package jalview.gui;
import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.util.*;
import jalview.analysis.*;
import java.awt.*;
import java.awt.geom.*;
import java.util.*;

public class CpGRenderer implements RendererI {
    protected Color   color = Color.black;

    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {
	Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);
	return c;
    }

    public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText,Vector pid, int seqnum,AlignViewport av) {

	int i      = start;
	int length = seq.getLength();

	Color currentColor = Color.white;

	g.setColor(Color.black);

        int window = 1000;
        int max    = window/5;

        int step = window/10;

        if (step > window) {
          step = window;
        }

        if (window < 2) {
           window = 2;
           step = 1;
        }

        int cpgstart = start;
        int cpgend   = end;

	if (cpgstart <= window/2 ) {
	    cpgstart = window/2;
	}
	if (cpgend+window/2 >= length) {
	    cpgend = length-window/2;
	}

	Hashtable vals = AAFrequency.findKmerCount(seq,cpgstart,cpgend,window,step,av.getKmers());

	Enumeration en = vals.keys();

	Vector valset = new Vector();

	while (en.hasMoreElements()) {
	    valset.add((Integer)en.nextElement());
	}
	Collections.sort(valset);

	g.setColor(Color.black);

	int j = 0;

	while (j < valset.size()) {

	    Integer posInt = (Integer)valset.elementAt(j);
	    int     count  = ((Integer)vals.get(posInt)).intValue();
	    int     pos    = posInt.intValue();

            if (count > 40) {
               g.setColor(Color.red);
            } else {
               g.setColor(Color.black);
            }

	    g.fillRect(x1 + (int)(width*(pos-start-width/2)),
		       y1+height - (int)(count*height/max),
		       (int)(step*width),
		       (int)(count*height/max));

	    j++;
	}
    }

}