+ // verify MappedPositions includes discontinuity
+ int[] mappedCl = newseq.getContactListFor(newaa, 5).getMappedPositionsFor(0, 4);
+ assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+ // make it harder.
+
+ SequenceI alseq = newseq.getSubSequence(6, 10);
+ alseq.insertCharAt(2, 2, '-');
+ AlignmentI alForSeq=new Alignment(new SequenceI[] { alseq });
+ newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa, null);
+ ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+ assertNotNull(alcl);
+ mappedCl = alcl.getMappedPositionsFor(0, 4);
+ assertNotNull(mappedCl);
+ assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+