return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
- (Map<String, Object>) pae_obj);
+ SequenceI seq = sm.getSequence();
+ Console.debug("##### SEQUENCE FOUND=" + seq.getName());
+ Map<String, Object> paeObject = (Map<String, Object>) pae_obj;
- AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ ContactMatrixI matrix = new PAEContactMatrix(seq, paeObject);
+ AlignmentAnnotation cmannot = seq.addContactList(matrix);
if (label != null)
{
- Console.debug("Setting annotation label to '" + label + "'");
cmannot.label = label;
}
- sm.getSequence().addAlignmentAnnotation(cmannot);
+ // seq.addAlignmentAnnotation(cmannot);
return true;
}