- jalview.util.Format.print(System.out, "%7.3f",\r
- scores[i][j] / totscore);\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+\r
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
+ seqs[j], seqStrings[j], "pep");\r
+\r
+ if(as.s1str.length()==0 || as.s2str.length()==0)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\r
+\r
+\r
+ as.printAlignment(System.out);\r
+ scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
+ totscore = totscore + scores[i][j];\r
+\r
+ textarea.append(as.getOutput());\r
+ seq = new Sequence(as.getS1().getName(),\r
+ as.getAStr1(),\r
+ as.getS1().getStart(),\r
+ as.getS1().getEnd()\r
+ );\r
+ sequences.add(seq);\r
+\r
+ seq = new Sequence(as.getS2().getName(),\r
+ as.getAStr2(),\r
+ as.getS2().getStart(),\r
+ as.getS2().getEnd() );\r
+ sequences.add(seq);\r
+ }\r