fullseq = osp.substring(0, ipos) + nogaprep
+ osp.substring(ipos + nogaprep.length());
newds.setSequence(fullseq.toUpperCase());
- // TODO: ensure newly created dataset sequence is added to the set of
+ // TODO: JAL-1131 ensure newly created dataset sequence is added to the set of
// dataset sequences associated with the alignment.
+ // TODO: JAL-1131 fix up any annotation associated with new dataset
+ // sequence to ensure that original sequence/annotation relationships
+ // are preserved.
command.seqs[i].setDatasetSequence(newds);
}