code: @Override
  	public void actionPerformed(ActionEvent evt) {
  
  		//System.out.println("stopping!");
  		logStatus("terminating");
  		logStatus(" Total alignments processed: " + alignmentsProcessed);
  		stopButton.setEnabled(false);
  		setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
  		progressBar.setIndeterminate(true);
  		progressBar.setStringPainted(false);
  		System.out.println("terminating jobs");
  
  		farmJob.terminate();
  
  		setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
  		progressBar.setIndeterminate(false);
  
  	}
docs: Invoked when the user presses the stop button.