graph problem? in bioinformatics
Hi All,
I am a student of bioinformatics and i want to plot aminoAcid Sequence according to it's hydrophobicity values..
Alanine (A)1.8
Arginine (R) -4.5
Asparagine ( N)-3.5
Aspartic acid (D)-3.5
Cysteine (C)2.5
Glutamine (Q)-3.5
Glutamic acid(E)-3.5
Glycine(G)-0.4
Histidine(H)-3.2
Isoleucine (I) 4.5
Leucine (L)3.8
Lysine (K)-3.9
Methionine(M)1.9
Phenylalanine(F)2.8
Proline (P)-1.6
Serine (S)-0.8
Threonine(T)-0.7
Tryptophan (W)-0.9
Tyrosine (Y) -1.3
Valine(V)4.2
My sequence is for example:AITHYSTRAGETNMVAFSRDEA...
I want to plot this sequence or any other sequence like this on a graph to show it's hydrophobicity values...I tried and my code is as follows:
/*
* HydrophobicityViewer.java
*
* Created on December 16, 2006, 10:05 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package myapplics;
import java.awt.geom.Point2D;
import javax.swing.*;
import biomolecule.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JLabel;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JTextField;
import java.awt.GridLayout;
import java.awt.geom.Line2D;
import java.util.*;
import java.lang.Float;
import java.io.*;
public class HydrophobicityViewer extends JFrame implements ActionListener{
JButton plot=new JButton("PLOT");
JTextArea Sequence=new JTextArea(10,30);
JScrollPane scroll=new JScrollPane(Sequence,ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
private Object action;
/** Creates a new instance of HydrophobicityViewer */
public HydrophobicityViewer() {
super("Hydrophobicity Frame");
setSize(600,800);
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
plot.addActionListener(this);
JPanel pane=new JPanel();
JLabel SequenceLabel=new JLabel("Sequence");
RectangleComponent component = new RectangleComponent();
setLayout(new BorderLayout());
Sequence.setLineWrap(true);
Sequence.setWrapStyleWord(true);
pane.add(SequenceLabel);
pane.add(Sequence);
pane.add(scroll);
pane.add(plot);
add(pane,BorderLayout.NORTH);
add(component,BorderLayout.CENTER);
setVisible(true);
}
public void actionPerformed(ActionEvent evt)
{
Object source=evt.getSource();
if (source==plot)
{
}
repaint();
}
public static void main(String []args)
{
HydrophobicityViewer hydro=new HydrophobicityViewer();
}
}
/*
* RectangleComponent.java
*
* Created on December 16, 2006, 10:11 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package biomolecule;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Color;
import java.awt.Rectangle;
import java.awt.geom.Line2D;
import javax.swing.JPanel;
import javax.swing.JComponent;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.*;
/**
*
* @author rupesh
*/
public class RectangleComponent extends JComponent{
/** Creates a new instance of RectangleComponent */
protected String seq="aminoacid";
int x1,y1,x2,y2=0;
public RectangleComponent() {
}
public int length(){
int len=0;
len=seq.length();
return len;
}
public void paintComponent(Graphics g)
{
Graphics2D g2=(Graphics2D)g;
Rectangle box=new Rectangle(100,200,400,35);
g2.draw(box);
g2.setColor(Color.BLACK);
g2.draw(box);
g2.drawString("4.0",100,200);
Rectangle box1=new Rectangle(100,235,400,35);
g2.draw(box1);
g2.setColor(Color.BLACK);
g2.draw(box1);
g2.drawString("3.0",100,235);
Rectangle box2=new Rectangle(100,270,400,35);
g2.draw(box2);
g2.setColor(Color.BLACK);
g2.draw(box2);
g2.drawString("2.0",100,270);
Rectangle box3=new Rectangle(100,305,400,35);
g2.draw(box3);
g2.setColor(Color.BLACK);
g2.draw(box3);
g2.drawString("1.0",100,305);
Rectangle box4=new Rectangle(100,340,400,35);
g2.draw(box4);
g2.setColor(Color.BLACK);
g2.draw(box4);
g2.drawString("0.0",100,340);
Rectangle box5=new Rectangle(100,375,400,35);
g2.draw(box5);
g2.setColor(Color.BLACK);
g2.draw(box5);
g2.drawString("-1.0",100,375);
Rectangle box6=new Rectangle(100,410,400,35);
g2.draw(box6);
g2.setColor(Color.BLACK);
g2.draw(box6);
g2.drawString("-2.0",100,410);
Rectangle box7=new Rectangle(100,445,400,35);
g2.draw(box7);
g2.setColor(Color.BLACK);
g2.draw(box7);
g2.drawString("-3.0",100,445);
g2.drawString("-4.0",100,470);
}
}
I am not able to imagine anything more than this.....Also i am totally new to Java itself and it's a tall order for me to solve this..So i need some help...Assignments,Assignments!!!!!!!!
Rupesh...
