Program: 59238
Project: 59238
Buggy source:
public void initView(){
class PathwayMarqueeHandler extends BasicMarqueeHandler {
    public boolean isForceMarqueeEvent(    MouseEvent event){
      if (SwingUtilities.isLeftMouseButton(event) && event.getClickCount() == 1)       return true;
 else       return super.isForceMarqueeEvent(event);
    }
    public void mousePressed(    final MouseEvent event){
      DefaultGraphCell clickedCell=(DefaultGraphCell)refPathwayGraph.getFirstCellForLocation(event.getX(),event.getY());
      if (clickedCell != null) {
        final String sUrl=((PathwayVertex)clickedCell.getUserObject()).getVertexLink();
        String sSearchPattern="String_Node_Str";
        String sPathwayFilePath;
        if (sUrl.contains((CharSequence)sSearchPattern)) {
          int iFilePathStartIndex=sUrl.lastIndexOf(sSearchPattern) + sSearchPattern.length();
          sPathwayFilePath=sUrl.substring(iFilePathStartIndex);
          sPathwayFilePath=sPathwayFilePath.replaceFirst("String_Node_Str","String_Node_Str");
          System.out.println("String_Node_Str" + sPathwayFilePath);
          int iPathwayIdIndex=sUrl.lastIndexOf("String_Node_Str") + 5;
          System.out.println("String_Node_Str" + iPathwayIdIndex);
          iPathwayId=StringConversionTool.convertStringToInt(sUrl.substring(iPathwayIdIndex,iPathwayIdIndex + 3),0);
          refGeneralManager.getSingelton().getLoggerManager().logMsg("String_Node_Str" + iPathwayId);
          loadPathwayFromFile("String_Node_Str" + sPathwayFilePath);
        }
 else {
          final IViewManager tmpViewManager=refGeneralManager.getSingelton().getViewGLCanvasManager();
          refEmbeddedFrameComposite.getDisplay().asyncExec(new Runnable(){
            public void run(){
              ((HTMLBrowserViewRep)tmpViewManager.getItem(iHTMLBrowserId)).setUrl(sUrl);
            }
          }
);
          showNeighbourhood(clickedCell,iNeighbourhoodDistance);
        }
      }
      super.mousePressed(event);
    }
  }
  refGraphModel=new DefaultGraphModel();
  refGraphLayoutCache=new GraphLayoutCache(refGraphModel,new DefaultCellViewFactory());
  refPathwayGraph=new JGraph(refGraphModel,refGraphLayoutCache);
  refPathwayGraph.getGraphLayoutCache().setFactory(new GPCellViewFactory());
  refPathwayGraph.setCloneable(true);
  refPathwayGraph.setMarqueeHandler(new PathwayMarqueeHandler());
  refUndoManager=new GraphUndoManager();
  refGraphModel.addUndoableEditListener(refUndoManager);
}

Fixed version (ground truth):
public void initView(){
class PathwayMarqueeHandler extends BasicMarqueeHandler {
    public boolean isForceMarqueeEvent(    MouseEvent event){
      if (SwingUtilities.isLeftMouseButton(event) && event.getClickCount() == 1)       return true;
 else       return super.isForceMarqueeEvent(event);
    }
    public void mousePressed(    final MouseEvent event){
      DefaultGraphCell clickedCell=(DefaultGraphCell)refPathwayGraph.getFirstCellForLocation(event.getX(),event.getY());
      if (clickedCell != null) {
        final String sUrl=((PathwayVertex)clickedCell.getUserObject()).getVertexLink();
        String sSearchPattern="String_Node_Str";
        String sPathwayFilePath;
        if (sUrl.contains((CharSequence)sSearchPattern)) {
          int iFilePathStartIndex=sUrl.lastIndexOf(sSearchPattern) + sSearchPattern.length();
          sPathwayFilePath=sUrl.substring(iFilePathStartIndex);
          sPathwayFilePath=sPathwayFilePath.replaceFirst("String_Node_Str","String_Node_Str");
          System.out.println("String_Node_Str" + sPathwayFilePath);
          int iPathwayIdIndex=sUrl.lastIndexOf("String_Node_Str") + 5;
          System.out.println("String_Node_Str" + iPathwayIdIndex);
          iPathwayId=StringConversionTool.convertStringToInt(sUrl.substring(iPathwayIdIndex,iPathwayIdIndex + 3),0);
          refGeneralManager.getSingelton().getLoggerManager().logMsg("String_Node_Str" + iPathwayId);
          loadPathwayFromFile("String_Node_Str" + sPathwayFilePath);
          bNeighbourhoodShown=false;
        }
 else {
          final IViewManager tmpViewManager=refGeneralManager.getSingelton().getViewGLCanvasManager();
          refEmbeddedFrameComposite.getDisplay().asyncExec(new Runnable(){
            public void run(){
              ((HTMLBrowserViewRep)tmpViewManager.getItem(iHTMLBrowserId)).setUrl(sUrl);
            }
          }
);
          if (bNeighbourhoodShown == true) {
            for (int iUndoCount=0; iUndoCount < iNeighbourhoodUndoCount; iUndoCount++) {
              refUndoManager.undo(refGraphLayoutCache);
            }
            bNeighbourhoodShown=false;
          }
          showNeighbourhood(clickedCell,iNeighbourhoodDistance);
          bNeighbourhoodShown=true;
        }
      }
      super.mousePressed(event);
    }
  }
  refGraphModel=new DefaultGraphModel();
  refGraphLayoutCache=new GraphLayoutCache(refGraphModel,new DefaultCellViewFactory());
  refPathwayGraph=new JGraph(refGraphModel,refGraphLayoutCache);
  refPathwayGraph.getGraphLayoutCache().setFactory(new GPCellViewFactory());
  refPathwayGraph.setCloneable(true);
  refPathwayGraph.setMarqueeHandler(new PathwayMarqueeHandler());
  refUndoManager=new GraphUndoManager();
  refGraphModel.addUndoableEditListener(refUndoManager);
}