code: public static Last[][] setScoreVector(int x, int xb, int yb, int ye, int gep, int[] subs, boolean storing,
  			int[][][] scores, boolean startAnchored) {
  		Last[][] pointers = new Last[ye + 1][1];
  		ensureScoringMatrixColumn(x, storing, scores);
  		if (x == xb) {
  			if (startAnchored) {
  				assert (xb > 0 && yb > 0);
  				scores[xb][yb][0] = scores[xb - 1][yb - 1][0] + subs[yb];
  				pointers[yb][0] = Last.SUBSTITUTION;
  			}
  			for (int y = yb + 1; y <= ye; y++) {
  				scores[xb][y][0] = scores[xb][y - 1][0] + gep;
  				pointers[y][0] = Last.INSERTION;
  			}
  		} else {
  			scores[x][yb][0] = scores[x - 1][yb][0] + gep;
  			pointers[yb][0] = Last.DELETION;
  			for (int y = yb + 1; y <= ye; y++) {
  				pointers[y][0] = setScorePoint(x, y, gep, subs[y], scores);
  			}
  		}
  		return pointers;
  	}
docs: Score global alignment for a given position in the query sequence for a linear gap penalty
  @param x
  @param xb
  @param yb
  @param ye
  @param gep
  @param subs
  @param storing
  @param scores
  @param startAnchored
  @return