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);
}
}
}
@Override
public List<Integer> getChildren(int i) {
NodeRef n = tree.getNode(i);
int childCount = tree.getChildCount(n);
List<Integer> children = new ArrayList<Integer>(childCount);
for (int j = 0; j < childCount; ++j) children.add(tree.getChild(n, j).getNumber());
return children;
}
@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;
}
private static int mauCanonicalSub(
Tree tree, NodeRef node, int loc, NodeRef[] order, boolean[] wasSwaped) {
if (tree.isExternal(node)) {
order[loc] = node;
assert (loc & 0x1) == 0;
return loc + 1;
}
final boolean swap = MathUtils.nextBoolean();
// wasSwaped[(loc-1)/2] = swap;
int l = mauCanonicalSub(tree, tree.getChild(node, swap ? 1 : 0), loc, order, wasSwaped);
order[l] = node;
assert (l & 0x1) == 1;
wasSwaped[(l - 1) / 2] = swap;
l = mauCanonicalSub(tree, tree.getChild(node, swap ? 0 : 1), l + 1, order, wasSwaped);
return l;
}
private double getUniqueBranches(Tree tree, NodeRef node) {
if (tree.isExternal(node)) {
return tree.getBranchLength(node);
} else {
double length = 0;
if (isUnique(taxonList, tree, node)) {
length = tree.getBranchLength(node);
// System.out.println("length = " + length);
}
for (int i = 0; i < tree.getChildCount(node); i++) {
length += getUniqueBranches(tree, tree.getChild(node, i));
}
// System.out.println("length of node " + node + " = " + length);
return length;
}
}
private void getDescendants(NodeRef n, List<Integer> descendants) {
descendants.add(n.getNumber());
if (tree.isExternal(n)) return;
for (int i = 0; i < tree.getChildCount(n); ++i)
getDescendants(tree.getChild(n, i), descendants);
}
@Override
public int getRightChild(int i) {
return tree.getChild(tree.getNode(i), 1).getNumber();
}
@Override
public int getLeftChild(int i) {
return tree.getChild(tree.getNode(i), 0).getNumber();
}
/**
* Traverse the tree calculating partial likelihoods.
*
* @param tree tree
* @param node node
* @param operatorNumber operatorNumber
* @param flip flip
* @return boolean
*/
private boolean traverse(Tree tree, NodeRef node, int[] operatorNumber, boolean flip) {
boolean update = false;
int nodeNum = node.getNumber();
NodeRef parent = tree.getParent(node);
if (operatorNumber != null) {
operatorNumber[0] = -1;
}
// First update the transition probability matrix(ices) for this branch
if (parent != null && updateNode[nodeNum]) {
final double branchRate = branchRateModel.getBranchRate(tree, node);
final double parentHeight = tree.getNodeHeight(parent);
final double nodeHeight = tree.getNodeHeight(node);
// Get the operational time of the branch
final double branchLength = branchRate * (parentHeight - nodeHeight);
if (branchLength < 0.0) {
throw new RuntimeException("Negative branch length: " + branchLength);
}
if (flip) {
substitutionModelDelegate.flipMatrixBuffer(nodeNum);
}
branchUpdateIndices[branchUpdateCount] = nodeNum;
branchLengths[branchUpdateCount] = branchLength;
branchUpdateCount++;
update = true;
}
// If the node is internal, update the partial likelihoods.
if (!tree.isExternal(node)) {
// Traverse down the two child nodes
NodeRef child1 = tree.getChild(node, 0);
final int[] op1 = {-1};
final boolean update1 = traverse(tree, child1, op1, flip);
NodeRef child2 = tree.getChild(node, 1);
final int[] op2 = {-1};
final boolean update2 = traverse(tree, child2, op2, flip);
// If either child node was updated then update this node too
if (update1 || update2) {
int x = operationCount[operationListCount] * Beagle.OPERATION_TUPLE_SIZE;
if (flip) {
// first flip the partialBufferHelper
partialBufferHelper.flipOffset(nodeNum);
}
final int[] operations = this.operations[operationListCount];
operations[x] = partialBufferHelper.getOffsetIndex(nodeNum);
if (useScaleFactors) {
// get the index of this scaling buffer
int n = nodeNum - tipCount;
if (recomputeScaleFactors) {
// flip the indicator: can take either n or (internalNodeCount + 1) - n
scaleBufferHelper.flipOffset(n);
// store the index
scaleBufferIndices[n] = scaleBufferHelper.getOffsetIndex(n);
operations[x + 1] = scaleBufferIndices[n]; // Write new scaleFactor
operations[x + 2] = Beagle.NONE;
} else {
operations[x + 1] = Beagle.NONE;
operations[x + 2] = scaleBufferIndices[n]; // Read existing scaleFactor
}
} else {
if (useAutoScaling) {
scaleBufferIndices[nodeNum - tipCount] = partialBufferHelper.getOffsetIndex(nodeNum);
}
operations[x + 1] = Beagle.NONE; // Not using scaleFactors
operations[x + 2] = Beagle.NONE;
}
operations[x + 3] = partialBufferHelper.getOffsetIndex(child1.getNumber()); // source node 1
operations[x + 4] =
substitutionModelDelegate.getMatrixIndex(child1.getNumber()); // source matrix 1
operations[x + 5] = partialBufferHelper.getOffsetIndex(child2.getNumber()); // source node 2
operations[x + 6] =
substitutionModelDelegate.getMatrixIndex(child2.getNumber()); // source matrix 2
operationCount[operationListCount]++;
update = true;
if (hasRestrictedPartials) {
// Test if this set of partials should be restricted
if (updateRestrictedNodePartials) {
// Recompute map
computeNodeToRestrictionMap();
updateRestrictedNodePartials = false;
}
if (partialsMap[nodeNum] != null) {}
}
}
}
return update;
}
/**
* Traverse the tree calculating partial likelihoods.
