import of structural state check if data is not null

CHANGELOG

@@ -11,6 +11,8 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
     exporter violates SBGN specification (#707)
   * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are
     visualized with proper line type across all included modifiers (#957)
+  * Bug fix: dimension of the modifications is the same as in minerva when
+    exporting to SBGNML-PD (#554)
 
 minerva (15.0.0~alpha.0) stable; urgency=medium
   * Improvement: logs provided for validation data model are structurized (#325)

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

@@ -4,15 +4,14 @@ import java.awt.Color;
 import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
 import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.sbgn.*;
 import org.sbgn.bindings.*;
 import org.sbgn.bindings.Arc.*;
+import org.sbgn.bindings.Map;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -80,6 +79,8 @@ public class SbgnmlXmlParser {
    */
   private List<Arc> logicArcs = new ArrayList<Arc>();
 
+  Model model;
+
   /**
    * Method used to create a model from SBGN-ML file.
    *
@@ -94,7 +95,7 @@ public class SbgnmlXmlParser {
    */
   public Model createModel(String filename, File inputSbgnmlFile) throws InvalidInputDataExecption {
 
-    Model model = new ModelFullIndexed(null);
+    model = new ModelFullIndexed(null);
     model.setIdModel(filename);
 
     Sbgn sbgnData;
@@ -598,7 +599,7 @@ public class SbgnmlXmlParser {
               logger.warn("Only macromolecule elements can have state variables.");
             }
           } else {
-            StructuralState state = stateVariableToStructuralState(child);
+            StructuralState state = createStructuralState(child);
             if (newSpecies instanceof Protein) {
               ((Protein) newSpecies).setStructuralState(state);
             } else {
@@ -625,21 +626,12 @@ public class SbgnmlXmlParser {
 
   }
 
-  private StructuralState stateVariableToStructuralState(Glyph glyph) {
-    StructuralState state = new StructuralState();
-
-    state.setFontSize(10);
-    state.setPosition(new Point2D.Double(glyph.getBbox().getX(), glyph.getBbox().getY()));
-    state.setHeight((double) glyph.getBbox().getH());
-    state.setWidth((double) glyph.getBbox().getW());
-    if (glyph.getState() != null) {
-      state.setValue(glyph.getState().getValue());
-    }
-
-    return state;
-  }
-
   private StructuralState createStructuralState(Glyph glyph) {
+    if (glyph.getState() == null || glyph.getState().getValue() == null) {
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, glyph.getId(), "state", model.getName()),
+          "Invalid structural state");
+      return null;
+    }
     StructuralState structuralState = new StructuralState();
 
     double height = new Double(glyph.getBbox().getH());