Need Help for Dot Plot Graph

[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

/****************************************************************/
/*                      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

[CaptainMorgan]

From your file list, can you post here separately, lines 65 and 71 of DotPlot.java; and lines 98, 129, 168, 184, 220, and 257 of DotPlotUI.java. It appears the above lines have been cut short by the maximum page width. :(

Can you elaborate more on your GUI code.. for example, why do you have your GUI code which named after DotPlot.java, and yet you link to a complete DotPlot.java file?

[BHCluster]

Thanks for taking interest in this but I have found this online with the code like it is that's why I don't know how to do it and that's why I am so desperate for this if you know any way around this I would appreciate it.

[CaptainMorgan]

BH, actually.... what I did was complete those lines that were cut off saying (floa with: (float)10;

Those lines that were cut off with strings I just closed the string and then it all compiled and ran. The GUI runs but it requires a "Fasta" file type which I don't have and I assume you'll need to open a graph.

Best of luck. :)

[CaptainMorgan]

As requested:

GraphPane

/** 
 *  File:         GraphPane.java
 *  Created:      Apr 10, 2008, at 10:54:12 PM
 *
 *  Description:  See the comments before the class below. 
 */

import java.awt.*;
import javax.swing.*;
import java.util.*;
import java.io.*;

/* This class extends teh JPanel class and is
 * used primarily to contain the Graphical dot-plot
 */
class GraphPane extends JPanel {
  /* These are the attributes required for this class.
  * Their primary purpose is to fit the graph to the
  * panel.
  */
  int scaleWidth = 600;
  int scaleHeight = 600;
  final int PAD = 20;
  Image scaledImage;
  DotPlot dp;
  String sequence_1 = "";
  String sequence_2 = "";
  int window;
  int threshold;
  /* This is the sole constructor for GraphPane. The
  * class is populted from these initial parameters.
  *
  */
  public GraphPane(String sequence_1, String sequence_2, int window, int threshold)
  {
    this.window = window;
    this.threshold = threshold;
    this.sequence_1 = sequence_1;
    this.sequence_2 = sequence_2;
  }
  // Paints the graph to a panel
  public void paint(Graphics g)
  {
    DotPlot dp = new DotPlot();
    dp = new DotPlot();
    dp.readInGenome(this.sequence_1,this.sequence_2,this.window,this.threshold);
    dp.setDimensions();
    Panel panel = new Panel();
    panel.setBackground(new Color(235,235,235));
    add(panel);
    g.setColor(Color.red);
    dp.draw(panel);
    scaledImage = dp.img.getScaledInstance(scaleWidth,scaleHeight,0);
    g.drawImage(scaledImage,0,0,panel);
  }
}

DotPlotUI

/** 
 *  File:         DotPlotUI.java
 *  Created:      Apr 10, 2008, at 10:52:47 PM
 *
 *  Description:  See the comments before the class below. 
 */

import java.awt.*;
import javax.swing.*;
import java.util.*;
import java.io.*;
import java.awt.event.*;

/* This is the main driver for the Dot-Plot program.
 * Compilation: javac DotPlotUI.java
 * Usage:        java DotPlotUI
 *
 */
public class DotPlotUI implements ActionListener
{
  // the following are the components used to make
  // up the application UI
  GraphPane graphPane;
  JTabbedPane tabbedPane;
  TextField tfDirectory = new TextField();
  TextField tfFile = new TextField();
  TextField tfFilter = new TextField();
  FileDialog fd;
  JFrame f;
  final JButton button1;
  final JButton button2;
  final JButton button3;
  TextArea textArea1;
  TextArea textArea2;
  JLabel window_label;
  JTextField window;
  JLabel threshold_label;
  JTextField threshold;
  TextArea status;
  JLabel status_label;
  JPanel pre_plot;
     
