@Override
public void initAndValidate() {
meanRate = meanRateInput.get();
speciesTreeRatesX = speciesTreeRatesInput.get();
geneTree = geneTreeInput.get();
geneNodeCount = geneTree.getNodeCount();
branchRates = new double[geneNodeCount];
storedBranchRates = new double[geneNodeCount];
needsUpdate = true;
}
private void update() {
final double geneTreeRate = meanRate.getValue();
final double[] speciesTreeRates = speciesTreeRatesX.getRatesArray();
final double[] speciesOccupancy = geneTree.getSpeciesOccupancy();
final int speciesNodeCount = speciesTreeRates.length;
for (int i = 0; i < geneNodeCount - 1; i++) {
double weightedSum = 0.0;
double branchLength = 0.0;
for (int j = 0; j < speciesNodeCount; j++) {
// System.out.println(String.format("%d, %d: %f, %f", i, j, speciesTreeRates[j],
// speciesOccupancy[i * speciesNodeCount + j]));
weightedSum += speciesTreeRates[j] * speciesOccupancy[i * speciesNodeCount + j];
branchLength += speciesOccupancy[i * speciesNodeCount + j];
}
branchRates[i] = geneTreeRate * weightedSum / branchLength;
}
// set the rate for the root branch of this gene to equal the input mean rate
branchRates[geneNodeCount - 1] = geneTreeRate;
needsUpdate = false;
}
