How to use

getChildrenMap

method

in

phylo.tree.model.TreeUtils

public static Map<Set<String>, TreeNode> getChildrenMap(final Tree tree) {
  return getChildrenMap(tree, false);
}

addingEnabled = false;
for (Tree treeTopology : topologies) {
  mergedSets.put(getChildrenMap(treeTopology, true), treeTopology);
Map<Set<String>, TreeNode> treeAsMap = getChildrenMap(tree);
treeSetToNode.put(treeAsMap, tree);
Set<Set<String>> treeAsSet = treeAsMap.keySet();

public static Tree addCladewiseSplitFit(List<WeightedTreePartitions> biparts, Tree tree) {
  Map<Set<String>, TreeNode> labelsToClade = getChildrenMap(tree);
  Set<String> all = getLeafLabels(tree);
  Map<WeightedTreePartitions, AtomicDouble> partitionsToConflicts = new HashMap<>(labelsToClade.size());
  for (Set<String> leafesInClade : labelsToClade.keySet()) {
    partitionsToConflicts.put(new WeightedTreePartitions(leafesInClade, all), new AtomicDouble(0));
  }
  double numberOfChars = 0;
  for (WeightedTreePartitions sourcePartition : biparts) {
    numberOfChars += sourcePartition.weight;
    for (Map.Entry<WeightedTreePartitions, AtomicDouble> e : partitionsToConflicts.entrySet()) {
      if (e.getKey().isIncompatible(sourcePartition)) {
        e.getValue().addAndGet(e.getKey().weight);
      }
    }
  }
  for (Map.Entry<WeightedTreePartitions, AtomicDouble> entry : partitionsToConflicts.entrySet()) {
    TreeNode first = labelsToClade.remove(entry.getKey().getGroupA());
    TreeNode second = labelsToClade.remove(entry.getKey().getGroupB());
    String l = String.valueOf(1 - (entry.getValue().doubleValue() / numberOfChars));
    if (first != null)
      first.setLabel(l);
    if (second != null)
      second.setLabel(l);
  }
  return tree;
}