AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
null);
- ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+ // check for null on out of bounds
+ ContactListI alcl = alForSeq.getContactListFor(newaa, newaa.annotations.length);
+ assertNull(alcl,"Should've gotten null!");
+ // now check for mapping
+ alcl = alForSeq.getContactListFor(newaa, 1);
assertNotNull(alcl);
mappedCl = alcl.getMappedPositionsFor(0, 4);
assertNotNull(mappedCl);