/**
* creates a clade system from a tree (using a pre-specified order of sequences)
*
* @param idGroup sequence order for the matrix
* @param tree
*/
public static CladeSystem getClades(IdGroup idGroup, Tree tree) {
tree.createNodeList();
int size = tree.getInternalNodeCount() - 1;
CladeSystem cladeSystem = new CladeSystem(idGroup, size);
boolean[][] clades = cladeSystem.getCladeArray();
for (int i = 0; i < size; i++) {
getClade(idGroup, tree.getInternalNode(i), clades[i]);
}
return cladeSystem;
}
public static void calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems) {
CladeSystem cladeSystem = getClades(cladeSystems[0].getIdGroup(), tree);
for (int i = 0; i < tree.getInternalNodeCount() - 1; i++) {
Node node = tree.getInternalNode(i);
boolean[] clade = cladeSystem.getClade(i);
if (node.isRoot()) throw new RuntimeException("Root node does not have clade probability!");
int cladeCount = 0;
for (int j = 0; j < cladeSystems.length; j++) {
if (cladeSystems[j].hasClade(clade)) cladeCount += 1;
}
double pr = (double) cladeCount / (double) cladeSystems.length;
tree.setAttribute(node, AttributeNode.CLADE_PROBABILITY, new Double(pr));
}
}