- if (ala.sequenceRef != null)
- {
- SequenceI seq = running.getSeqNames()
- .get(ala.sequenceRef.getName());
- aseq = seq;
- // This part doesn't do anything. I suppose bad merge.
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- }
- /* Prepare an array for annotations and copy returned annotations to it.
- * Similar process happens in develop:JabawsCalcWorker#constructAnnotationFromScore.
- * However, JabawsCalcWorker fills the array form the beginning, not
- * the start position (start - column of the submitted region).
- * Also, JabawsCalcWorker adds those annotations to an AlignmentAnnotation
- * retrieved from the current alignment. */