- for (int i = 1; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- acount++;\r
-\r
- AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),\r
- (SequenceI) selsubset.elementAt(j), "pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
- totscore = totscore + scores[i][j];\r
-\r
- textarea.append(as.getOutput());\r
- sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
- sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
- }\r
- }\r
-\r
- if (count > 2)\r
- {\r
- System.out.println(\r
- "Pairwise alignment scaled similarity score matrix\n");\r
+ for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)\r
+ {\r
+ if (av.getAlignment().getSequences().contains(av.getSelectionGroup()\r
+ .getSequenceAt(i)))\r
+ {\r
+ selsubset.add(av.getSelectionGroup().getSequenceAt(i));\r
+ }\r
+ }\r