+ // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data
+ cl = al.getContactListFor(alan, 3);
+ assertNotNull(
+ "Contact matrix should have data for last position in sequence",
+ cl);
+
+ ContactMatrixI cm2 = new SeqDistanceContactMatrix(4);
+ dssq.addContactList(cm2);
+ tipEntries = new TreeMap<>();
+ candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+ tipEntries, candidates, al);
+ AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+ assertTrue("Expected two contact map annotation transferred",
+ al.getAlignmentAnnotation() != null
+ && al.getAlignmentAnnotation().length == 2);