- AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
- "Contact Matrix", _aa);
- aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
- aa.graphMin = cm.getMin();
- aa.graphMax = cm.getMax();
- aa.editable = false;
- // aa.autoCalculated = true;
- contactmaps.put(aa.annotationId, cm);
- // TODO: contact matrices could be intra or inter - more than one refseq
- // possible!
- if (cm.hasReferenceSeq())
- {
- aa.setSequenceRef(cm.getReferenceSeq());
- }