- int score = 0;
-
- for (int k = 0; k < end; k++)
- {
- try
- {
- score += ResidueProperties.getBLOSUM62(
- sequenceString[i].substring(k, k + 1),
- sequenceString[j].substring(k, k + 1));
- }
- catch (Exception ex)
- {
- System.err.println("err creating BLOSUM62 tree");
- ex.printStackTrace();
- }
- }
-
- distance[i][j] = (float) score;
-
- if (score > maxscore)
- {
- maxscore = score;
- }
+ score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
+ sequenceString[j].charAt(k));