output.append("Length of alignment = " + (aseq1.length - count) + "\n");\r
output.append("Sequence ");\r
output.append(new Format("%" + maxid + "s").form(s1.getName()));\r
- output.append(" : " + seq1start + " - " + seq1end + " (Sequence length = " +\r
+ output.append(" : " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +\r
s1str.length() + ")\n");\r
output .append("Sequence ");\r
output.append(new Format("%" + maxid + "s").form(s2.getName()));\r
- output .append(" : " + seq2start + " - " + seq2end + " (Sequence length = " +\r
+ output.append(" : " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +\r
s2str.length() + ")\n\n");\r
\r
for (int j = 0; j < nochunks; j++)\r
int count = ap.av.getSelectionGroup().getSize();\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
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
+ 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
\r
int count = selsubset.size();\r
\r
int acount = 0;\r
+ Sequence seq;\r
\r
for (int i = 1; i < count; i++)\r
{\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
+ seq = new Sequence(as.getS1().getName(),\r
+ as.getAStr1(),\r
+ as.getS1().getStart(), as.getS1().getEnd()\r
+ );\r
+ sequences.add(seq);\r
+\r
+ seq = new Sequence(as.getS2().getName(),\r
+ as.getAStr2(),\r
+ as.getS2().getStart(), as.getS2().getEnd()\r
+ );\r
+ sequences.add(seq);\r
}\r
}\r
\r