structural state should be between species and reaction

converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java

@@ -4,6 +4,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -13,12 +14,13 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
 import lcsb.mapviewer.model.map.species.field.StructuralState;
 
 /**
@@ -41,18 +43,7 @@ public class ZIndexPopulator {
    * z-values.
    */
   public void populateZIndex(final Model model) {
-    List<Drawable> drawables = new ArrayList<>();
-    for (Layer layer : model.getLayers()) {
-      drawables.addAll(layer.getOvals());
-      drawables.addAll(layer.getRectangles());
-      drawables.addAll(layer.getTexts());
-    }
-    drawables.addAll(model.getBioEntities());
-    for (Species species : model.getSpeciesList()) {
-      if (species.getStructuralState() != null) {
-        drawables.add(species.getStructuralState());
-      }
-    }
+    Set<Drawable> drawables = model.getDrawables();
 
     populateZIndex(drawables);
 
@@ -129,6 +120,16 @@ public class ZIndexPopulator {
     for (final Drawable drawable : sortedDrawables) {
       if (drawable.getZ() == null) {
         drawable.setZ(++maxZIndex);
+        if (drawable instanceof Species) {
+          if (((Species) drawable).getStructuralState() != null) {
+            ((Species) drawable).getStructuralState().setZ(++maxZIndex);
+          }
+        }
+        if (drawable instanceof SpeciesWithModificationResidue) {
+          for (ModificationResidue mr : ((SpeciesWithModificationResidue) drawable).getModificationResidues()) {
+            mr.setZ(++maxZIndex);
+          }
+        }
       }
     }
   }

converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java

@@ -96,7 +96,7 @@ public class ZIndexPopulatorTest {
   }
 
   @Test
-  public void testZIndexReactionShouldBeBeforeElement() {
+  public void testZIndexReactionShouldBeAfterStructuralState() {
     Model model = new ModelFullIndexed(null);
     Species species = createProtein();
     StructuralState state = new StructuralState();
@@ -114,8 +114,9 @@ public class ZIndexPopulatorTest {
     populator.populateZIndex(model);
 
     assertTrue(reaction.getZ() > species.getZ());
-    // structural state should be over reaction and species
-    assertTrue(species.getStructuralState().getZ() > reaction.getZ());
+    // structural state should be below reaction and above species
+    assertTrue(species.getStructuralState().getZ() < reaction.getZ());
+    assertTrue(species.getStructuralState().getZ() > species.getZ());
   }
 
   @Test