Resolve "Poor handling of modification states when exporting to SBGN-ML"

Closes #554 (closed)

@david.hoksza,

I fixed the size problem of modifications. However, the position in my opinion is encoded properly and the problem is on newt.

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -15,6 +15,7 @@ import org.sbgn.bindings.Map;
 
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
 import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.PolylineData;
@@ -205,7 +206,7 @@ public class SbgnmlXmlExporter {
     glyph.setState(state);
 
     Bbox bbox = new Bbox();
-    
+
     float width = structuralState.getWidth().floatValue();
     float height = structuralState.getHeight().floatValue();
     bbox.setH(height);
@@ -400,32 +401,28 @@ public class SbgnmlXmlExporter {
     glyph.setId(mr.getIdModificationResidue());
     glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
 
+    double width = SpeciesConverter.DEFAULT_MODIFICATION_DIAMETER;
+    double height = SpeciesConverter.DEFAULT_MODIFICATION_DIAMETER;
     if (mr instanceof AbstractSiteModification) {
       AbstractSiteModification modification = (AbstractSiteModification) mr;
+      Glyph.State state = new Glyph.State();
+      state.setVariable(mr.getName());
+      glyph.setState(state);
       if (modification.getState() != null) {
-        Glyph.State state = new Glyph.State();
         state.setValue(modification.getState().getAbbreviation());
-        state.setVariable(mr.getName());
-        glyph.setState(state);
       }
+    } else if (mr instanceof AbstractRegionModification) {
+      width = ((AbstractRegionModification) mr).getWidth();
+      height = ((AbstractRegionModification) mr).getHeight();
     }
 
     Bbox bbox = new Bbox();
 
-    final float filledWidth = 70.0f;
-    final float filledHeight = 28.0f;
-    final float emptyWidth = 20.0f;
-    final float emptyHeight = 22.0f;
-    if (glyph.getState() != null) {
-      bbox.setH(filledHeight);
-      bbox.setW(filledWidth);
-    } else {
-      bbox.setH(emptyHeight);
-      bbox.setW(emptyWidth);
-    }
+    bbox.setH((float) width);
+    bbox.setW((float) height);
 
-    bbox.setX((float) mr.getPosition().getX());
-    bbox.setY((float) mr.getPosition().getY());
+    bbox.setX((float) (mr.getPosition().getX() - width / 2));
+    bbox.setY((float) (mr.getPosition().getY() - height / 2));
 
     glyph.setBbox(bbox);