code: @Override
  	protected void setProfile(List<Step> sx, List<Step> sy) {
  		profile = pair = new SimpleSequencePair<S, C>(getQuery(), getTarget(), sx, xyStart[0],
  				getQuery().getLength() - xyMax[0], sy, xyStart[1], getTarget().getLength() - xyMax[1]);
  	}
docs: method for AbstractMatrixAligner