+ ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
+ if (cm == null && _aa.groupRef != null)
+ {
+ cm = _aa.groupRef.getContactMatrixFor(_aa);
+ }
+ if (cm == null && _aa.sequenceRef != null)
+ {
+ cm = _aa.sequenceRef.getContactMatrixFor(_aa);
+ if (cm == null && _aa.sequenceRef.getDatasetSequence()!=null)
+ {
+ // TODO fix up this logic and unify with getContactListFor
+ cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
+ }
+ }
+ return cm;