  /* The is the sole constructionfor the DotPlotUI
  * In this constructor all the components are added
  * sequentially/
  */
  public DotPlotUI()
  {
    f = new JFrame("Dot-plot Comparative Sequence Analysis");
    f.getContentPane().setLayout(null);
    f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    GraphicsEnvironment env = GraphicsEnvironment.getLocalGraphicsEnvironment();
    Rectangle bounds = env.getMaximumWindowBounds();
    button1 = new JButton("Fasta File 1");
    button2 = new JButton("Fasta File 2");
    button3 = new JButton("Create Dot-plot");
    textArea1 = new TextArea("Fasta File 1", 10,10,TextArea.SCROLLBARS_NONE);
    textArea2 = new TextArea("Fasta File 2", 10,10,TextArea.SCROLLBARS_NONE);
    status = new TextArea("", 10,bounds.width,TextArea.SCROLLBARS_VERTICAL_ONLY);
    status.setEditable(false);
    window_label = new JLabel("Windows Size");
    window = new JTextField(10);
    threshold_label = new JLabel("Threshold Size");
    threshold = new JTextField(10);
    status_label = new JLabel("Process Status/Error Info");
    pre_plot = new JPanel();
    pre_plot.setBackground(new Color(235,235,235));
    f.getContentPane().add(textArea1);
    f.getContentPane().add(button1);
    f.getContentPane().add(textArea2);
    f.getContentPane().add(button2);
    f.getContentPane().add(window_label);
    f.getContentPane().add(window);
    f.getContentPane().add(threshold_label);
    f.getContentPane().add(threshold);
    f.getContentPane().add(button3);
    f.getContentPane().add(status);
    f.getContentPane().add(status_label);
    f.getContentPane().add(pre_plot);
    button1.addActionListener(this);
    button2.addActionListener(this);
    window.addActionListener(this);
    threshold.addActionListener(this);
    button3.addActionListener(this);
    textArea1.setBounds(10,10,182,150);
    Dimension size = button1.getPreferredSize();
    button1.setBounds(10,170,size.width,size.height);
    textArea2.setBounds(10,180+size.height,182,150);
    size = button1.getPreferredSize();
    button2.setBounds(10,340+size.height,size.width,size.height);
    size = threshold_label.getPreferredSize();
    window_label.setBounds(10,420+size.height,size.width,size.height );
    window.setBounds(10+size.width+10,420+size.height,size.width,size.height );
    threshold_label.setBounds(10,445+size.height,size.width,size.height );
    threshold.setBounds(10+size.width+10,445+size.height,size.width,size.height );
    size = button3.getPreferredSize();
    button3.setBounds(10,485+size.height,size.width+5,size.height+5);
    button3.setBackground(new Color(153,153,153));
    size = status_label.getPreferredSize();
    //status_label.setBounds((int)((bounds.width/2)-(size.width/2)),bounds.height-115,size);
    status.setBounds(10,bounds.height-100,bounds.width-30,65);
    status.setBackground(new Color(255,255,204));
    status.setForeground(Color.red);
    pre_plot.setBounds(300,10, 600, 600);
    f.setSize((int)bounds.getWidth(),(int)bounds.getHeight());
    f.setLocation(0,0);
    f.setVisible(true);
  }
  
  /* This handles all action events to the Application UI.
  * It poulates the Fasta File TextFields, and ultimatley
  * produces the dot-plot.
  */
  public void actionPerformed(ActionEvent evt)
  {
    // load the first fasta file
    if ((evt.getActionCommand()).equals("Fasta File 1")) {
      fd = new FileDialog(f, null, FileDialog.LOAD);
      fd.setDirectory(".\\");
    }
    // load the second fasta file
    else if ((evt.getActionCommand()).equals("Fasta File 2"))
    {
      fd = new FileDialog(f, null, FileDialog.LOAD);
      fd.setDirectory(".\\");
    }
    // display the dot-plot of the previously loaded data
    else if ((evt.getActionCommand()).equals("Create Dot-plot"))
    {
      graphPane = new GraphPane(textArea1.getText(),textArea2.getText(),getWindow(),getWindow());
      f.getContentPane().add(graphPane);
      graphPane.setBounds(300,10, 600, 600);
      // display program status
      status.append("Info: Dot-plot sequence analysis diagram created!");
    }
    // Populate textArea_1 with sequences
    if ((evt.getActionCommand()).equals("Fasta File 1"))
    {
      fd.show();
      String sequence = this.readFile(fd.getDirectory()+fd.getFile());
      textArea1.replaceRange(sequence,0,textArea1.getText().length());
      // display program status
      status.append("Info: Fast File 1 sequence data loaded, " + sequence.length()
        + " characters in length.\n");
    }
    // Populate textArea_2 with sequences
    else if((evt.getActionCommand()).equals("Fasta File 2"))
    {
      fd.show();
      String sequence = this.readFile(fd.getDirectory()+fd.getFile());
      textArea2.replaceRange(sequence,0,textArea2.getText().length());
      // display program status
      status.append("Info: Fast File 2 sequence data loaded, " + sequence.length()
        +" characters in length.\n");
    }
  }
  
