- // copy before we do any mapping business.
- // TODO: verify that undo/redo with 1:many sequence associated
- // annotations can be undone correctly
- AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
- annotation
- .createSequenceMapping(referedSeq, refSeqIndex, false);
- annotation.adjustForAlignment();
- referedSeq.addAlignmentAnnotation(annotation);
- al.addAnnotation(annotation);
- al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
- if (groupRef != null)