- if(getSequenceAt(i).getDatasetSequence()!=null)
- {
- seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
- }
- else
- {
- seqs[i] = new Sequence(getSequenceAt(i).getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- getSequenceAt(i).getSequence()
- ),
- getSequenceAt(i).getStart(),
- getSequenceAt(i).getEnd());
- seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures();
- getSequenceAt(i).setSequenceFeatures(null);
- getSequenceAt(i).setDatasetSequence(seqs[i]);
- }
+ seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ }
+ else
+ {
+ seqs[i] = new Sequence(currentSeq.getName(),
+ AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ currentSeq.getSequenceAsString()
+ ),
+ currentSeq.getStart(),
+ currentSeq.getEnd());
+ seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+ seqs[i].setDescription(currentSeq.getDescription());
+ getSequenceAt(i).setSequenceFeatures(null);
+ getSequenceAt(i).setDatasetSequence(seqs[i]);