Program: 17168
Project: 17168
Buggy source:
public StructureAlignmentJmol(AFPChain afpChain,Atom[] ca1,Atom[] ca2){
  jmolPanel=new JmolPanel();
  frame=new JFrame();
  JMenuBar menu=MenuCreator.initMenu(frame,this,afpChain);
  frame.setJMenuBar(menu);
  frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
  this.afpChain=afpChain;
  this.ca1=ca1;
  this.ca2=ca2;
  Container contentPane=frame.getContentPane();
  Box vBox=Box.createVerticalBox();
  jmolPanel.addMouseMotionListener(this);
  jmolPanel.addMouseListener(this);
  jmolPanel.setPreferredSize(new Dimension(500,500));
  vBox.add(jmolPanel);
  JTextField field=new JTextField();
  field.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  field.setText(COMMAND_LINE_HELP);
  RasmolCommandListener listener=new RasmolCommandListener(jmolPanel,field);
  field.addActionListener(listener);
  field.addMouseListener(listener);
  field.addKeyListener(listener);
  vBox.add(field);
  Box hBox=Box.createHorizontalBox();
  status=new JTextField();
  status.setBackground(Color.white);
  status.setEditable(false);
  status.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  hBox.add(status);
  text=new JTextField();
  text.setBackground(Color.white);
  text.setMaximumSize(new Dimension(220,30));
  text.setSize(new Dimension(220,30));
  text.setMinimumSize(new Dimension(220,30));
  text.setText("String_Node_Str");
  text.setEditable(false);
  hBox.add(text);
  vBox.add(hBox);
  contentPane.add(vBox);
  MyJmolStatusListener li=(MyJmolStatusListener)jmolPanel.getStatusListener();
  li.setTextField(status);
  frame.pack();
  frame.setVisible(true);
  initCoords();
  resetDisplay();
}

Fixed version (ground truth):
public StructureAlignmentJmol(AFPChain afpChain,Atom[] ca1,Atom[] ca2){
  jmolPanel=new JmolPanel();
  frame=new JFrame();
  JMenuBar menu=MenuCreator.initMenu(frame,this,afpChain);
  frame.setJMenuBar(menu);
  frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
  this.afpChain=afpChain;
  this.ca1=ca1;
  this.ca2=ca2;
  Container contentPane=frame.getContentPane();
  Box vBox=Box.createVerticalBox();
  jmolPanel.addMouseMotionListener(this);
  jmolPanel.addMouseListener(this);
  jmolPanel.setPreferredSize(new Dimension(500,500));
  vBox.add(jmolPanel);
  JTextField field=new JTextField();
  field.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  field.setText(COMMAND_LINE_HELP);
  RasmolCommandListener listener=new RasmolCommandListener(jmolPanel,field);
  field.addActionListener(listener);
  field.addMouseListener(listener);
  field.addKeyListener(listener);
  vBox.add(field);
  Box hBox=Box.createHorizontalBox();
  status=new JTextField();
  status.setBackground(Color.white);
  status.setEditable(false);
  status.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  hBox.add(status);
  text=new JTextField();
  text.setBackground(Color.white);
  text.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
  text.setText("String_Node_Str");
  text.setEditable(false);
  hBox.add(text);
  vBox.add(hBox);
  contentPane.add(vBox);
  MyJmolStatusListener li=(MyJmolStatusListener)jmolPanel.getStatusListener();
  li.setTextField(status);
  frame.pack();
  frame.setVisible(true);
  initCoords();
  resetDisplay();
}