// compute scale factor
private void computeFactor() {
// scale mean rate to 1.0 or separate parameter
double treeRate = 0.0;
double treeTime = 0.0;
// normalizeBranchRateTo = 1.0;
for (int i = 0; i < treeModel.getNodeCount(); i++) {
NodeRef node = treeModel.getNode(i);
if (!treeModel.isRoot(node)) {
// d int rateCategory = (int)
// Math.round(rateCategories.getNodeValue(treeModel, node));
// d treeRate += rates[rateCategory] * treeModel.getBranchLength(node);
treeTime += treeModel.getBranchLength(node);
// d System.out.println("rates and time\t" + rates[rateCategory] + "\t" +
// treeModel.getBranchLength(node));
}
}
// treeRate /= treeTime;
scaleFactor = normalizeBranchRateTo / (treeRate / treeTime);
System.out.println("scaleFactor\t\t\t\t\t" + scaleFactor);
}
private void setup() {
DataType dataType = baseSubstitutionModel.getDataType();
FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel();
Parameter kappaParameter = new Parameter.Default("kappa", 1, baseSubstitutionModel.getKappa());
substitutionModels = new LinkedList<SubstitutionModel>();
branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>();
int branchClass = 0;
for (NodeRef node : treeModel.getNodes()) {
if (!treeModel.isRoot(node)) {
double nodeHeight = treeModel.getNodeHeight(node);
double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
double time = 0.5 * (parentHeight + nodeHeight);
double baseOmega = baseSubstitutionModel.getOmega();
double fixed = baseOmega * time;
double epsilon =
(Math.log(1 - random.nextDouble())
/ (-rate)); // Math.exp((random.nextGaussian() * stdev + mean));
double value = fixed + epsilon;
Parameter omegaParameter = new Parameter.Default("omega", 1, value);
GY94CodonModel gy94 =
new GY94CodonModel((Codons) dataType, omegaParameter, kappaParameter, freqModel);
substitutionModels.add(gy94);
branchAssignmentMap.put(node, branchClass);
branchClass++;
} // END: root check
} // END: nodes loop
} // END: setup