CpGPainter.java

package org.seqcode.projects.seqview.paintable;

import java.awt.*;
import java.util.*;

import org.seqcode.genome.location.Region;
import org.seqcode.gseutils.*;
import org.seqcode.projects.seqview.model.RegionMapperModel;


public class CpGPainter extends RegionPaintable {

    private RegionMapperModel<String> model;
    private CpGProperties props;
    
    public CpGPainter(RegionMapperModel<String> model) {
        super();
        this.model = model;
        props = new CpGProperties();
        model.addEventListener(this);
    }
    
    public void cleanup() { 
        super.cleanup();
        model.removeEventListener(this);
    }

    public CpGProperties getProperties() {
        return props;
    }

    public void removeEventListener(Listener<EventObject> l) {
        super.removeEventListener(l);
        if (!hasListeners()) {
            model.removeEventListener(this);
        }
    }

    public synchronized void eventRegistered(EventObject e) {
        if (e.getSource() == model &&
            model.isReady()) {
            setCanPaint(true);
            setWantsPaint(true);
            notifyListeners();
        }
    }    

    public int getMaxVertSpace() { 
        return 40;
    }
    public int getMinVertSpace() { 
        return 40;
    }

    public void paintItem(Graphics2D g, 
                          int x1, int y1, 
                          int x2, int y2) {
        if (!canPaint()) {
            return;
        }
        int w = x2 - x1;
        double h = y2 - y1;
        Region region = getRegion();
        int regionstart = region.getStart(), regionend = region.getEnd();
        int regionwidth = regionend - regionstart;
        int pixwidth = props.PixWidth;
        if (pixwidth < 1) {
            pixwidth = 1;
        }

        String wholestring = model.getResults();
        if (wholestring == null) {
            return;
        }
        char[] chars = wholestring.toUpperCase().toCharArray();
        g.setColor(Color.BLUE);
        int pixHeights[] = new int[w / pixwidth];
        double f = ((double)w ) / ((double)(regionwidth*pixwidth));
        for (int i = 0; i < chars.length - 1; i++) {
            int pix = (int)(i * f);
            if (pix >= 0 && pix < pixHeights.length && chars[i] == 'C' && chars[i+1] == 'G') {
                pixHeights[pix]++;
            }
        }
        for (int i = 0; i < pixHeights.length; i++) {
            double frac = ((double)pixHeights[i]) * f;
            if (frac > 1) {
                frac = 1;
            }
            int fill = (int) (h * frac);
            g.fillRect(i*pixwidth,y1,pixwidth,fill);
        }
        if (props.DrawTrackLabel) {
            g.setColor(Color.BLACK);
            g.drawString(getLabel(),x1,y2);
        }
    }
}