- for (int j = 0; j < i; j++)
- {
-
- AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
- seqs[j], seqStrings[j], type);
-
- if(as.s1str.length()==0 || as.s2str.length()==0)
- {
- continue;
- }
-
- as.calcScoreMatrix();
- as.traceAlignment();
-
-
- as.printAlignment(System.out);
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
- totscore = totscore + scores[i][j];
-
- textarea.append(as.getOutput());
- seq = new Sequence(as.getS1().getName(),
- as.getAStr1(),
- as.getS1().getStart(),
- as.getS1().getEnd()
- );
- sequences.add(seq);
-
- seq = new Sequence(as.getS2().getName(),
- as.getAStr2(),
- as.getS2().getStart(),
- as.getS2().getEnd() );
- sequences.add(seq);
- }