- SequenceI aseq = null;
- if (ala.sequenceRef != null) {
- SequenceI seq = job.seqNames.get(ala.sequenceRef.getName());
- aseq = seq.getRootDatasetSequence();
- }
- ala.sequenceRef = aseq;
- Annotation[] gappedAnnots = createGappedAnnotations(ala.annotations, job.start, job.gapMap);
- ala.annotations = gappedAnnots;
-
- AlignmentAnnotation newAnnot = viewport.getAlignment()
- .updateFromOrCopyAnnotation(ala);
- if (aseq != null)
+ SequenceI seq = (ala.sequenceRef == null) ? null
+ : job.seqNames.get(ala.sequenceRef.getName());
+ if (job.gapMap != null && job.gapMap.length > 0)
+ ala.annotations = createGappedAnnotations(ala.annotations,
+ job.gapMap);
+ if (seq != null)