when there are multiple input operators in reaction one operator ends where the next start

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java

@@ -749,11 +749,9 @@ public class ReactionFromXml {
       inputOperator.setLine(ld);
       applyStylingToLine(new LineProperties(nodes.iterator().next().getLine()), ld);
       inputOperator.addInputs(nodes);
-      for (Reactant reactant : result.getReactants()) {
-        if (!toExclude.contains(reactant)) {
-          reactant.getLine().getEndPoint().setLocation(reactantAndOperatorBeginPoint.getX(),
-              reactantAndOperatorBeginPoint.getY());
-        }
+      for (AbstractNode node : nodes) {
+        node.getLine().getEndPoint().setLocation(reactantAndOperatorBeginPoint.getX(),
+            reactantAndOperatorBeginPoint.getY());
       }
       if (lineType != null) {
         inputOperator.getLine().setType(lineType);
@@ -935,26 +933,28 @@ public class ReactionFromXml {
 
       operator.addInputs(andOperator.getInputs());
 
-      //operator line
+      // operator line
       PolylineData line = new PolylineData();
       line.addPoint(pointTransformation.copyPoint(product.getLine().getBeginPoint()));
 
-      double secondX = (product.getLine().getPoints().get(1).getX() + product.getLine().getPoints().get(0).getX())*0.4;
-      double secondY = (product.getLine().getPoints().get(1).getY() + product.getLine().getPoints().get(0).getY())*0.4;
-      double thirdX = (product.getLine().getPoints().get(1).getX() + product.getLine().getPoints().get(0).getX())*0.6;
-      double thirdY = (product.getLine().getPoints().get(1).getY() + product.getLine().getPoints().get(0).getY())*0.6;
+      double secondX = (product.getLine().getPoints().get(1).getX() + product.getLine().getPoints().get(0).getX())
+          * 0.4;
+      double secondY = (product.getLine().getPoints().get(1).getY() + product.getLine().getPoints().get(0).getY())
+          * 0.4;
+      double thirdX = (product.getLine().getPoints().get(1).getX() + product.getLine().getPoints().get(0).getX()) * 0.6;
+      double thirdY = (product.getLine().getPoints().get(1).getY() + product.getLine().getPoints().get(0).getY()) * 0.6;
       Point2D secondPoint = new Point2D.Double(secondX, secondY);
       Point2D thirdPoint = new Point2D.Double(thirdX, thirdY);
       line.addPoint(pointTransformation.copyPoint(secondPoint));
       operator.setLine(line);
-      
-      //center line
+
+      // center line
       PolylineData centerLine = new PolylineData();
       centerLine.addPoint(pointTransformation.copyPoint(secondPoint));
       centerLine.addPoint(pointTransformation.copyPoint(thirdPoint));
       result.setLine(centerLine);
-      
-      //product line is not trimmed
+
+      // product line is not trimmed
       product.getLine().getPoints().get(0).setLocation(thirdPoint);
 
       result.addNode(operator);

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java

@@ -19,6 +19,7 @@ import org.junit.Before;
 import org.junit.Test;
 import org.w3c.dom.Node;
 
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
@@ -884,47 +885,41 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
       NodeOperator operator2 = reaction.getOperators().get(1);
       NodeOperator operator3 = reaction.getOperators().get(2);
 
-      // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
-      // false).saveToPNG("tmp.png");
-      // Desktop.getDesktop().open(new File("tmp.png"));
+      Product product1 = reaction.getProducts().get(0);
+      Product product2 = reaction.getProducts().get(1);
 
-      assertEquals(operator1.getLine().getPoints().get(0).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+      assertEquals(0, operator1.getLine().getPoints().get(0).distance(new Point2D.Double(287.0, 242.00000000000009)),
           EPSILON);
-      assertEquals(
+      assertEquals(0,
           operator1.getLine().getPoints().get(1).distance(new Point2D.Double(287.97349260719136, 204.40292958328325)),
-          0, EPSILON);
-      assertEquals(
-          operator1.getLine().getPoints().get(2).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
           EPSILON);
+      assertEquals(0, operator1.getLine().getEndPoint().distance(operator2.getLine().getBeginPoint()), EPSILON);
 
-      assertEquals(
-          operator2.getLine().getPoints().get(0).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
+      assertEquals(0,
+          operator2.getLine().getPoints().get(0).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)),
           EPSILON);
-      assertEquals(
-          operator2.getLine().getPoints().get(1).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
+      assertEquals(0,
+          operator2.getLine().getPoints().get(1).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)),
           EPSILON);
 
-      assertEquals(
+      assertEquals(0,
           operator3.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)),
-          0, EPSILON);
-      assertEquals(
-          operator3.getLine().getPoints().get(1).distance(new Point2D.Double(380.9866634960982, 203.80442011470782)), 0,
+          EPSILON);
+      assertEquals(0,
+          operator3.getLine().getPoints().get(1).distance(new Point2D.Double(380.9866634960982, 203.80442011470782)),
           EPSILON);
 
-      Product product1 = reaction.getProducts().get(0);
-      Product product2 = reaction.getProducts().get(1);
-
-      assertEquals(
-          product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+      assertEquals(0,
+          product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)),
           EPSILON);
-      assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
+      assertEquals(0, product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)),
           EPSILON);
 
-      assertEquals(
-          product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+      assertEquals(0,
+          product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)),
           EPSILON);
-      assertEquals(
-          product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
+      assertEquals(0,
+          product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)),
           EPSILON);
 
     } catch (Exception e) {
@@ -1779,6 +1774,25 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testHeterodimerWithAdditionalReactant() throws Exception {
+    Model model;
+    try {
+      model = getModelForFile("testFiles/reactions/heterodimer_association_with_additional_reactant.xml");
+      assertEquals(1, model.getReactions().size());
+      Reaction reaction = model.getReactions().iterator().next();
+
+      NodeOperator o1 = reaction.getOperators().get(0);
+      NodeOperator o2 = reaction.getOperators().get(1);
+
+      assertEquals(0, o1.getLine().getEndPoint().distance(o2.getLine().getBeginPoint()), Configuration.EPSILON);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testProblematicDrawing() throws Exception {
     Model model;

converter-CellDesigner/testFiles/reactions/heterodimer_association_with_additional_reactant.xml

+<?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"/>
+<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="181.0" y="274.0" 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="444.0" y="176.0" 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="271.0" y="13.0" 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="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>
+<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:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re2" id="re2" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s4" alias="sa4" targetLineIndex="2,0">
+<celldesigner:linkAnchor position="INACTIVE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</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>