@Test
public void testOperator2() throws Exception {
Tree tree;
int taxaSize = 3;
// make a caterpillar
Node left = new ZeroBranchSANode();
left.setNr(0);
left.setHeight(0.0);
for (int i = 1; i < taxaSize; i++) {
Node right = new ZeroBranchSANode();
right.setNr(i);
right.setHeight(i);
Node parent = new ZeroBranchSANode();
parent.setNr(taxaSize + i - 1);
parent.setHeight(i);
left.setParent(parent);
parent.setLeft(left);
right.setParent(parent);
parent.setRight(right);
left = parent;
}
left.setHeight(left.getRight().getHeight() + 2);
tree = new Tree(left);
System.out.println("Tree was = " + tree.getRoot().toShortNewick(false));
TreeDimensionJump operator = new TreeDimensionJump();
operator.initByName("tree", tree);
double logHastingsRatio = operator.proposal();
System.out.println("Proposed tree = " + tree.getRoot().toShortNewick(false));
System.out.println("Log Hastings ratio = " + logHastingsRatio);
}
// identify nodes that can serve as graft branches as part of a coordinated exchange move
protected SetMultimap<Integer, Node> getGraftBranches(Node yNode) {
final int yNumber = yNode.getNr();
final Set<String> cousinDescendants = findDescendants(yNode, yNumber);
final SetMultimap<Integer, Node> allGraftBranches = HashMultimap.create();
final List<Tree> geneTrees = geneTreeInput.get();
for (int j = 0; j < nGeneTrees; j++) {
final Tree geneTree = geneTrees.get(j);
final Node geneTreeRootNode = geneTree.getRoot();
final Set<Node> jGraftBranches = new LinkedHashSet<>();
findGraftBranches(geneTreeRootNode, jGraftBranches, cousinDescendants);
allGraftBranches.putAll(j, jGraftBranches);
}
return allGraftBranches;
}
/**
* extract coalescent times and tip information into array times from beast.tree.
*
* @param tree the beast.tree
* @param times the times of the nodes in the beast.tree
* @param childCounts the number of children of each node
*/
protected static void collectTimes(Tree tree, double[] times, int[] childCounts) {
Node[] nodes = tree.getNodesAsArray();
for (int i = 0; i < nodes.length; i++) {
Node node = nodes[i];
times[i] = node.getHeight();
childCounts[i] = node.isLeaf() ? 0 : 2;
}
}
@Override
public double proposal() {
Tree tree = treeInput.get(this);
// randomly select leaf node
int i = Randomizer.nextInt(taxonIndices.length);
Node node = tree.getNode(taxonIndices[i]);
double upper = node.getParent().getHeight();
// double lower = 0.0;
// final double newValue = (Randomizer.nextDouble() * (upper -lower)) + lower;
// scale node
double scale = (scaleFactor + (Randomizer.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
final double newValue = node.getHeight() * scale;
// check the tree does not get negative branch lengths
if (newValue > upper) {
return Double.NEGATIVE_INFINITY;
}
node.setHeight(newValue);
return -Math.log(scale);
}
/** Ensure the class behaves properly, even when inputs are not specified. */
@Override
public void initAndValidate() throws Exception {
boolean sortNodesAlphabetically = false;
if (dataInput.get() != null) {
labels = dataInput.get().getTaxaNames();
} else if (m_taxonset.get() != null) {
if (labels == null) {
labels = m_taxonset.get().asStringList();
} else { // else labels were set by TreeParser c'tor
sortNodesAlphabetically = true;
}
} else {
if (isLabelledNewickInput.get()) {
if (m_initial.get() != null) {
labels = m_initial.get().getTaxonset().asStringList();
} else {
labels = new ArrayList<>();
createUnrecognizedTaxa = true;
sortNodesAlphabetically = true;
}
} else {
if (m_initial.get() != null) {
// try to pick up taxa from initial tree
final Tree tree = m_initial.get();
if (tree.m_taxonset.get() != null) {
labels = tree.m_taxonset.get().asStringList();
} else {
// m_sLabels = null;
}
} else {
// m_sLabels = null;
}
}
// m_bIsLabelledNewick = false;
}
final String newick = newickInput.get();
