/*
* Salichos Stamatakis and Rokas, MBE v31 p1261 (2014)
* If only two splits are listed, returns IC, the Internode Certainty.
* If more splits are listed, returns ICA, (IC All).
*/
private double internodeCertainty(DoubleList<Split, Integer> splits) {
int sum = 0;
int n = splits.size(); // number of splits under consideration
for (int i = 0; i < n; i++) sum += splits.getB(i);
double ic = 1;
if (n > 1) {
ic = Math.log(n);
for (int i = 0; i < n; i++) {
double p = ((double) splits.getB(i)) / sum;
ic += p * Math.log(p);
}
ic /= Math.log(n); // convert from natural log to log base n
}
return ic;
}
/**
* Returns the sum of Internode Certainties over a greedy consensus tree.
*
* @return
*/
public double treeCertainty() {
double tc = 0;
DoubleList<Split, Double> ic = getICs();
for (int i = 0; i < ic.size(); i++) {
tc += ic.getB(i);
}
return tc;
}
/**
* Returns the sum of Internode Certainty All over a greedy consensus tree.
*
* @return
*/
public double treeCertaintyAll(int threshold) {
double tca = 0;
DoubleList<Split, Double> ic = getICAs(threshold);
for (int i = 0; i < ic.size(); i++) {
tca += ic.getB(i);
}
return tca;
}
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());
}
}