modification glyphs reference glyph is provided properly and bounding box is defined

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

@@ -527,8 +527,14 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     GeneralGlyph modificationGlyph = getLayout().createGeneralGlyph("modification_" + (idCounter++),
         modificationFeatureValue.getId());
     ReferenceGlyph referenceGlyph = new ReferenceGlyph("modification_reference_" + (idCounter++));
-    referenceGlyph.setReference(speciesGlyph.getId());
+    referenceGlyph.setGlyph(speciesGlyph.getId());
+    referenceGlyph.setBoundingBox(createBoundingBoxForModification(mr));
+    
     modificationGlyph.addReferenceGlyph(referenceGlyph);
+    modificationGlyph.setBoundingBox(createBoundingBoxForModification(mr));
+  }
+
+  private BoundingBox createBoundingBoxForModification(ModificationResidue mr) {
     double width, height;
     if (mr instanceof AbstractRegionModification) {
       width = ((AbstractRegionModification) mr).getWidth();
@@ -545,7 +551,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     dimensions.setWidth(width);
     dimensions.setHeight(height);
     boundingBox.setDimensions(dimensions);
-    modificationGlyph.setBoundingBox(boundingBox);
+    return boundingBox;
   }
 
   private int modificationResidueCounter = 0;

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

@@ -414,7 +414,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
           if (((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().size() > 0) {
             // find a reference to the alias in layout, so we know it's the proper value
             ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
-            if (referenceGlyph.getReference().equals(mr.getSpecies().getElementId())) {
+            if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
               residueGlyph = (GeneralGlyph) graphicalObject;
             }
           } else {