// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
Vector algn = align.getSequences();\r
\r
+ int index = 0;\r
for (int i = 0; i < seqs.length; i++)\r
{\r
- algn.setElementAt(seqs[i], i);\r
+ if(algn.contains(seqs[i]))\r
+ algn.setElementAt(seqs[i], index++);\r
}\r
}\r
\r