Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
for (SequenceI seq : aligned.getSequences())
{
+ // JAL-2110: fail if two or more alignment sequences have a common dataset
+ // sequence.
alignedDatasets.put(seq.getDatasetSequence(), seq);
}
{
SequenceI alignedSequence = alignedDatasets.get(seq
.getDatasetSequence());
+ // JAL-2110: fail if two or more alignment sequences have common dataset
+ // sequence.
// TODO: getSequenceAsString() will be deprecated in the future
// TODO: need to leave to SequenceI implementor to update gaps
seq.setSequence(alignedSequence.getSequenceAsString());