[BHCluster]

I have a little problem at the moment what I am trying to do is plot a graph from two sequences and plot it onto the jPanel but I can't. I have the gui done and the link to a certain file but can't make sense out of it if somebody knows how to do this please help.

The two sequences should look like this
A B C D E F G .....Z
A
B
C
D
E
F
G
.
.
.
.
.
Z

An the inputs are going to be letters in stead of numbers so every time the program encounters the same letter on both axis it will put a line like the photo shows.



File 1
File 2
File 3

and here is my Gui code

Code:

/****************************************************************/
/*                      DotPlot	                            */
/*                                                              */
/****************************************************************/
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
/**
 * Summary description for DotPlot
 *
 */
public class DotPlot extends JFrame
{
	// Variables declaration
	private JLabel jLabel1;
	private JLabel jLabel2;
	private JLabel jLabel3;
	private JTextArea jTextArea1;
	private JScrollPane jScrollPane1;
	private JTextArea jTextArea2;
	private JScrollPane jScrollPane2;
	private JButton jButton1;
	private JPanel contentPane;
	//-----
	private JPanel jPanel1;
	//-----
	// End of variables declaration


	public DotPlot()
	{
		super();
		initializeComponent();
		//
		// Add any constructor code after initializeComponent call
		//

		this.setVisible(true);
	}

	/**
	 * This method is called from within the constructor to initialize the form.
	 */
	private void initializeComponent()
	{
		jLabel1 = new JLabel();
		jLabel2 = new JLabel();
		jLabel3 = new JLabel();
		jTextArea1 = new JTextArea();
		jScrollPane1 = new JScrollPane();
		jTextArea2 = new JTextArea();
		jScrollPane2 = new JScrollPane();
		jButton1 = new JButton();
		contentPane = (JPanel)this.getContentPane();
		//-----
		jPanel1 = new JPanel();
		//-----

		//
		// jLabel1
		//
		jLabel1.setBackground(new Color(105, 188, 246));
		jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
		jLabel1.setHorizontalTextPosition(SwingConstants.CENTER);
		jLabel1.setOpaque(true);
		jLabel1.setText("FASTA Sequences File 1 ");
		//
		// jLabel2
		//
		jLabel2.setBackground(new Color(105, 188, 246));
		jLabel2.setHorizontalAlignment(SwingConstants.CENTER);
		jLabel2.setHorizontalTextPosition(SwingConstants.CENTER);
		jLabel2.setOpaque(true);
		jLabel2.setText("FASTA Sequences File 2 ");
		//
		// jLabel3
		//
		jLabel3.setBackground(new Color(105, 188, 246));
		jLabel3.setHorizontalAlignment(SwingConstants.CENTER);
		jLabel3.setOpaque(true);
		jLabel3.setText("Dot-Plot Graph");
		//
		// jTextArea1
		//
		jTextArea1.setWrapStyleWord(true);
		//
		// jScrollPane1
		//
		jScrollPane1.setViewportView(jTextArea1);
		//
		// jTextArea2
		//
		jTextArea2.setLineWrap(true);
		//
		// jScrollPane2
		//
		jScrollPane2.setViewportView(jTextArea2);
		//
		// jButton1
		//
		jButton1.setText("Plot the Sequance");
		jButton1.addActionListener(new ActionListener() {
			public void actionPerformed(ActionEvent e)
			{
				jButton1_actionPerformed(e);
			}

		});
		//
		// contentPane
		//
		contentPane.setLayout(null);
		addComponent(contentPane, jLabel1, 19,10,249,18);
		addComponent(contentPane, jLabel2, 18,229,249,18);
		addComponent(contentPane, jLabel3, 284,11,500,18);
		addComponent(contentPane, jScrollPane1, 18,29,250,160);
		addComponent(contentPane, jScrollPane2, 18,247,250,160);
		addComponent(contentPane, jButton1, 658,422,127,28);
		addComponent(contentPane, jPanel1, 284,30,500,379);
		//
		// jPanel1
		//
		jPanel1.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5));
		jPanel1.setBorder(BorderFactory.createLineBorder(Color.blue));
		//
		// DotPlot
		//
		this.setTitle("DotPlot");
		this.setLocation(new Point(0, 0));
		this.setSize(new Dimension(800, 486));
		this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
	}


	private void addComponent(Container container,Component c,int x,int y,int width,int height)
	{
		c.setBounds(x,y,width,height);
		container.add(c);
	}

	//
	// Add any appropriate code in the following Event Handling Methods
	//
	private void jButton1_actionPerformed(ActionEvent e)
	{
		System.out.println("\njButton1_actionPerformed(ActionEvent e) called.");
		// Add any handling code here

	}

	//
	// Add any method code to meet your needs in the following area
	//


	public static void main(String[] args)
	{
		JFrame.setDefaultLookAndFeelDecorated(true);
		JDialog.setDefaultLookAndFeelDecorated(true);
		try
		{
			UIManager.setLookAndFeel("com.sun.java.swing.plaf.windows.WindowsLookAndFeel");
		}
		catch (Exception ex)
		{
			System.out.println("Failed loading L&F: ");
			System.out.println(ex);
		}
		new DotPlot();
	}

}

Your help is appreciated