+ nodegroups = clusterer.groupNodes(cut);
+ }
+ else
+ {
+ nodegroups = new ArrayList<BinaryNode>();
+ nodegroups.add(clusterer.getTopNode());
+ }
+ this.abs=abs;
+ this.thresh=thresh;
+ groups = new ArrayList<>();
+ for (BinaryNode root:nodegroups)
+ {
+ BitSet gpset=new BitSet();
+ for (BinaryNode leaf:clusterer.findLeaves(root))
+ {
+ gpset.set((Integer)leaf.element());
+ }
+ groups.add(gpset);
+ }
+ }
+ @Override
+ public void updateGroups(List<BitSet> colGroups)
+ {
+ if (colGroups!=null)
+ {
+ groups=colGroups;
+ }
+ }
+ @Override
+ public BitSet getGroupsFor(int column)
+ {
+ for (BitSet gp:groups) {
+ if (gp.get(column))
+ {
+ return gp;
+ }
+ }
+ return ContactMatrixI.super.getGroupsFor(column);
+ }
+
+ HashMap<BitSet,Color> colorMap = new HashMap<>();
+ @Override
+ public Color getColourForGroup(BitSet bs)
+ {
+ if (bs==null) {
+ return Color.white;
+ }
+ Color groupCol=colorMap.get(bs);
+ if (groupCol==null)
+ {
+ return Color.white;
+ }
+ return groupCol;
+ }
+ @Override
+ public void setColorForGroup(BitSet bs,Color color)
+ {
+ colorMap.put(bs,color);
+ }
+ public void restoreGroups(List<BitSet> newgroups, String treeMethod,
+ String tree, double thresh2)
+ {
+ treeType=treeMethod;
+ groups = newgroups;
+ thresh=thresh2;
+ newick =tree;
+
+ }
+ @Override
+ public boolean hasCutHeight() {
+ return groups!=null && thresh!=0;
+ }
+ @Override
+ public double getCutHeight()
+ {
+ return thresh;
+ }
+ @Override
+ public String getTreeMethod()
+ {
+ return treeType;