if (newick == null || newick.equals("")) {
// can happen while initalising Beauti
final Node dummy = new Node();
setRoot(dummy);
} else {
try {
setRoot(parseNewick(newickInput.get()));
} catch (ParseCancellationException e) {
throw new RuntimeException(
"TreeParser cannot make sense of the Newick string "
+ "provided. It gives the following clue:\n"
+ e.getMessage());
}
}
super.initAndValidate();
if (sortNodesAlphabetically) {
// correct for node ordering: ensure order is alphabetical
for (int i = 0; i < getNodeCount() && i < labels.size(); i++) {
m_nodes[i].setID(labels.get(i));
}
Node[] nodes = new Node[labels.size()];
System.arraycopy(m_nodes, 0, nodes, 0, labels.size());
Arrays.sort(nodes, (o1, o2) -> o1.getID().compareTo(o2.getID()));
for (int i = 0; i < labels.size(); i++) {
m_nodes[i] = nodes[i];
nodes[i].setNr(i);
}
}
if (m_initial.get() != null) processTraits(m_initial.get().m_traitList.get());
else processTraits(m_traitList.get());
if (timeTraitSet != null) {
adjustTreeNodeHeights(root);
} else if (adjustTipHeightsInput.get()) {
double treeLength = TreeUtils.getTreeLength(this, getRoot());
double extraTreeLength = 0.0;
double maxTipHeight = 0.0;
// all nodes should be at zero height if no date-trait is available
for (int i = 0; i < getLeafNodeCount(); i++) {
double height = getNode(i).getHeight();
if (maxTipHeight < height) {
maxTipHeight = height;
}
extraTreeLength += height;
getNode(i).setHeight(0);
}
double scaleFactor = (treeLength + extraTreeLength) / treeLength;
final double SCALE_FACTOR_THRESHOLD = 0.001;
// if the change in total tree length is more than 0.1% then give the user a warning!
if (scaleFactor > 1.0 + SCALE_FACTOR_THRESHOLD) {
DecimalFormat format = new DecimalFormat("#.##");
Log.info.println(
"WARNING: Adjust tip heights attribute set to 'true' in " + getClass().getSimpleName());
Log.info.println(
" has resulted in significant (>"
+ format.format(SCALE_FACTOR_THRESHOLD * 100.0)
+ "%) change in tree length.");
Log.info.println(
" Use "
+ adjustTipHeightsInput.getName()
+ "='false' to override this default.");
Log.info.printf(" original max tip age = %8.3f\n", maxTipHeight);
Log.info.printf(" new max tip age = %8.3f\n", 0.0);
Log.info.printf(" original tree length = %8.3f\n", treeLength);
Log.info.printf(" new tree length = %8.3f\n", treeLength + extraTreeLength);
Log.info.printf(" TL scale factor = %8.3f\n", scaleFactor);
}
}
if (m_taxonset.get() == null && labels != null && isLabelledNewickInput.get()) {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(labels)), this);
}
initStateNodes();
} // init
/**
* override this for proposals,
*
* @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
*/
@Override
public double proposal() {
testing = isTestInput.get();
speciesTreeNodes = speciesTree.getNodesAsArray();
nLeafNodes = speciesTree.getLeafNodeCount();
nInternalNodes = speciesTree.getInternalNodeCount();
nSpeciesNodes = speciesTree.getNodeCount();
boolean isNarrow = isNarrowInput.get();
double logHastingsRatio = 0.0;
if (isNarrow) {
// only proceed to rearrange gene trees if the species tree can be changed
// doesn't execute if testing
if (!testing && !pickNarrow()) return Double.NEGATIVE_INFINITY;
int validGP = 0;
for (int i = nLeafNodes; i < nSpeciesNodes; ++i) {
validGP += isg(speciesTree.getNode(i));
}
final int c2 = sisg(yNode) + sisg(cNode);
fillNodes(); // fills in movedNodes and graftNodes
pruneAndRegraft(yNode, cNode, bNode);
final int validGPafter = validGP - c2 + sisg(yNode) + sisg(cNode);
logHastingsRatio += Math.log(validGP) - Math.log(validGPafter);
} else {
// only proceed to rearrange gene trees if the species tree can be changed
// doesn't execute if testing
if (!testing && !pickWide()) return Double.NEGATIVE_INFINITY;
fillNodes(); // fills in movedNodes and graftNodes
