// TODO: cope with recovering hidden sequences from
// resultContext
{
- Vector sqs = sg.getSequences(null);
- for (int sqsi = 0, iSize = sqs.size(); sqsi < iSize; sqsi++)
+ for (SequenceI oseq : sg.getSequences(null))
{
- SequenceI oseq = (SequenceI) sqs.get(sqsi);
SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
ordermap[nrj], destAl);
if (nseq != null)