drug shape in CellDesigner is slightly different

CHANGELOG

@@ -3,6 +3,8 @@ minerva (15.1.4) stable; urgency=medium
     (#1476)
   * Bug fix: orthogonal reactions to phenotypes from CellDesigner were drawn
     incorrectly (#1454)
+  * Bug fix: orthogonal reactions to drugs from CellDesigner were drawn
+    incorrectly (#1454)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 30 Apr 2021 17:00:00 +0200
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java

 package lcsb.mapviewer.converter.model.celldesigner.geometry;
 
-import java.awt.*;
+import java.awt.Shape;
 import java.awt.geom.*;
 import java.util.ArrayList;
+import java.util.List;
 
 import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
 import lcsb.mapviewer.model.map.species.Element;
@@ -37,7 +38,7 @@ public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
     if (invalidAnchorPosition(alias, anchor)) {
       return alias.getCenter();
     }
-    ArrayList<Point2D> list = getDrugPoints(alias);
+    List<Point2D> list = getDrugPoints(alias);
 
     return getPolygonTransformation().getPointOnPolygonByAnchor(list, anchor);
   }
@@ -54,23 +55,25 @@ public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
    *          alias for which we are looking for a border
    * @return list of points defining border of the given alias
    */
-  protected ArrayList<Point2D> getDrugPoints(Species alias) {
-    ArrayList<Point2D> list = new ArrayList<Point2D>();
+  protected List<Point2D> getDrugPoints(Species alias) {
+    List<Point2D> list = new ArrayList<>();
 
     double x = alias.getX();
     double y = alias.getY();
     double width = alias.getWidth();
     double height = alias.getHeight();
 
+    double cutSize = width*1/5;
+
     // CHECKSTYLE:OFF
     list.add(new Point2D.Double(x, y + height / 2));
-    list.add(new Point2D.Double(x + width / 12, y));
+    list.add(new Point2D.Double(x + cutSize, y));
     list.add(new Point2D.Double(x + width / 2, y));
-    list.add(new Point2D.Double(x + width * 11 / 12, y));
+    list.add(new Point2D.Double(x + width - cutSize, y));
     list.add(new Point2D.Double(x + width, y + height / 2));
-    list.add(new Point2D.Double(x + width * 11 / 12, y + height));
+    list.add(new Point2D.Double(x + width - cutSize, y + height));
     list.add(new Point2D.Double(x + width / 2, y + height));
-    list.add(new Point2D.Double(x + width / 12, y + height));
+    list.add(new Point2D.Double(x + cutSize, y + height));
     // CHECKSTYLE:ON
     return list;
   }

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

@@ -936,5 +936,13 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     assertEquals(r.getReactants().get(0).getLine().getBeginPoint().getY(), r.getProducts().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
   }
 
+  @Test
+  public void testOrthogonalReactionToDrug() throws Exception {
+    CellDesignerXmlParser parser = new CellDesignerXmlParser();
+    Model model = parser.createModel(new ConverterParams().filename("testFiles/orthogonal_reaction_to_drug.xml"));
+    Reaction r = model.getReactionByReactionId("re3");
+    assertEquals(r.getReactants().get(0).getLine().getBeginPoint().getY(), r.getProducts().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
+  }
+
 
 }

converter-CellDesigner/testFiles/orthogonal_reaction_to_drug.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:complexSpeciesAlias id="csa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="29.0" y="213.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:structuralState angle="1.5707963267948966"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" 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="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="219.0" y="46.0" w="375.0" h="74.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="375.0" height="74.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffff00ff" 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: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"/>
+</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>COMPLEX</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="open"/>
+</celldesigner:listOfStructuralStates>
+</celldesigner:state>
+</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>DRUG</celldesigner:class>
+<celldesigner:name>s3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re3" id="re3" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="csa1">
+<celldesigner:linkAnchor position="ESE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa2">
+<celldesigner:linkAnchor position="SSW"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="square" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="horizontal"/>
+<celldesigner:lineDirection index="1" value="vertical"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.5937800642735791,0.49112656163645174</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00008" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>csa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00009" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>