+ @Override
+ public AlignmentAnnotation addContactList(ContactMatrixI cm)
+ {
+ AlignmentAnnotation aa;
+
+ if (datasetSequence != null)
+ {
+ aa = datasetSequence.addContactList(cm);
+ // clone the annotation for the local sequence
+ aa = new AlignmentAnnotation(aa);
+ aa.restrict(start, end);
+ aa.adjustForAlignment();
+ getContactMapHolder().addContactListFor(aa,cm);
+ addAlignmentAnnotation(aa);
+ return aa;
+ }
+
+ // construct new annotation for matrix on dataset sequence
+ aa = getContactMapHolder().addContactList(cm);
+
+ Annotation _aa[] = new Annotation[getLength()];
+
+ for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
+ {
+ ;
+ }
+ aa.annotations = _aa;
+ aa.setSequenceRef(this);
+ if (cm instanceof MappableContactMatrix
+ && !((MappableContactMatrix) cm).hasReferenceSeq())
+ {
+ ((MappableContactMatrix) cm).setRefSeq(this);
+ }
+ aa.createSequenceMapping(this, getStart(), false);
+ addAlignmentAnnotation(aa);
+ return aa;
+ }
+
+ @Override
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm)
+ {
+ getContactMapHolder().addContactListFor(annotation, cm);