  /* This method is used to collect the window size in the
  * text-fields. If they are empty or erroneous a default value
  * of 100 is chosen, and a warning message outputted.
  */
  public int getWindow()
  {
    String win_val = window.getText();
    if(win_val.equals("") || win_val == null)
    {
      status.append("Warning: No window size selected, using default window size of 10");
      return 100;
    }
    win_val.trim();
    boolean is_number = true;
    for(int i=0; i<win_val.length(); i++)
    {
      if(Character.isDigit(win_val.charAt(i)) == false)
      {
        is_number = false;
        break;
      }
    }
    if(is_number == false)
    {
      status.append("Error: The chosen window size is not a number, using default windoow");
      return 100;
    }
    else
    {
      status.append("Info: Window size set at: " + win_val + ".\n");
      return Integer.parseInt(win_val);
    }
  }
  
  /* This method is used to collect the threshold size in the
  * text-fields. If they are empty or erroneous a default value
  * of 100 is chosen, and a warning message outputted.
  */
  public int getThreshold()
  {
    String thres_val = window.getText();
    if(thres_val.equals("") || thres_val == null)
    {
      status.append("Warning: No threshold size selected, using default threshold size");
      return 100;
    }
    thres_val.trim();
    boolean is_number = true;
    for(int i=0; i<thres_val.length(); i++)
    {
      if(Character.isDigit(thres_val.charAt(i)) == false)
      {
        is_number = false;
        break;
      }
    }
    if(is_number == false)
    {
      status.append("Error: The chosen threshold size is not a number, using default th?");
      return 100;
    }
    else
    {
      status.append("Info: Threshold size set at: " + thres_val + ".\n");
      return Integer.parseInt(thres_val);
    }
  }
  
  /* This method reads the genomic sequences from the file
  * passed in the argument. The file must be of FASTA formatting.
  */
  public String readFile(String file)
  {
    BufferedReader inFile = null;
    String sequence = "";
    try{
      inFile = new BufferedReader(new FileReader(file));
      String str = null;
      while((str = inFile.readLine()) != null)
      {
        if(!str.equals(""))
        {
          if(str.substring(0,1).equals(">"))
          {
            while((str = inFile.readLine()) != null && !str.equals(""))
              sequence = sequence.concat(str);
          }
        }
      }
    }
    catch (IOException e)
    {
      System.out.println("INPUT ERROR: Input file not recognized at DotPlotUI.readFile");
      System.exit(1);
    }
    return sequence;
  }
  
  public static void main(String[] args)
  {
    new DotPlotUI();
  }
}

DotPlot

/** 
 *  File:         DotPlot.java
 *  Created:      Apr 10, 2008, at 10:51:43 PM
 *
 *  Description:  See the comments before the class below. 
 */

import  java.awt.*;
import  javax.swing.*;
import  java.util.*;
import  java.io.*;

/* Class DotPlot works out the technical aspects of the graph
 * by computing the thresholds, window size and where sequences match.
 * It is also responsible for drawing the points of the Dot-plot.
 */
class DotPlot
{
  // Required attibutes including the Image to be displayed,seq_1, seq_2
  // window and threshold vlaues
  Image img;
  String seq1 = null;
  String seq2 = null;
  int windowSize = 0;
  int threshold = 0;
  Vector vecPoints = new Vector();
  int index = 0;
  int noOfCoors = 0;
  int imageWidth = 1000;
  int imageHeight = 1000;
  int scale = 1000;
  // Initialise the classes attributes
  public void readInGenome(String seq1, String seq2, int windowSize, int threshold)
  {
    this.windowSize = windowSize;
    this.threshold = threshold;
    this.seq1 = seq1;
    this.seq2 = seq2;
  }
  
