code: public void drawBoxes(Graphics g){
  		if ( fragmentPairs == null )
  			return;
  
  		g.setColor(Color.yellow);
  
  
  		for (int i = 0; i < fragmentPairs.length; i++) {
  			FragmentPair fp =fragmentPairs[i];
  			int xp = fp.getPos1();
  			int yp = fp.getPos2();
  
  			int width = Math.round(scale);
  
  			g.drawRect(Math.round(xp*scale),Math.round(yp*scale),width, width);
  
  		}
  	}
docs: draw high scoring fragments that are used for the initial alignment seed
  selection
  
  @param g