/*
* Return a twin list of the greedy consensus tree splits and their internode certainties
*/
public DoubleList<Split, Double> getICs() {
DoubleList<Split, Double> ic = new DoubleList<Split, Double>();
List<DoubleList<Split, Integer>> greedyTreeConflicts = findConflictingSplitCounts(2, true);
for (DoubleList<Split, Integer> splitList : greedyTreeConflicts) {
ic.add(splitList.getA(0), internodeCertainty(splitList));
}
return ic;
}
/*
* Return a twin list of the greedy consensus tree splits and their ICA (internode certainty all)
* scores, with a threshold for which incompatible splits are included in the ICA calculation
*/
public DoubleList<Split, Double> getICAs(int threshold) {
DoubleList<Split, Double> ica = new DoubleList<Split, Double>();
List<DoubleList<Split, Integer>> greedyTreeConflicts =
findConflictingSplitCounts(threshold, false);
for (DoubleList<Split, Integer> splitList : greedyTreeConflicts) {
ica.add(splitList.getA(0), internodeCertainty(splitList));
}
return ica;
}
public void printInternodeCertainties(PrintWriter out) {
DoubleList<Split, Double> ic = getICs();
for (int i = 0; i < ic.size(); i++) {
out.printf("IC = %f for split %s\n", ic.getB(i), ic.getA(i).toString());
}
}