Program: 88750
Project: 88750
Buggy source:
public void run(){
  IAnnotationModel model=getEditor().getDocumentProvider().getAnnotationModel(getEditor().getEditorInput());
  if (model instanceof AbstractMarkerAnnotationModel) {
    setModel((AbstractMarkerAnnotationModel)model);
  }
  int markerLine=getRulerInfo().getLineOfLastMouseButtonActivity();
  IResource rec=getResource(getEditor());
  try {
    IMarker[] markers=rec.findMarkers("String_Node_Str",true,IResource.DEPTH_INFINITE);
    for (int i=0; i < markers.length; i++) {
      setLineNumber(getDocument().getLineOfOffset(getModel().getMarkerPosition(markers[i]).getOffset()));
      if (getLineNumber() == markerLine) {
        System.out.println("String_Node_Str");
        ArrayList links=getMarkerLinks();
        Iterator lit=links.iterator();
        while (lit.hasNext()) {
          System.out.println("String_Node_Str" + lit.next());
        }
        String[] list=getMarkerLabels(links);
        if ((list == null) || (list.length == 0)) {
          System.out.println("String_Node_Str");
        }
 else {
          IWorkbenchWindow window=SootPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage().getWorkbenchWindow();
          if (window == null) {
            System.out.println("String_Node_Str");
          }
          PopupListSelector popup=new PopupListSelector(window.getShell());
          popup.setItems(list);
          if (getEditor() instanceof JimpleEditor) {
            int topIndex=((JimpleEditor)getEditor()).getViewer().getTopIndex();
            Rectangle rect=new Rectangle(400,(getLineNumber() + 1 - topIndex),650,45);
            popup.open(rect);
          }
 else {
            System.out.println(getEditor().getClass());
            System.out.println("String_Node_Str" + getModel().getMarkerPosition(markers[i]).getOffset());
            int pos=getModel().getMarkerPosition(markers[i]).getOffset();
            pos=pos / getLineNumber();
            Rectangle rect=new Rectangle(380,16,650,45);
            popup.open(rect);
          }
          handleSelection(popup.getSelected(),links);
        }
      }
    }
  }
 catch (  CoreException e) {
  }
catch (  BadLocationException e1) {
  }
}

Fixed version (ground truth):
public void run(){
  IAnnotationModel model=getEditor().getDocumentProvider().getAnnotationModel(getEditor().getEditorInput());
  if (model instanceof AbstractMarkerAnnotationModel) {
    setModel((AbstractMarkerAnnotationModel)model);
  }
  int markerLine=getRulerInfo().getLineOfLastMouseButtonActivity();
  IResource rec=getResource(getEditor());
  try {
    IMarker[] markers=rec.findMarkers("String_Node_Str",true,IResource.DEPTH_INFINITE);
    for (int i=0; i < markers.length; i++) {
      System.out.println("String_Node_Str" + getDocument());
      System.out.println("String_Node_Str" + getModel());
      System.out.println("String_Node_Str" + getModel().getMarkerPosition(markers[i]));
      if (getModel().getMarkerPosition(markers[i]) == null)       continue;
      setLineNumber(getDocument().getLineOfOffset(getModel().getMarkerPosition(markers[i]).getOffset()));
      if (getLineNumber() == markerLine) {
        System.out.println("String_Node_Str");
        ArrayList links=getMarkerLinks();
        Iterator lit=links.iterator();
        while (lit.hasNext()) {
          System.out.println("String_Node_Str" + lit.next());
        }
        String[] list=getMarkerLabels(links);
        if ((list == null) || (list.length == 0)) {
          System.out.println("String_Node_Str");
        }
 else {
          IWorkbenchWindow window=SootPlugin.getDefault().getWorkbench().getActiveWorkbenchWindow().getActivePage().getWorkbenchWindow();
          if (window == null) {
            System.out.println("String_Node_Str");
          }
          PopupListSelector popup=new PopupListSelector(window.getShell());
          popup.setItems(list);
          if (getEditor() instanceof JimpleEditor) {
            int topIndex=((JimpleEditor)getEditor()).getViewer().getTopIndex();
            Rectangle rect=new Rectangle(400,(getLineNumber() + 1 - topIndex),650,45);
            popup.open(rect);
          }
 else {
            System.out.println(getEditor().getClass());
            System.out.println("String_Node_Str" + getModel().getMarkerPosition(markers[i]).getOffset());
            int pos=getModel().getMarkerPosition(markers[i]).getOffset();
            pos=pos / getLineNumber();
            Rectangle rect=new Rectangle(380,16,650,45);
            popup.open(rect);
          }
          handleSelection(popup.getSelected(),links);
        }
      }
    }
  }
 catch (  CoreException e) {
  }
catch (  BadLocationException e1) {
  }
}