Program: 57732
Project: 57732
Buggy source:
/** 
 * Reacts on the elements of the graphics tag. An example graphics tag looks like this: <graphics name="1.8.4.1" fgcolor="#000000" bgcolor="#FFFFFF" type="rectangle" x="142" y="304" width="45" height="17"/>
 */
protected void handleGraphicsTag(){
  String name="String_Node_Str";
  String shapeType="String_Node_Str";
  short height=0;
  short width=0;
  short x=0;
  short y=0;
  for (int attributeIndex=0; attributeIndex < attributes.getLength(); attributeIndex++) {
    attributeName=attributes.getLocalName(attributeIndex);
    try {
      if ("String_Node_Str".equals(attributeName)) {
        attributeName=attributes.getQName(attributeIndex);
      }
      if (attributeName.equals("String_Node_Str")) {
        name=attributes.getValue(attributeIndex);
      }
 else       if (attributeName.equals("String_Node_Str")) {
        height=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        width=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        x=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        y=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        shapeType=attributes.getValue(attributeIndex);
      }
    }
 catch (    NumberFormatException e) {
      e.printStackTrace();
    }
  }
  if (currentVertices.isEmpty()) {
    return;
  }
  if (currentVertices.get(0).getType().equals(EPathwayVertexType.group)) {
    currentVertexGroupRep=pathwayItemManager.createVertexGroupRep(currentPathway);
    hashKgmlEntryIdToVertexRep.put(currentEntryId,currentVertexGroupRep);
    hashKgmlNameToVertexRep.put(currentVertices.get(0).getName(),currentVertexGroupRep);
  }
 else {
    PathwayVertexRep vertexRep=pathwayItemManager.createVertexRep(currentPathway,currentVertices,name,shapeType,x,y,width,height);
    hashKgmlEntryIdToVertexRep.put(currentEntryId,vertexRep);
    hashKgmlNameToVertexRep.put(currentVertices.get(0).getName(),vertexRep);
    if (currentReactionName != null && !currentReactionName.isEmpty()) {
      if (hashKgmlReactionNameToVertexRep.get(currentReactionName) != null) {
        PathwayVertexRep alreadyPresentReactionNode=hashKgmlReactionNameToVertexRep.get(currentReactionName);
        if (alreadyPresentReactionNode instanceof PathwayVertexGroupRep) {
          ((PathwayVertexGroupRep)alreadyPresentReactionNode).addVertexRep(vertexRep);
        }
 else {
          PathwayVertexGroupRep vertexGroupRep=pathwayItemManager.createVertexGroupRep(currentPathway);
          vertexGroupRep.addVertexRep(alreadyPresentReactionNode);
          vertexGroupRep.addVertexRep(vertexRep);
          hashKgmlReactionNameToVertexRep.remove(alreadyPresentReactionNode);
          hashKgmlReactionNameToVertexRep.put(currentReactionName,vertexGroupRep);
        }
      }
 else {
        hashKgmlReactionNameToVertexRep.put(currentReactionName,vertexRep);
      }
    }
  }
}

Fixed version (ground truth):
/** 
 * Reacts on the elements of the graphics tag. An example graphics tag looks like this: <graphics name="1.8.4.1" fgcolor="#000000" bgcolor="#FFFFFF" type="rectangle" x="142" y="304" width="45" height="17"/>
 */
protected void handleGraphicsTag(){
  String name="String_Node_Str";
  String shapeType="String_Node_Str";
  short height=0;
  short width=0;
  short x=0;
  short y=0;
  for (int attributeIndex=0; attributeIndex < attributes.getLength(); attributeIndex++) {
    attributeName=attributes.getLocalName(attributeIndex);
    try {
      if ("String_Node_Str".equals(attributeName)) {
        attributeName=attributes.getQName(attributeIndex);
      }
      if (attributeName.equals("String_Node_Str")) {
        name=attributes.getValue(attributeIndex);
      }
 else       if (attributeName.equals("String_Node_Str")) {
        height=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        width=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        x=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        y=new Short(attributes.getValue(attributeIndex));
      }
 else       if (attributeName.equals("String_Node_Str")) {
        shapeType=attributes.getValue(attributeIndex);
      }
    }
 catch (    NumberFormatException e) {
      e.printStackTrace();
    }
  }
  if (currentVertices.isEmpty()) {
    return;
  }
  if (currentVertices.get(0).getType().equals(EPathwayVertexType.group)) {
    currentVertexGroupRep=pathwayItemManager.createVertexGroupRep(currentPathway);
    hashKgmlEntryIdToVertexRep.put(currentEntryId,currentVertexGroupRep);
  }
 else {
    PathwayVertexRep vertexRep=pathwayItemManager.createVertexRep(currentPathway,currentVertices,name,shapeType,x,y,width,height);
    hashKgmlEntryIdToVertexRep.put(currentEntryId,vertexRep);
    if (currentReactionName != null && !currentReactionName.isEmpty()) {
      if (hashKgmlReactionNameToVertexRep.get(currentReactionName) != null) {
        PathwayVertexRep alreadyPresentReactionNode=hashKgmlReactionNameToVertexRep.get(currentReactionName);
        if (alreadyPresentReactionNode instanceof PathwayVertexGroupRep) {
          ((PathwayVertexGroupRep)alreadyPresentReactionNode).addVertexRep(vertexRep);
        }
 else {
          PathwayVertexGroupRep vertexGroupRep=pathwayItemManager.createVertexGroupRep(currentPathway);
          vertexGroupRep.addVertexRep(alreadyPresentReactionNode);
          vertexGroupRep.addVertexRep(vertexRep);
          hashKgmlReactionNameToVertexRep.remove(alreadyPresentReactionNode);
          hashKgmlReactionNameToVertexRep.put(currentReactionName,vertexGroupRep);
        }
      }
 else {
        hashKgmlReactionNameToVertexRep.put(currentReactionName,vertexRep);
      }
    }
  }
}