InteractionArcPainter.java

package org.seqcode.projects.seqview.paintable;

import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.Stroke;
import java.awt.geom.QuadCurve2D;
import java.io.File;
import java.util.EventObject;
import java.util.HashMap;
import java.util.List;

import org.seqcode.data.readdb.PairedHit;
import org.seqcode.gseutils.Listener;
import org.seqcode.projects.seqview.model.InteractionArcModel;
import org.seqcode.projects.seqview.model.SeqPairedEndModel;
import org.seqcode.viz.DynamicAttribute;


public class InteractionArcPainter extends RegionPaintable {

	private InteractionArcModel model;
	private InteractionArcProperties props;
	private DynamicAttribute attrib;

	public InteractionArcPainter (InteractionArcModel model) {
		super();
		this.model = model;
		props = new InteractionArcProperties();
		model.addEventListener(this);
		attrib = DynamicAttribute.getGlobalAttributes();
	}

	public InteractionArcProperties getProperties() {return props;}
	public void setProperties(InteractionArcProperties p) {props = p;}
	public void savePropsInDir(File dir) {
		super.savePropsInDir(dir);
		saveModelPropsInDir(dir,model);
	}
	public void loadPropsInDir(File dir) {
		super.loadPropsInDir(dir);
		loadModelPropsInDir(dir,model);
	}    
	public void cleanup() { 
		super.cleanup();
		model.removeEventListener(this);
	}
	public synchronized void eventRegistered(EventObject e) {        
		if (e.getSource() == model && model.isReady()) {
			setCanPaint(true);
			setWantsPaint(true);
			notifyListeners();
		}
	}
	public void removeEventListener(Listener<EventObject> l) {
		super.removeEventListener(l);
		if (!hasListeners()) {
			model.removeEventListener(this);
		}
	}

	public void paintItem(Graphics2D g, int x1, int y1, int x2, int y2) {
		if (!canPaint()) {
			return;
		}
		if(!model.isReady()) { return; }

		boolean differential = getProperties().Differential;


		int width = x2 - x1;
		int height = Math.max(y2 - y1,1);
		int halfy = y2 - (height/2);
		int regionStart = model.getRegion().getStart();
		int regionEnd = model.getRegion().getEnd();
		int regionWidth = model.getRegion().getWidth();
		int linewidth = Math.max(getProperties().LineWidth,1);
		Stroke oldStroke = g.getStroke();
		g.setStroke(new BasicStroke((float)linewidth));        
		List<PairedHit> hits = model.getResults();
		if(model.isDataError()){
			g.setFont(attrib.getLargeLabelFont(width,height));
			g.setColor(Color.RED);
			g.drawString("ReadDB Data Error: " +getLabel(),x1 + g.getFont().getSize()*2,y1 + g.getFont().getSize());
		}else if (getProperties().DrawTrackLabel) {
			g.setFont(attrib.getLargeLabelFont(width,height));
			g.setColor(Color.BLACK);
			g.drawString("Paired " +getLabel(),x1 + g.getFont().getSize()*2,y1 + g.getFont().getSize());
		}
		int h = height;
		float maxweight = 0;
		g.setStroke(new BasicStroke(1.0f));
		if (differential) {
			g.setColor(Color.black);
			g.drawLine(x1, halfy, x2, halfy);
			for (int i = 0; i < hits.size(); i++) {
				PairedHit hit = hits.get(i);
				float tmpweight = hit.weight;
				int leftx = getXPos(hit.leftPos, regionStart, regionEnd, x1, x2);
				int rightx = getXPos(hit.rightPos, regionStart, regionEnd, x1, x2);
				int midx = (leftx+rightx)/2;
				int midy;
				if (tmpweight>=0) {
					midy = halfy - (int)(((double)(rightx-leftx)/(double)width) * height);
				} else {
					midy = halfy + (int)(((double)(rightx-leftx)/(double)width) * height);
				}
				tmpweight = Math.abs(tmpweight);
				g.setStroke(new BasicStroke(tmpweight));
				//g.setColor(new Color(0.0f, 0.0f, 0.0f, Math.min(1.0f, tmpweight/25f)));
				g.setColor(new Color(0.0f, 0.0f, 0.0f, Math.min(1.0f, props.Alpha.floatValue())));
				QuadCurve2D loop = new QuadCurve2D.Float(leftx, halfy, midx, midy, rightx, halfy);
				g.draw(loop);
			}
		} else {
			HashMap<PairedHit, Float> pairedReadCounter = new HashMap<PairedHit, Float>();
			for (int i = 0; i < hits.size(); i++) {
				PairedHit hit = hits.get(i);
				if(pairedReadCounter.containsKey(hit))
					pairedReadCounter.put(hit, pairedReadCounter.get(hit)+hit.weight);
				else
					pairedReadCounter.put(hit, hit.weight);
				
				//If under the de-duplicate limit, draw the arc
				if(pairedReadCounter.get(hit)<= props.DeDuplicate.floatValue()){
					int leftx = getXPos(hit.leftPos, regionStart, regionEnd, x1, x2);
					int rightx = getXPos(hit.rightPos, regionStart, regionEnd, x1, x2);
					int midx = (leftx+rightx)/2;
					int midy = y2 - (int)(((double)(rightx-leftx)/(double)width) * 2*height);
					g.setColor(Color.BLACK);
					float tmpweight = hit.weight;
					if (tmpweight>maxweight) {
						maxweight = tmpweight;
					}
					if (tmpweight>0.0f) {
						g.setStroke(new BasicStroke(tmpweight/15f));
						tmpweight = Math.max(0.0f, tmpweight);
						//g.setColor(new Color(0.0f, 0.0f, 0.0f, Math.min(1.0f, tmpweight/100f)));
						g.setColor(new Color(0.4f, 0.4f, 0.4f, props.Alpha.floatValue()));
						QuadCurve2D loop = new QuadCurve2D.Float(leftx, y2, midx, midy, rightx, y2);
						g.draw(loop);
					}
				}
			}
			//System.err.println("maxweight: "+maxweight);
		}
		g.setStroke(oldStroke);
	}

}