code: public static Last[][] setScoreVector(int x, int gep, int[] subs, boolean storing, int[][][] scores,
  			int[] xyMax, int score) {
  		return setScoreVector(x, 0, 0, scores[0].length - 1, gep, subs, storing, scores, xyMax, score);
  	}
docs: Score local alignment for a given position in the query sequence for a linear gap penalty
  @param x
  @param gep
  @param subs
  @param storing
  @param scores
  @param xyMax
  @param score
  @return