+ ////
+ //// Contact Matrix Holder Boilerplate
+ ////
+ ContactMapHolder cmholder = new ContactMapHolder();
+
+ @Override
+ public Collection<ContactMatrixI> getContactMaps()
+ {
+ return cmholder.getContactMaps();
+ }
+
+ @Override
+ public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
+ {
+ 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;
+ }
+
+ @Override
+ public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+ {
+ if (_aa.annotations == null || column >= _aa.annotations.length
+ || column < 0)
+ {
+ return null;
+ }
+ ContactListI cl = cmholder.getContactListFor(_aa, column);
+ if (cl == null && _aa.groupRef != null)
+ {
+ cl = _aa.groupRef.getContactListFor(_aa, column);
+ }
+ if (cl == null && _aa.sequenceRef != null)
+ {
+ if (_aa.annotations[column] != null)
+ {
+ // sequence associated
+ cl = _aa.sequenceRef.getContactListFor(_aa, column);
+ if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+ {
+ int spos = _aa.sequenceRef.findPosition(column);
+ if (spos >= _aa.sequenceRef.getStart()
+ && spos <= 1 + _aa.sequenceRef.getEnd())
+ {
+ cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+ spos - _aa.sequenceRef.getStart());
+ }
+ }
+ }
+ }
+ return cl;
+ }
+
+ @Override
+ public AlignmentAnnotation addContactList(ContactMatrixI cm)
+ {
+ AlignmentAnnotation aa = cmholder.addContactList(cm);
+
+ Annotation _aa[] = new Annotation[getWidth()];
+ for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
+ {
+ ;
+ }
+ aa.annotations = _aa;
+ addAnnotation(aa);
+ return aa;
+ }
+
+ @Override
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm)
+ {
+ cmholder.addContactListFor(annotation, cm);
+
+ }