pruneAndRegraft(yNode, cNode, bNode);
}
for (final Tree geneTree : geneTreeInput.get())
geneTree.startEditing(null); // hack to stop beast.core.State.Trie memory leak
for (int i = 0; i < czBranchCount; i++) {
final List<SortedMap<Node, Node>> perBranchMovedNodes = movedNodes.get(i);
final SetMultimap<Integer, Node> perBranchGraftNodes = graftNodes.get(i);
final double logForward = rearrangeGeneTrees(perBranchMovedNodes, perBranchGraftNodes, true);
assert logForward != Double.NEGATIVE_INFINITY;
if (logForward == Double.NEGATIVE_INFINITY) return Double.NEGATIVE_INFINITY;
else logHastingsRatio += logForward;
}
// compute reverse move (Hastings ratio denominator)
final Node bNodeTmp = bNode;
final Node cNodeTmp = cNode;
bNode = cNodeTmp;
cNode = bNodeTmp;
fillNodes(); // fills in movedNodes and graftNodes for reverse move
for (int i = 0; i < czBranchCount; i++) {
final List<SortedMap<Node, Node>> perBranchMovedNodes = movedNodes.get(i);
final SetMultimap<Integer, Node> perBranchGraftNodes = graftNodes.get(i);
final double logReverse = rearrangeGeneTrees(perBranchMovedNodes, perBranchGraftNodes, false);
assert logReverse != Double.NEGATIVE_INFINITY;
if (logReverse == Double.NEGATIVE_INFINITY) return Double.NEGATIVE_INFINITY;
else logHastingsRatio -= logReverse;
}
return logHastingsRatio;
}
/** Recalculates all the intervals for the given beast.tree. */
@SuppressWarnings("unchecked")
protected void calculateIntervals() {
Tree tree = treeInput.get();
final int nodeCount = tree.getNodeCount();
times = new double[nodeCount];
int[] childCounts = new int[nodeCount];
collectTimes(tree, times, childCounts);
indices = new int[nodeCount];
HeapSort.sort(times, indices);
if (intervals == null || intervals.length != nodeCount) {
intervals = new double[nodeCount];
lineageCounts = new int[nodeCount];
lineagesAdded = new List[nodeCount];
lineagesRemoved = new List[nodeCount];
// lineages = new List[nodeCount];
storedIntervals = new double[nodeCount];
storedLineageCounts = new int[nodeCount];
} else {
for (List<Node> l : lineagesAdded) {
if (l != null) {
l.clear();
}
}
for (List<Node> l : lineagesRemoved) {
if (l != null) {
l.clear();
}
}
}
// start is the time of the first tip
double start = times[indices[0]];
int numLines = 0;
int nodeNo = 0;
intervalCount = 0;
while (nodeNo < nodeCount) {
int lineagesRemoved = 0;
int lineagesAdded = 0;
double finish = times[indices[nodeNo]];
double next;
do {
final int childIndex = indices[nodeNo];
final int childCount = childCounts[childIndex];
// don't use nodeNo from here on in do loop
nodeNo += 1;
if (childCount == 0) {
addLineage(intervalCount, tree.getNode(childIndex));
lineagesAdded += 1;
} else {
lineagesRemoved += (childCount - 1);
// record removed lineages
final Node parent = tree.getNode(childIndex);
// assert childCounts[indices[nodeNo]] == beast.tree.getChildCount(parent);
// for (int j = 0; j < lineagesRemoved + 1; j++) {
for (int j = 0; j < childCount; j++) {
Node child = j == 0 ? parent.getLeft() : parent.getRight();
removeLineage(intervalCount, child);
}
// record added lineages
addLineage(intervalCount, parent);
// no mix of removed lineages when 0 th
if (multifurcationLimit == 0.0) {
break;
}
}
if (nodeNo < nodeCount) {
next = times[indices[nodeNo]];
} else break;
} while (Math.abs(next - finish) <= multifurcationLimit);
if (lineagesAdded > 0) {
if (intervalCount > 0 || ((finish - start) > multifurcationLimit)) {
intervals[intervalCount] = finish - start;
lineageCounts[intervalCount] = numLines;
intervalCount += 1;
}
start = finish;
}
// add sample event
numLines += lineagesAdded;
if (lineagesRemoved > 0) {
intervals[intervalCount] = finish - start;
lineageCounts[intervalCount] = numLines;
intervalCount += 1;
start = finish;
}
// coalescent event
numLines -= lineagesRemoved;
}
intervalsKnown = true;
}