fix on kinetics in reactions with complex modifiers

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

@@ -55,15 +55,18 @@ public class KineticsXmlParser extends XmlParser {
       if (element == null) {
         element = model.getFunctionById(id);
       }
+      if (element == null) {
+        element = model.getElementByElementId(id);
+      }
       if (element != null) {
         ciNode.setTextContent(element.getElementId());
-      } else {
+        elementsUsedInKinetics.add(element);
+      } else if (!id.equals("default")) {
         throw new InvalidXmlSchemaException("Unknown symbol in kinetics: " + id);
       }
-      elementsUsedInKinetics.add(element);
     }
     result.addArguments(elementsUsedInKinetics);
-    
+
     String definition = super.nodeToString(mathNode, true);
     definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
     definition = definition.replace("<math>", "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">");

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

@@ -233,20 +233,30 @@ public class ReactionFromXml extends XmlParser {
       String aliasId = super.getNodeAttr("alias", node);
       addElementMapping(model, result, speciesId, aliasId);
     }
-    
+
     for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:productLink", annotationNode)) {
       String speciesId = super.getNodeAttr("product", node);
       String aliasId = super.getNodeAttr("alias", node);
       addElementMapping(model, result, speciesId, aliasId);
     }
-    
+    for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:modification", annotationNode)) {
+      String speciesId = super.getNodeAttr("modifiers", node);
+      String aliasId = super.getNodeAttr("aliases", node);
+      addElementMapping(model, result, speciesId, aliasId);
+    }
+
     return result;
   }
 
   private void addElementMapping(Model model, Map<String, Element> result, String speciesId, String aliasId) {
-    Element element = model.getElementByElementId(aliasId);
-    result.put(speciesId, element);
-    addCompartmentMapping(result, element);
+    String[] aliasIds = aliasId.split(",");
+    String[] speciesIds = speciesId.split(",");
+    for (int i = 0; i < aliasIds.length; i++) {
+
+      Element element = model.getElementByElementId(aliasIds[i]);
+      result.put(speciesIds[i], element);
+      addCompartmentMapping(result, element);
+    }
   }
 
   private void addCompartmentMapping(Map<String, Element> result, Element element) {