Program: 46796
Project: 46796
Buggy source:
/** 
 * Set the main sequence area to the give string
 * @param newSequence
 */
public void setSequence(NucSeq newSequence){
  int actionChoice;
  String currentText=((SequenceViewGUI)_sequenceview).get_TextArea().getText();
  if ((currentText == null) || (currentText.equalsIgnoreCase("String_Node_Str"))) {
    actionChoice=0;
  }
 else {
    String[] options={"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"};
    actionChoice=javax.swing.JOptionPane.showOptionDialog(new JFrame(),"String_Node_Str","String_Node_Str",javax.swing.JOptionPane.YES_NO_CANCEL_OPTION,javax.swing.JOptionPane.QUESTION_MESSAGE,null,options,options[0]);
  }
  if (!this.checkValidSequence(newSequence.toString(),this.getDegeneracy())) {
    String[] choices={"String_Node_Str","String_Node_Str"};
    int getChoice=javax.swing.JOptionPane.showOptionDialog(new JFrame(),"String_Node_Str","String_Node_Str",javax.swing.JOptionPane.YES_NO_CANCEL_OPTION,javax.swing.JOptionPane.QUESTION_MESSAGE,null,choices,choices[1]);
    if (getChoice == 1) {
      return;
    }
  }
  if (actionChoice == 0) {
    ((SequenceViewGUI)_sequenceview).get_TextArea().setText(newSequence.toString());
  }
 else   if (actionChoice == 1) {
    ((SequenceViewGUI)_sequenceview).get_TextArea().replaceSelection(newSequence.toString());
  }
 else   if (actionChoice == 2) {
    ((SequenceViewGUI)_sequenceview).get_TextArea().setText(((SequenceViewGUI)_sequenceview).get_TextArea().getText() + newSequence);
  }
 else   if (actionChoice == 3) {
    return;
  }
  _sequence=newSequence;
  _sequenceview.setVisible(true);
}

Fixed version (ground truth):
/** 
 * Set the main sequence area to the give string
 * @param newSequence
 */
public void setSequence(NucSeq newSequence){
  int actionChoice;
  String currentText=((SequenceViewGUI)_sequenceview).get_TextArea().getText();
  if ((currentText == null) || (currentText.equalsIgnoreCase("String_Node_Str"))) {
    actionChoice=0;
  }
 else {
    String[] options={"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"};
    actionChoice=javax.swing.JOptionPane.showOptionDialog(new JFrame(),"String_Node_Str","String_Node_Str",javax.swing.JOptionPane.YES_NO_CANCEL_OPTION,javax.swing.JOptionPane.QUESTION_MESSAGE,null,options,options[0]);
  }
  if (!this.checkValidSequence(newSequence.toString(),this.getDegeneracy())) {
    String[] choices={"String_Node_Str","String_Node_Str"};
    int getChoice=javax.swing.JOptionPane.showOptionDialog(new JFrame(),"String_Node_Str","String_Node_Str",javax.swing.JOptionPane.YES_NO_CANCEL_OPTION,javax.swing.JOptionPane.QUESTION_MESSAGE,null,choices,choices[1]);
    if (getChoice == 1) {
      return;
    }
  }
  if (actionChoice == 0) {
    ((SequenceViewGUI)_sequenceview).get_TextArea().setText(newSequence.toString());
  }
 else   if (actionChoice == 1) {
    ((SequenceViewGUI)_sequenceview).get_TextArea().replaceSelection(newSequence.toString());
  }
 else   if (actionChoice == 2) {
    ((SequenceViewGUI)_sequenceview).get_TextArea().setText(((SequenceViewGUI)_sequenceview).get_TextArea().getText() + newSequence);
  }
 else   if (actionChoice == 3) {
    return;
  }
  _sequence=newSequence;
}