PKU journal Task5

Plot of the mapping

We used the java library Graphics2D here and apart from some parsing, and preprocessing of the data, the plot is pretty much the following class. For the complete sourcecode please write to Sebastian.

<source lang="java"> package SNPMapping;

import java.awt.Color; import java.awt.Font; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.geom.RoundRectangle2D; import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.LinkedList; import javax.imageio.ImageIO;

/**

* Created on 09.06.2012, 15:03:25
* @author Sebastian Hollizeck <sebastian.hollizeck@campus.lmu.de>
*/

public class MapPainter {

   public static void paint(LinkedList<Residue> input,String output) throws IOException {
       int multi = 10;
       //get maximal residue position
       Residue last = input.peekLast();
       int max = last.getPosition();
       max *= multi;
       //drawing default picture;
       BufferedImage off_Image = new BufferedImage(900, max + 150, BufferedImage.TYPE_INT_ARGB);
       Graphics2D g2 = off_Image.createGraphics();
       g2.setBackground(Color.white);
       g2.setColor(Color.white);
       g2.fillRect(0, 0, max + 100, max + 150);
       RoundRectangle2D sequence = new RoundRectangle2D.Double(70, 100, 20, max, 10, 10);
       g2.setColor(Color.black);
       g2.draw(sequence);
       
       Font original = g2.getFont();
       //print caption
       Font caption = new Font("SanSerif",Font.BOLD,24);
       g2.setFont(caption);
       g2.drawString("SNP mapping for PAH",300,50);

       //revert font
       g2.setFont(original);

       for (Residue r : input) {
           int pos = r.getPosition();
           ArrayList<String> muts = r.getMutations();
           String effect = r.getEffect();
           int paintpos = 100 + pos * multi;
           if (pos % 10 == 0) {
               g2.drawString(pos + "", 40, paintpos);
           }
           if (muts == null&&effect==null) {
               //muts is only null if nothing but the position is in the file;
               continue;
           }

           g2.drawLine(70, paintpos, 140, paintpos);
           int offset = 75;
           int count = 1;
           for (String s : muts) {
               if (s.endsWith("*")) {
                   g2.setColor(Color.red);
               } else if (s.endsWith("+")) {
                   g2.setColor(Color.orange);
               } else if (s.endsWith("#")) {
                   g2.setColor(Color.green);
               }
               if (s.length() > 1) {
                   String mut = s.substring(0, s.length() - 1);
                   g2.drawString(mut, 90 + offset * count, paintpos);
                   count++;
               }
           }
           g2.setColor(Color.black);
           if (effect != null) {
               if (effect.equals("*")) {
                   g2.setColor(Color.red);
                   g2.drawString("conserved, probably disease effect", 90 + offset * 6, paintpos);
               } else if (effect.equals("+")) {
                   g2.setColor(Color.green);
                   g2.drawString("not conserved, little effect", 90 + offset * 6, paintpos);
               }
           }
           g2.setColor(Color.black);
       }

       File out = new File(output);
       ImageIO.write(off_Image, "png", out);
   }

}

</source>