- super();\r
- this.av = av;\r
- float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];\r
- double totscore = 0;\r
- int count = av.getSelectionGroup().getSize();\r
-\r
- int acount = 0;\r
- for (int i = 1; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- acount++;\r
- AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
- av.getSelectionGroup().getSequenceAt(j),"pep");\r
-\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.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) );\r
- sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) );\r
-\r
-\r
- }\r
- }\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+ this.ap = ap;\r
+ float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
+ getHeight()];\r
+ double totscore = 0;\r
+ int count = ap.av.getSelectionGroup().getSize(false);\r
+\r
+ int acount = 0;\r
+ Sequence seq;\r
+ for (int i = 1; i < count; i++)\r
+ {\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+ acount++;\r
+ AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
+ ap.av.getSelectionGroup().getSequenceAt(j),\r
+ "pep");\r
+\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\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
+\r
+ seq = new Sequence(as.getS1().getName(),\r
+ as.getAStr1(),\r
+ as.getS1().getStart(), as.getS1().getEnd()\r
+ );\r
+ sequences.addElement(seq);\r
+\r
+ seq = new Sequence(as.getS2().getName(),\r
+ as.getAStr2(),\r
+ as.getS2().getStart(), as.getS2().getEnd()\r
+ );\r
+\r
+ sequences.addElement(seq);\r
+ }\r
+ }\r