code: protected int[] getSubstitutionScoreVector(int queryColumn, Subproblem subproblem) {
  		int[] subs = new int[subproblem.getTargetEndIndex() + 1];
  		if (queryColumn > 0) {
  			for (int y = Math.max(1, subproblem.getTargetStartIndex()); y <= subproblem.getTargetEndIndex(); y++) {
  				subs[y] = getSubstitutionScore(queryColumn, y);
  			}
  		}
  		return subs;
  	}
docs: Returns score for the alignment of the query column to all target columns
  @param queryColumn
  @param subproblem
  @return