element are differntaite also on the complex in which they are placed

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java

@@ -49,10 +49,14 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
   @Override
   protected String getSbmlIdKey(Species element) {
     String compartmentName = null;
+    String complexName = null;
     if (element.getCompartment() != null) {
       compartmentName = element.getCompartment().getName();
     }
-    return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName;
+    if (element.getComplex() != null) {
+      complexName = element.getComplex().getName();
+    }
+    return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName+ "\n" + complexName;
   }
 
   protected LocalStyle createStyle(Species element) {

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java

 package lcsb.mapviewer.converter.model.sbml.species;
 
-import java.awt.Color;
 import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.List;
@@ -35,7 +34,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
     Class<? extends Species> clazz = SBOTermSpeciesType.getTypeSBOTerm(sboTerm);
     try {
       Species result = clazz.getConstructor(String.class).newInstance(species.getId());
-      result.setInitialAmount(species.getInitialAmount());
+      if (!Double.isNaN(species.getInitialAmount())) {
+        result.setInitialAmount(species.getInitialAmount());
+      }
       assignBioEntityData(species, result);
       if (layout == null) {
         assignCompartment(result, species.getCompartment());
@@ -101,7 +102,6 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
     return result;
   }
 
-
   @Override
   protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
     super.applyStyleToElement(elementWithLayout, style);