- *
- * @return DOCUMENT ME!
- */
- public float[][] findDistances(String[] sequenceString)
- {
- float[][] distance = new float[noseqs][noseqs];
-
- if (pwtype.equals("PID"))
- {
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- if (j == i)
- {
- distance[i][i] = 0;
- }
- else
- {
- distance[i][j] = 100 - Comparison.PID(sequenceString[i],
- sequenceString[j]);
-
- distance[j][i] = distance[i][j];
- }
- }
- }
- }
- else
- {
- // Pairwise substitution score (with no gap penalties)
- ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
- if (pwmatrix == null)
- {
- pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- int maxscore = 0;
- int end = sequenceString[0].length();
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- int score = 0;
-
- for (int k = 0; k < end; k++)
- {
- try
- {
- score += pwmatrix.getPairwiseScore(
- sequenceString[i].charAt(k),
- sequenceString[j].charAt(k));
- } catch (Exception ex)
- {
- System.err.println("err creating BLOSUM62 tree");
- ex.printStackTrace();
- }
- }
-
- distance[i][j] = (float) score;
-
- if (score > maxscore)
- {
- maxscore = score;
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = (float) maxscore - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
-
- }
- return distance;
-
- // else
- /*
- * else if (pwtype.equals("SW")) { float max = -1;
- *
- * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- * { AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
- * as.calcScoreMatrix(); as.traceAlignment(); as.printAlignment(System.out);
- * distance[i][j] = (float) as.maxscore;
- *
- * if (max < distance[i][j]) { max = distance[i][j]; } } }
- *
- * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- * { distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j];
- * } } }/
- */
- }
-
- /**
- * DOCUMENT ME!