFromGateMembers(result, gateMembers);
}
if (reactantsLinkNode != null) { if (reactantsLinkNode != null) {
parseReactantLinks(result, reactantsLinkNode, model); parseReactantLinks(result, reactantsLinkNode, model);
} }
...@@ -927,6 +930,36 @@ public class ReactionFromXml { ...@@ -927,6 +930,36 @@ public class ReactionFromXml {
} }
} }
private void assignColorFromGateMembers(Reaction result, Node gateMembers) {
int elementIndex = 0;
for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
Node child = gateMembers.getChildNodes().item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
Node lineNode = XmlParser.getNode("celldesigner:line", child);
if (lineNode != null) {
LineProperties line = getLineProperties(lineNode);
PolylineData polyline = null;
if (elementIndex == 0) {
if (result.getOperators().size() > 0) {
polyline = result.getOperators().get(result.getOperators().size() - 1).getLine();
}
} else {
if (result.getReactants().size() >= elementIndex) {
polyline = result.getReactants().get(elementIndex - 1).getLine();
}
}
if (polyline != null) {
polyline.setColor(line.getColor());
polyline.setWidth(line.getWidth());
}
}
elementIndex++;
}
}
}
}
/** /**
* Creates lines for reaction that belongs to * Creates lines for reaction that belongs to
* {@link TwoProductReactionInterface}. * {@link TwoProductReactionInterface}.
......
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+ 15
− 0
View file @ 54cf87c4
...@@ -759,4 +759,19 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions { ...@@ -759,4 +759,19 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
assertEquals(0, new ModelComparator().compare(model, model2)); assertEquals(0, new ModelComparator().compare(model, model2));
} }
@Test
public void testParseBooleanReactionWithColors() throws Exception {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = parser.createModel(new ConverterParams().filename("testFiles/reactions/boolean-colors.xml"));
Reaction r1 = model.getReactionByReactionId("re1");
Set<Color> colors = new HashSet<>();
for (AbstractNode node : r1.getNodes()) {
colors.add(node.getLine().getColor());
}
assertEquals("Three different colors were used to draw the reaction", 3, colors.size());
assertFalse("Black wasn't used in reaction coloring", colors.contains(Color.BLACK));
}
} }
converter-CellDesigner/testFiles/reactions/boolean-colors.xml 0 → 100644
+ 224
− 0
View file @ 54cf87c4
<?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="86.0" y="110.0" 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="91.0" y="220.0" 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="371.0" y="157.0" 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: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>BOOLEAN_LOGIC_GATE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s2" alias="sa2"/>
<celldesigner:baseReactant species="s1" alias="sa1"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s3" alias="sa3"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct"/>
<celldesigner:editPoints>264.66666666666663,177.0</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ffff00ff"/>
<celldesigner:listOfGateMember>
<celldesigner:GateMember type="BOOLEAN_LOGIC_GATE_AND" aliases="sa2,sa1" modificationType="REDUCED_TRIGGER" targetLineIndex="-1,-1" editPoints="264.66666666666663,177.0">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ffff00ff"/>
</celldesigner:GateMember>
<celldesigner:GateMember type="REDUCED_TRIGGER" aliases="sa2">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff00cc33"/>
</celldesigner:GateMember>
<celldesigner:GateMember type="REDUCED_TRIGGER" aliases="sa1" targetLineIndex="-1,0">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ffff9999"/>
</celldesigner:GateMember>
</celldesigner:listOfGateMember>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00003" species="s3">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa3</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
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