layout for reaction is taken into consideration

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java

@@ -95,18 +95,9 @@ public class SbmlParser implements IConverter {
       if (sbmlModel.getParameterCount() > 0) {
         throw new NotImplementedException("Parameter not implemented for model");
       }
-      if (sbmlModel.getModifierSpeciesReferenceCount() > 0) {
-        throw new NotImplementedException("ModifierSpeciesReference not implemented for model");
-      }
-      if (sbmlModel.getReactionCount() > 0) {
-        throw new NotImplementedException("Reaction not implemented for model");
-      }
       if (sbmlModel.getRuleCount() > 0) {
         throw new NotImplementedException("Rule not implemented for model");
       }
-      if (sbmlModel.getSpeciesReferenceCount() > 0) {
-        throw new NotImplementedException("SpeciesReference not implemented for model");
-      }
       if (sbmlModel.getUnitDefinitionCount() > 0) {
         logger.warn("Units are not supported");
       }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java

 package lcsb.mapviewer.converter.model.sbml;
 
+import java.awt.geom.Point2D;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -14,14 +15,18 @@ import org.sbml.jsbml.ListOf;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ModifierSpeciesReference;
 import org.sbml.jsbml.SpeciesReference;
+import org.sbml.jsbml.ext.layout.CurveSegment;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.ReactionGlyph;
+import org.sbml.jsbml.ext.layout.SpeciesGlyph;
 import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
 import org.sbml.jsbml.util.NotImplementedException;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
 import lcsb.mapviewer.model.map.reaction.Modifier;
 import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
@@ -76,27 +81,35 @@ public class SbmlReactionParser {
       used.add(source);
       Reaction reactionWithLayout = source.copy();
       reactionWithLayout.setIdReaction(glyph.getId());
-      for (SpeciesReferenceGlyph speciesGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
+      for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
+        SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
         ReactionNode minervaNode = null;
-        Element minervaElement = minervaModel.getElementByElementId(speciesGlyph.getSpeciesReference());
-        if (minervaElement == null) {
-          throw new InvalidInputDataExecption("Cannot find source reaction node for layouted reaction: "
-              + speciesGlyph.getSpeciesReference() + ", " + glyph.getId());
-        }
         for (ReactionNode node : reactionWithLayout.getReactionNodes()) {
-          if (node.getElement().equals(minervaElement)) {
+          if (node.getElement().getElementId().equals(speciesGlyph.getSpecies())) {
             minervaNode = node;
           }
         }
         if (minervaNode == null) {
-          throw new InvalidInputDataExecption("Cannot find reaction node for layouted reaction: "
-              + speciesGlyph.getSpeciesReference() + ", " + glyph.getId());
+          throw new InvalidInputDataExecption(
+              "Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
         }
-        minervaElement = minervaModel.getElementByElementId(speciesGlyph.getId());
+        Element minervaElement = minervaModel.getElementByElementId(speciesGlyph.getId());
         if (minervaElement == null) {
           throw new InvalidInputDataExecption("Cannot find layouted reaction node for layouted reaction: "
               + speciesGlyph.getId() + ", " + glyph.getId());
         }
+
+        PolylineData line = null;
+        for (CurveSegment segment : speciesRefernceGlyph.getCurve().getListOfCurveSegments()) {
+          Point2D start = new Point2D.Double(segment.getStart().getX(), segment.getStart().getY());
+          Point2D end = new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY());
+          if (line == null) {
+            line = new PolylineData(start, end);
+          } else {
+            line.addPoint(end);
+          }
+        }
+        minervaNode.setLine(line);
         minervaNode.setElement(minervaElement);
       }
       try {
@@ -131,7 +144,7 @@ public class SbmlReactionParser {
 
     for (ModifierSpeciesReference modifier : sbmlReaction.getListOfModifiers()) {
       Species element = minervaModel.getElementByElementId(modifier.getSpecies());
-      reaction.addModifier(new Modifier(element));
+      reaction.addModifier(new Catalysis(element));
     }
 
     return reaction;

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java

@@ -15,6 +15,8 @@ import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class SbmlParserTest {
@@ -89,6 +91,18 @@ public class SbmlParserTest {
     assertEquals(new Point(1, 2), parser.nextCoordinates());
     assertEquals(new Point(2, 2), parser.nextCoordinates());
     assertEquals(new Point(3, 0), parser.nextCoordinates());
-    
   }
+
+  @Test
+  public void testParseReaction() throws FileNotFoundException, InvalidInputDataExecption {
+    Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/Complete_Example.xml"));
+    assertNotNull(model);
+    assertEquals(1, model.getReactions().size());
+    Reaction reaction = model.getReactions().iterator().next();
+    for (ReactionNode node : reaction.getReactionNodes()) {
+      assertNotNull(node.getLine());
+      assertTrue(node.getLine().length() > 0);
+    }
+  }
+
 }