Merge branch '604-improve-information-in-exception' into 'master'

Resolve "improve information in exception"

Closes #604

See merge request !538

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java

@@ -64,6 +64,7 @@ import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
 import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 /**
  * This is a part of {@link ReactionXmlParser} class functionality that allows
@@ -216,9 +217,9 @@ public class ReactionFromXml extends XmlParser {
       }
     }
     try {
-    assignStochiometry(result.getReactants(), reactantsNode, elements);
-    assignStochiometry(result.getProducts(), productsNode, elements);
-    assignStochiometry(result.getModifiers(), modifiersNode, elements);
+      assignStochiometry(result.getReactants(), reactantsNode, elements);
+      assignStochiometry(result.getProducts(), productsNode, elements);
+      assignStochiometry(result.getModifiers(), modifiersNode, elements);
     } catch (InvalidStateException e) {
       throw new ReactionParserException(result, e);
     }
@@ -476,7 +477,7 @@ public class ReactionFromXml extends XmlParser {
           result.removeModifier(modifier);
           i--;
         } else if (modifier.getLine() == null) {
-          createLineForModifier(result, modifier);
+          createLineForModifier(modifier);
         }
       }
 
@@ -579,26 +580,29 @@ public class ReactionFromXml extends XmlParser {
   /**
    * Creates line information for the modifier.
    * 
-   * @param reaction
-   *          reaction where modifier is placed
    * @param modifier
    *          modifier to update
+   * @throws ReactionParserException 
    */
-  private void createLineForModifier(Reaction reaction, Modifier modifier) {
-    Element element = modifier.getElement();
-    CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
-    Point2D startPoint = converter.getPointCoordinates(element, anchorsByNodes.get(modifier));
-    ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
-
-    Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(),
-        lineTypeByModifier.get(modifier));
-    PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p,
-        pointsByModifier.get(modifier));
-
-    startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
-    line.setStartPoint(startPoint);
-    modifier.setLine(line);
-    modifierTypeUtils.updateLineEndPoint(modifier);
+  private void createLineForModifier(Modifier modifier) throws ReactionParserException {
+    try {
+      Element element = modifier.getElement();
+      CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
+      Point2D startPoint = converter.getPointCoordinates(element, anchorsByNodes.get(modifier));
+      ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+
+      Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(),
+          lineTypeByModifier.get(modifier));
+      PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p,
+          pointsByModifier.get(modifier));
+
+      startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
+      line.setStartPoint(startPoint);
+      modifier.setLine(line);
+      modifierTypeUtils.updateLineEndPoint(modifier);
+    } catch (Exception e) {
+      throw new ReactionParserException("Problem with creating layout for modifier.", modifier.getReaction());
+    }
   }
 
   /**