/** Calculates the actual rates corresponding to the category indices. */
protected void setupRates() {
// System.out.println("BRRRTTZZZ " + distributionIndexParameter.getValue(0));
for (int i = 0; i < tree.getNodeCount(); i++) {
// rates[i] = distributionModel.quantile(rateCategoryQuantiles.getNodeValue(
// rateCategoryQuantiles.getTreeModel(), rateCategoryQuantiles.getTreeModel().getNode(i) ));
if (!tree.isRoot(tree.getNode(i))) {
if (useQuantilesForRates) {
/* Using quantiles to represent rates */
rates[tree.getNode(i).getNumber()] =
distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].quantile(
rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i)));
} else {
/* Not using quantiles to represent rates. This is practically useless for anything else other than simulation */
rates[tree.getNode(i).getNumber()] =
rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i));
}
}
}
/*System.out.print(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName() + "\t" + (int) Math.round(distributionIndexParameter.getValue(0)) + "\t" + rates[1] + "\t" + rateCategoryQuantiles.getNodeValue(tree, tree.getNode(1)));// + "\t" + distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].);
if(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.LogNormalDistributionModel")) {
LogNormalDistributionModel lndm = (LogNormalDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
System.out.println("\t" + lndm.getS());
}
else if (distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.InverseGaussianDistributionModel")) {
InverseGaussianDistributionModel lndm = (InverseGaussianDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
System.out.println("\t" + lndm.getS());
}*/
if (normalize) computeFactor();
}
/** @return cenancestor */
public final double getCenancestorBranch() {
return cenancestorBranch.getValue(0);
}
/** @return cenancestor */
public final double getCenancestorHeight() {
return cenancestorHeight.getValue(0);
}