export of structural state should use structural state z index

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

@@ -277,7 +277,7 @@ public class ModificationResidueExporter {
     double x = structuralState.getPosition().getX();
     double y = structuralState.getPosition().getY();
     BoundingBox boundingBox = new BoundingBox();
-    boundingBox.setPosition(new Point(x, y, structuralState.getSpecies().getZ() + 1));
+    boundingBox.setPosition(new Point(x, y, structuralState.getZ()));
     Dimensions dimensions = new Dimensions();
     dimensions.setWidth(width);
     dimensions.setHeight(height);

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

@@ -536,6 +536,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
     structuralState.setWidth(element.getWidth());
     structuralState.setHeight(20.0);
     structuralState.setFontSize(10.0);
+    structuralState.setZ(element.getZ() + 2);
     return structuralState;
   }
 

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

@@ -64,6 +64,7 @@ public class SbmlModelUtilsTest {
     }
   }
 
+  @SuppressWarnings("deprecation")
   private Model createModelWithLayoutAndRender() {
     SBMLDocument doc = new SBMLDocument(3, 1);
     Model result = doc.createModel();