+ for (AlignmentAnnotation ana : shadow.getAnnotation())
+ {
+ List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+ ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana = new AlignmentAnnotation(ana);
+ ana.liftOver(sequence, shadowMap);
+ ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ else
+ {
+ if (sequence != null && sequence.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ana : sequence.getAnnotation())
+ {
+ List<AlignmentAnnotation> transfer = sq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana = new AlignmentAnnotation(ana);
+ ana.liftOver(dsq, sqmpping);
+ // mapping.transfer(ana);
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ }
+ if (false)
+ {
+ // Useful for debugging mappings - adds annotation for mapped position
+ float min = -1, max = 0;
+ Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+ for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)