  /* Sets up the dimensions for the to be
  * displayed image depending on whether the sequence
  * is longer, shoter or equla to the default image dimensions
  */
  public void setDimensions()
  {
    if(seq1.length() == seq2.length())//Both seqs same length
    {
      if(seq1.length() > scale)//Both greater than scale
      {
        imageWidth = scale;
        imageHeight = scale;
      }
      else//Both less than scale
      {
        imageWidth = seq1.length();
        imageHeight = seq2.length();
      }
    }
    else//Different sized seqs
    {
      if(seq1.length() < scale && seq2.length() < scale)//seq_1 = seq_2
      {
        imageWidth = seq1.length();
        imageHeight = seq2.length();
      }
      else if(seq1.length() > seq2.length())//seq_1 > seq_2
      {
        imageWidth = scale;
        float fHeight = (float) ( (float)seq2.length()/(float)seq1.length() ) * (float)10;
        imageHeight = (int) fHeight;
      }
      else if(seq2.length() > seq1.length())//seq_2 > seq_1
      {
        imageHeight = scale;
        float fWidth = (float) ( (float)seq1.length()/(float)seq2.length() ) * (float)10;
        imageWidth = (int) fWidth;
      }
    }
  }
  
  /* Calculates if the sequential seegment starting
   * at 'a' and ending at 'b' meeets the current
   * threshold
   */
  public boolean satisfiesThreshold(int a, int b)
  {
    int outCount = 0;
    int matchCount = 0;
    for(int d=1; d<=windowSize; d++)
    {
      if(inBounds(a-d,b-d))
      {
        if(isMatch(a-d,b-d))
          matchCount++;
      }
      else
        outCount++;
      if(inBounds(a+d,b+d))
      {
        if(isMatch(a+d,b+d))
          matchCount++;
      }
      else
        outCount++;
      }
      if(matchCount >= threshold)
        return true;
      else
        return false;
  }
  
  /* Check if the base indexes match
  * True or False is returned.
  */
  public boolean isMatch(int a, int b)
  {
    String base1 = seq1.substring(a,a+1);
    String base2 = seq2.substring(b,b+1);
    if(base1.equals(base2))
      return true;
    else return false;
  }
  
  /* This makes sure we don't run over bounds with our
  * windowing.
  * True or False is returned.
  */
  public boolean inBounds(int a, int b)
  {
    if(a < 0 || b < 0 || a > seq1.length()-1 || b > seq2.length()-1)
      return false;
    else return true;
  }
  
  /* Uses java.Grphics to draw the points
  * tothe screen using the fore-mentioned
  * integers a and b
  */
  public void drawPoint(int a, int b, Graphics g)
  {
    int xcoor = 0;
    int ycoor = 0;
    if(seq1.length() > imageWidth)
    {
      float xx = (float) ( (float)a/(float)seq1.length() * (float)imageWidth );
      xcoor = (int) xx;
    }
    else
      xcoor = a;
    if(seq2.length() > imageHeight)
    {
      float yy = (float) ( (float)b/(float)seq2.length() * (float)imageHeight );
      ycoor = (int)yy;
    }
    else
      ycoor = b;
    g.drawLine(xcoor,ycoor,xcoor,ycoor);
  }
  
  /* Uses java.Graphics to set the points
  * for the Gragh. this is somewhat of a culmination
  * of methods.
  */
  public void setUpPoints(Graphics g)
  {
    String base1 = null;
    String base2 = null;
    for(int i=0; i<seq1.length(); i++)
    {
      for(int j=0; j<seq2.length(); j++)
      {
        base1 = seq1.substring(i,i+1);
        base2 = seq2.substring(j,j+1);
        if(base1.equals(base2))
        {
          if(satisfiesThreshold(i,j))
            drawPoint(i,j,g);
        }
      }
    }
  }

  public void draw(Component c)
  {
    img = c.createImage(imageWidth,imageHeight);
    Graphics g = img.getGraphics();
    g.setColor(new Color(38,0,133));
    setUpPoints(g);
  }
}

[BHCluster]

Thanks alot man.