*
* @return whether the partials for this node were recalculated.
*/
protected boolean traverse(Tree tree, NodeRef node) {
boolean update = false;
boolean rootUpdated = false;
int nodeNum = node.getNumber();
NodeRef parent = tree.getParent(node);
// First update the transition probability matrix(ices) for this branch if it is a normal branch
if (parent != null && updateNode[nodeNum]) {
final double branchRate = branchRateModel.getBranchRate(tree, node);
// Get the operational time of the branch
final double branchTime =
branchRate * (tree.getNodeHeight(parent) - tree.getNodeHeight(node));
if (branchTime < 0.0) {
throw new RuntimeException("Negative branch length: " + branchTime);
}
cenancestorlikelihoodCore.setNodeMatrixForUpdate(nodeNum);
for (int i = 0; i < categoryCount; i++) {
double branchLength = siteModel.getRateForCategory(i) * branchTime;
siteModel.getSubstitutionModel().getTransitionProbabilities(branchLength, probabilities);
cenancestorlikelihoodCore.setNodeMatrix(nodeNum, i, probabilities);
}
update = true;
} else if (parent == null
&& cenancestorHeight != null
&& updateNode[nodeNum]) // The root has to be updated
{
// First update the transition probability matrix(ices) for the root-cenancestor fake branch
rootUpdated = true;
// Get the operational time of the fake branch from the root to the cenancestor
double rootHeight = treeModel.getNodeHeight(treeModel.getRoot());
double branchRate =
branchRateModel.getBranchRate(
rootHeight,
getCenancestorHeight()); // TODO: Could this be easily improved? I would do to adapt
// the tree structure and abstact tree likelihood
double branchTime =
branchRate
* getCenancestorBranch(); // TODO: Could this be easily improved? The same as before
for (int i = 0; i < categoryCount; i++) {
double branchLength = siteModel.getRateForCategory(i) * branchTime;
siteModel.getSubstitutionModel().getTransitionProbabilities(branchLength, probabilities);
cenancestorlikelihoodCore.setNodeMatrix(nodeNum, i, probabilities);
}
}
// If the node is internal, update the partial likelihoods.
if (!tree.isExternal(node)) {
// Traverse down the two child nodes
NodeRef child1 = tree.getChild(node, 0);
final boolean update1 = traverse(tree, child1);
NodeRef child2 = tree.getChild(node, 1);
final boolean update2 = traverse(tree, child2);
// If either child node was updated then update this node too
if (update1 || update2 || rootUpdated) {
if (update1 || update2) {
final int childNum1 = child1.getNumber();
final int childNum2 = child2.getNumber();
cenancestorlikelihoodCore.setNodePartialsForUpdate(nodeNum);
if (integrateAcrossCategories) {
cenancestorlikelihoodCore.calculatePartials(childNum1, childNum2, nodeNum);
} else {
cenancestorlikelihoodCore.calculatePartials(
childNum1, childNum2, nodeNum, siteCategories);
}
if (COUNT_TOTAL_OPERATIONS) {
totalOperationCount++;
}
}
if (parent == null) {
// No parent this is the root of the tree
double[] partials;
int nodeNumCenan = getCenancestorIndex();
if (cenancestorHeight != null) {
if (rootUpdated) {
// Calculate the partials at the cenancestor. The transition matrix of the root was
// calculated before.
cenancestorlikelihoodCore.setNodePartialsForUpdate(nodeNumCenan);
if (integrateAcrossCategories) {
cenancestorlikelihoodCore.calculatePartials(nodeNum, nodeNumCenan);
} else {
cenancestorlikelihoodCore.calculatePartials(nodeNum, nodeNumCenan, siteCategories);
}
}
partials = getCenancestorPartials();
} else { // Using the cenancestor model without cenancestor date. It assumes that the root
// of the tree is the cenancestor. Not tested. It shouldn't be normally used
// either.
partials = getRootPartials();
}
// calculate the pattern likelihoods
double[] frequencies = frequencyModel.getFrequencies();
cenancestorlikelihoodCore.calculateLogLikelihoods(
partials, frequencies, patternLogLikelihoods);
}
update = true;
}
}
return update;
}