package jalview.ws.datamodel.alphafold;
+import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import jalview.analysis.AverageDistanceEngine;
+import jalview.bin.Console;
+import jalview.datamodel.BinaryNode;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
{
return length;
}
+ List<BitSet> groups=null;
+ @Override
+ public boolean hasGroups()
+ {
+ return groups!=null;
+ }
+ String newick=null;
+ public String getNewickString()
+ {
+ return newick;
+ }
+ public void makeGroups(float thresh,boolean abs)
+ {
+ AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
+ double height = clusterer.findHeight(clusterer.getTopNode());
+ newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
+
+ Console.trace("Newick string\n"+newick);
+
+ List<BinaryNode> nodegroups;
+ if (abs ? height > thresh : 0 < thresh && thresh < 1)
+ {
+ float cut = abs ? (float) (thresh / height) : thresh;
+ Console.debug("Threshold "+cut+" for height="+height);
+
+ nodegroups = clusterer.groupNodes(cut);
+ }
+ else
+ {
+ nodegroups = new ArrayList<BinaryNode>();
+ nodegroups.add(clusterer.getTopNode());
+ }
+
+ 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 BitSet getGroupsFor(int column)
+ {
+ for (BitSet gp:groups) {
+ if (gp.get(column))
+ {
+ return gp;
+ }
+ }
+ return ContactMatrixI.super.getGroupsFor(column);
+ }
}