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Commit c017f87a authored by Piotr Gawron's avatar Piotr Gawron
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export of reaction with two modifiers connected with operator was skipping some points

parent 9d49eb0b
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CHANGELOG
View file @ c017f87a
......@@ -2,8 +2,11 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
* Feature: log4j is replaced with log4j2 logging mechanism (#291)
* Feature: database installed via debian package is done via dbconfig-commons
(#469)
* Feature: Replaced connection pool manager C3P0 with better maintained Hikari (#564)
* Feature: Replaced connection pool manager C3P0 with better maintained
Hikari (#564)
* Feature removal: BioCompendium annotator removed (#32)
* Bug fix: export to CellDesigner of reaction with two modifiers connected
with boolean operator resulted was skipping some layout information
-- Sascha Herzinger <sascha.herzinger@uni.lu> Wed, 22 May 2019 10:30:00 +0200
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
View file @ c017f87a
......@@ -292,7 +292,7 @@ public class ReactionToXml {
line = line.reverse();
List<Point2D> points = lineTransformation.getPointsFromLine(line);
sb.append(" editPoints=\"");
for (int i = 1; i < points.size() - 1; i++) {
for (int i = 0; i < points.size(); i++) {
sb.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
}
sb.append(line.getEndPoint().getX() + "," + line.getEndPoint().getY());
......
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
View file @ c017f87a
......@@ -1843,6 +1843,25 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
}
}
@Test
public void testModifierWithOperator() throws Exception {
try {
Model model = getModelForFile("testFiles/reactions/modifier_with_operator.xml");
Reaction reaction = model.getReactionByReactionId("re1");
assertEquals(3, reaction.getOperators().iterator().next().getLine().getPoints().size());
assertEquals(3, reaction.getModifiers().get(0).getLine().getPoints().size());
assertEquals(3, reaction.getModifiers().get(1).getLine().getPoints().size());
Model model2 = super.serializeModel(model);
reaction = model2.getReactionByReactionId("re1");
assertEquals(3, reaction.getOperators().iterator().next().getLine().getPoints().size());
assertEquals(3, reaction.getModifiers().get(0).getLine().getPoints().size());
assertEquals(3, reaction.getModifiers().get(1).getLine().getPoints().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProblematicHeterodimerAssociation() throws Exception {
Model model;
......
converter-CellDesigner/testFiles/reactions/modifier_with_operator.xml 0 → 100644
View file @ c017f87a
<?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="74.0" y="204.0" 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="306.0" y="207.0" 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="59.0" y="49.0" 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="sa4" species="s4">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="254.0" y="75.0" 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:protein id="pr4" name="s4" 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="CDMT00005" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00006" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00007" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00008" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00009" 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:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re1"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re1"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="BOOLEAN_LOGIC_GATE_AND" modifiers="s3,s4" aliases="sa3,sa4" modificationType="CATALYSIS" targetLineIndex="-1,2" editPoints="0.3679805529917881,0.3895642712552996 206.66666666666666,126.0">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="CATALYSIS" modifiers="s3" aliases="sa3" editPoints="0.5027027027027031,-0.31493598862019895">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s3" alias="sa3">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="CATALYSIS" modifiers="s4" aliases="sa4" editPoints="0.6153467972520144,0.6324634831097264">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s4" alias="sa4">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00001" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</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>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00003" species="s3">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa3</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
<modifierSpeciesReference metaid="CDMT00004" species="s4">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa4</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
</listOfReactions>
</model>
</sbml>
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