- Console.debug("##### SEQUENCE FOUND=" + seq.getName());
- Map<String, Object> paeObject = (Map<String, Object>) pae_obj;
-
- ContactMatrixI matrix = new PAEContactMatrix(seq, paeObject);
- AlignmentAnnotation cmannot = seq.addContactList(matrix);
- if (label != null)
- {
- cmannot.label = label;
- }
- // seq.addAlignmentAnnotation(cmannot);
-
+ ContactMatrixI matrix = new PAEContactMatrix(seq,
+ (Map<String, Object>) pae_obj);
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ /* this already happens in Sequence.addContactList()
+ seq.addAlignmentAnnotation(cmannot);
+ */