Program: 13655
Project: 13655
Buggy source:
public boolean openFile(){
  statusPanel.progressUpdated("String_Node_Str",0,100);
  JFileChooser chooser;
  if (lastUsedDir == null) {
    chooser=new JFileChooser();
  }
 else {
    chooser=new JFileChooser(lastUsedDir);
  }
  chooser.setMultiSelectionEnabled(true);
  BAMFileFilter bff=new BAMFileFilter();
  chooser.removeChoosableFileFilter(chooser.getFileFilter());
  chooser.addChoosableFileFilter(bff);
  chooser.setFileFilter(bff);
  int result=chooser.showOpenDialog(this);
  if (result == JFileChooser.CANCEL_OPTION)   return false;
  FileFilter chosenFilter=chooser.getFileFilter();
  if (chosenFilter instanceof BAMFileFilter) {
    System.setProperty("String_Node_Str","String_Node_Str");
  }
  if (fileTabs.getTabCount() == 0) {
    getContentPane().remove(welcomePanel);
    getContentPane().add(fileTabs,BorderLayout.CENTER);
    validate();
    repaint();
  }
  File[] files=chooser.getSelectedFiles();
  for (int i=0; i < files.length; i++) {
    lastUsedDir=files[i].getParentFile();
    SequenceFile sequenceFile;
    try {
      sequenceFile=SequenceFactory.getSequenceFile(files[i]);
    }
 catch (    SequenceFormatException e) {
      JPanel errorPanel=new JPanel();
      errorPanel.setLayout(new BorderLayout());
      errorPanel.add(new JLabel("String_Node_Str" + e.getLocalizedMessage(),JLabel.CENTER),BorderLayout.CENTER);
      fileTabs.addTab(files[i].getName(),errorPanel);
      log.error(e,e);
      continue;
    }
catch (    IOException e) {
      log.error("String_Node_Str",e);
      JOptionPane.showMessageDialog(this,"String_Node_Str" + e.getLocalizedMessage(),"String_Node_Str",JOptionPane.ERROR_MESSAGE);
      continue;
    }
    AnalysisRunner runner=new AnalysisRunner(sequenceFile);
    ResultsPanel rp=new ResultsPanel(sequenceFile);
    runner.addProgressListener(rp);
    runner.addAnalysisListener(rp);
    fileTabs.addTab(sequenceFile.name(),rp);
    QCModule[] moduleList=ModuleFactory.getStandardModuleList();
    runner.startAnalysis(moduleList);
  }
  return true;
}

Fixed version (ground truth):
public boolean openFile(){
  statusPanel.progressUpdated("String_Node_Str",0,100);
  JFileChooser chooser;
  if (lastUsedDir == null) {
    chooser=new JFileChooser();
  }
 else {
    chooser=new JFileChooser(lastUsedDir);
  }
  chooser.setMultiSelectionEnabled(true);
  BAMFileFilter bff=new BAMFileFilter();
  chooser.removeChoosableFileFilter(chooser.getFileFilter());
  chooser.addChoosableFileFilter(bff);
  chooser.setFileFilter(bff);
  int result=chooser.showOpenDialog(this);
  if (result == JFileChooser.CANCEL_OPTION)   return false;
  FileFilter chosenFilter=chooser.getFileFilter();
  if (chosenFilter instanceof BAMFileFilter) {
    System.setProperty("String_Node_Str","String_Node_Str");
  }
  if (fileTabs.getTabCount() == 0) {
    getContentPane().remove(welcomePanel);
    getContentPane().add(fileTabs,BorderLayout.CENTER);
    validate();
    repaint();
  }
  File[] files=chooser.getSelectedFiles();
  for (int i=0; i < files.length; i++) {
    lastUsedDir=files[i].getParentFile();
    SequenceFile sequenceFile;
    try {
      sequenceFile=SequenceFactory.getSequenceFile(files[i]);
      AnalysisRunner runner=new AnalysisRunner(sequenceFile);
      ResultsPanel rp=new ResultsPanel(sequenceFile);
      runner.addProgressListener(rp);
      runner.addAnalysisListener(rp);
      fileTabs.addTab(sequenceFile.name(),rp);
      QCModule[] moduleList=ModuleFactory.getStandardModuleList();
      runner.startAnalysis(moduleList);
    }
 catch (    SequenceFormatException e) {
      JPanel errorPanel=new JPanel();
      errorPanel.setLayout(new BorderLayout());
      errorPanel.add(new JLabel("String_Node_Str" + e.getLocalizedMessage(),JLabel.CENTER),BorderLayout.CENTER);
      fileTabs.addTab(files[i].getName(),errorPanel);
      log.error(e,e);
      continue;
    }
catch (    IOException e) {
      log.error("String_Node_Str" + files[i].getAbsolutePath() + "String_Node_Str",e);
      JOptionPane.showMessageDialog(this,"String_Node_Str" + e.getLocalizedMessage(),"String_Node_Str",JOptionPane.ERROR_MESSAGE);
      continue;
    }
catch (    Exception e) {
      log.error("String_Node_Str" + files[i].getAbsolutePath(),e);
      JOptionPane.showMessageDialog(this,"String_Node_Str" + e.getLocalizedMessage(),"String_Node_Str",JOptionPane.ERROR_MESSAGE);
      continue;
    }
  }
  return true;
}