double totscore = 0;\r
int count = seqs.length;\r
\r
- int acount = 0;\r
Sequence seq;\r
\r
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(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
textarea.append(as.getOutput());\r
seq = new Sequence(as.getS1().getName(),\r
as.getAStr1(),\r
- as.getS1().getStart(), as.getS1().getEnd()\r
+ as.getS1().getStart(),\r
+ as.getS1().getEnd()\r
);\r
sequences.add(seq);\r
\r