\r
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
seqs[j], seqStrings[j], "pep");\r
\r
\r
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
seqs[j], seqStrings[j], "pep");\r
\r
as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\r
as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\r
textarea.append(as.getOutput());\r
seq = new Sequence(as.getS1().getName(),\r
as.getAStr1(),\r
textarea.append(as.getOutput());\r
seq = new Sequence(as.getS1().getName(),\r
as.getAStr1(),\r