Program: 58903
Project: 58903
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 sName="String_Node_Str";
  String sShapeType="String_Node_Str";
  short shHeight=0;
  short shWidth=0;
  short shXPosition=0;
  short shYPosition=0;
  for (int iAttributeIndex=0; iAttributeIndex < attributes.getLength(); iAttributeIndex++) {
    sAttributeName=attributes.getLocalName(iAttributeIndex);
    if ("String_Node_Str".equals(sAttributeName)) {
      sAttributeName=attributes.getQName(iAttributeIndex);
    }
    if (sAttributeName.equals("String_Node_Str")) {
      sName=attributes.getValue(iAttributeIndex);
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shHeight=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shWidth=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shXPosition=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shYPosition=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      sShapeType=attributes.getValue(iAttributeIndex);
    }
  }
  if (alCurrentVertex.isEmpty())   return;
  IGraphItem vertexRep=pathwayItemManager.createVertexRep(currentPathway,alCurrentVertex,sName,sShapeType,shXPosition,shYPosition,shWidth,shHeight);
  hashKgmlEntryIdToVertexRepId.put(iCurrentEntryId,vertexRep);
  hashKgmlNameToVertexRepId.put(((PathwayVertexGraphItem)currentVertex).getName(),vertexRep);
  hashKgmlReactionIdToVertexRepId.put(((PathwayVertexGraphItem)currentVertex).getReactionId(),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 sName="String_Node_Str";
  String sShapeType="String_Node_Str";
  short shHeight=0;
  short shWidth=0;
  short shXPosition=0;
  short shYPosition=0;
  for (int iAttributeIndex=0; iAttributeIndex < attributes.getLength(); iAttributeIndex++) {
    sAttributeName=attributes.getLocalName(iAttributeIndex);
    if ("String_Node_Str".equals(sAttributeName)) {
      sAttributeName=attributes.getQName(iAttributeIndex);
    }
    if (sAttributeName.equals("String_Node_Str")) {
      sName=attributes.getValue(iAttributeIndex);
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shHeight=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shWidth=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shXPosition=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      shYPosition=new Short(attributes.getValue(iAttributeIndex));
    }
 else     if (sAttributeName.equals("String_Node_Str")) {
      sShapeType=attributes.getValue(iAttributeIndex);
    }
  }
  if (alCurrentVertex.isEmpty())   return;
  IGraphItem vertexRep=pathwayItemManager.createVertexRep(currentPathway,alCurrentVertex,sName,sShapeType,shXPosition,shYPosition,shWidth,shHeight);
}