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);

		}
	}
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 ) ; } }
draw high scoring fragments that are used for the initial alignment seed
selection

@param g