assertNotNull(
"No contact matrix recovered after reference annotation transfer",
cl);
+ // 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);