private void writeNode(Tree tree, NodeRef node, boolean attributes, Map<String, Integer> idMap) {
if (tree.isExternal(node)) {
int k = node.getNumber() + 1;
if (idMap != null) k = idMap.get(tree.getTaxonId(k - 1));
out.print(k);
} else {
out.print("(");
writeNode(tree, tree.getChild(node, 0), attributes, idMap);
for (int i = 1; i < tree.getChildCount(node); i++) {
out.print(",");
writeNode(tree, tree.getChild(node, i), attributes, idMap);
}
out.print(")");
}
if (writeAttributesAs == AttributeType.BRANCH_ATTRIBUTES && !tree.isRoot(node)) {
out.print(":");
}
if (attributes) {
Iterator<?> iter = tree.getNodeAttributeNames(node);
if (iter != null) {
boolean first = true;
while (iter.hasNext()) {
if (first) {
out.print("[&");
first = false;
} else {
out.print(",");
}
String name = (String) iter.next();
out.print(name + "=");
Object value = tree.getNodeAttribute(node, name);
printValue(value);
}
out.print("]");
}
}
if (writeAttributesAs == AttributeType.NODE_ATTRIBUTES && !tree.isRoot(node)) {
out.print(":");
}
if (!tree.isRoot(node)) {
double length = tree.getBranchLength(node);
if (formatter != null) {
out.print(formatter.format(length));
} else {
out.print(length);
}
}
}
/** 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();
}
@Override
public int getSibling(int i) {
NodeRef n = tree.getNode(i);
if (tree.isRoot(n)) return RootedTree.NULL;
NodeRef p = tree.getParent(n);
int c1 = tree.getChild(p, 0).getNumber();
int c2 = tree.getChild(p, 1).getNumber();
return n.getNumber() == c2 ? c1 : c2;
}
double calculateNorm(Tree tree) {
double time = 0.0;
double rateTime = 0.0;
for (int i = 0; i < tree.getNodeCount(); i++) {
NodeRef node = tree.getNode(i);
if (!tree.isRoot(node)) {
double branchTime = tree.getBranchLength(node);
rateTime += getRawBranchRate(tree, node) * branchTime;
time += branchTime;
}
}
return rateTime / time;
}
public double[] getSummaryStatistic(Tree tree) {
double externalLength = 0.0;
double internalLength = 0.0;
int externalNodeCount = tree.getExternalNodeCount();
for (int i = 0; i < externalNodeCount; i++) {
NodeRef node = tree.getExternalNode(i);
externalLength += tree.getBranchLength(node);
}
int internalNodeCount = tree.getInternalNodeCount();
for (int i = 0; i < internalNodeCount; i++) {
NodeRef node = tree.getInternalNode(i);
if (!tree.isRoot(node)) {
internalLength += tree.getBranchLength(node);
}
}
return new double[] {internalLength + externalLength};
}
@Override
public boolean isRoot(int i) {
return tree.isRoot(tree.getNode(i));
}
public double getBranchRate(final Tree tree, final NodeRef node) {
assert !tree.isRoot(node) : "root node doesn't have a rate!";
// int rateCategory = (int) Math.round(rateCategories.getNodeValue(tree, node));
return rates[node.getNumber()] * scaleFactor;
}
