Java Tree.getNodeCount方法代码示例

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * change the parameter and return the hastings ratio.
 *
 * @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {
    final Tree tree = treeInput.get(this);

    // randomly select internal node
    final int nodeCount = tree.getNodeCount();
    
    // Abort if no non-root internal nodes
    if (tree.getInternalNodeCount()==1)
        return Double.NEGATIVE_INFINITY;
    
    Node node;
    do {
        final int nodeNr = nodeCount / 2 + 1 + Randomizer.nextInt(nodeCount / 2);
        node = tree.getNode(nodeNr);
    } while (node.isRoot() || node.isLeaf());
    final double upper = node.getParent().getHeight();
    final double lower = Math.max(node.getLeft().getHeight(), node.getRight().getHeight());
    final double newValue = (Randomizer.nextDouble() * (upper - lower)) + lower;
    node.setHeight(newValue);

    return 0.0;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
private void setupAttributes(Tree tree) {
    for (int i = 0; i < tree.getNodeCount(); i++) {
        Node node = tree.getNode(i);
        Set<String> iter = node.getMetaDataNames();
        if (iter != null) {
        	for (String name : iter) {
                attributeNames.add(name);
            }
        }
    }

    for (TreeAnnotationPlugin beastObject : beastObjects) {
        Set<String> claimed = beastObject.setAttributeNames(attributeNames);
        attributeNames.removeAll(claimed);
    }
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * change the parameter and return the hastings ratio.
 *
 * @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {
    final Tree tree = treeInput.get(this);
    final int nNodeCount = tree.getNodeCount();
    int leafNodeCount = tree.getLeafNodeCount();

    //make sure that there is at least one non-fake and non-root internal node
    int fakeNodeCount = ((ZeroBranchSATree)tree).getDirectAncestorNodeCount();
    if (fakeNodeCount == leafNodeCount-1 || (fakeNodeCount == leafNodeCount-2 && !((ZeroBranchSANode)tree.getRoot()).isFake())) {
        return Double.NEGATIVE_INFINITY;
    }

    // randomly select internal node
    Node node;
    do {
        node = tree.getNode(leafNodeCount + Randomizer.nextInt(nNodeCount / 2));
    } while (node.isRoot() || ((ZeroBranchSANode)node).isFake());
    final double fUpper = node.getParent().getHeight();
    final double fLower = Math.max(node.getLeft().getHeight(), node.getRight().getHeight());
    final double newValue = (Randomizer.nextDouble() * (fUpper - fLower)) + fLower;
    node.setHeight(newValue);

    return 0.0;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * change the parameter and return the hastings ratio.
 *
 * @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {
    final Tree tree = treeInput.get(this);
    final int nNodeCount = tree.getNodeCount();
    int leafNodeCount = tree.getLeafNodeCount();

    //make sure that there is at least one non-fake and non-root internal node
    int fakeNodeCount = tree.getDirectAncestorNodeCount();
    if (fakeNodeCount == leafNodeCount-1 || (fakeNodeCount == leafNodeCount-2 && !tree.getRoot().isFake())) {
        return Double.NEGATIVE_INFINITY;
    }

    // randomly select internal node
    Node node;
    do {
        node = tree.getNode(leafNodeCount + Randomizer.nextInt(nNodeCount / 2));
    } while (node.isRoot() || node.isFake());
    final double fUpper = node.getParent().getHeight();
    final double fLower = Math.max(node.getLeft().getHeight(), node.getRight().getHeight());
    final double newValue = (Randomizer.nextDouble() * (fUpper - fLower)) + fLower;
    node.setHeight(newValue);

    return 0.0;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
private SATreeComparingAnalysis.TreeSummary[] makeTreeSummaryForAllTrees(List<Tree> trees, int treeCount){
    SATreeComparingAnalysis.TreeSummary[] treeSummary = new TreeSummary[treeCount];
    for(int treeIndex=0; treeIndex < treeCount; treeIndex++) {
        Tree tree = trees.get(treeIndex);
        ArrayList<Integer> dAPattern = new ArrayList<Integer>();
        for (int i=tree.getLeafNodeCount(); i< tree.getNodeCount(); i++){
            if (((ZeroBranchSANode)tree.getNode(i)).isFake()) {
                int descendantsCount = tree.getNode(i).getLeafNodeCount() - 1;
                if (descendantsCount > 0) {
                    for(int j=dAPattern.size(); j<descendantsCount; j++){
                        dAPattern.add(0);
                    }
                    int tmp = dAPattern.get(descendantsCount-1);
                    tmp++;
                    dAPattern.set(descendantsCount - 1, tmp);
                }
            }
        }
        treeSummary[treeIndex] = new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - ((ZeroBranchSATree)tree).getDirectAncestorNodeCount(), dAPattern);
    }
    return treeSummary;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
public void countTreesWithDClades() throws Exception {

        int dCladeCount = 0;
        Tree tree;

        for (int i =0; i < trace.treeCount; i++) {
            tree = trace.beastTrees.get(i);
            int j;
            for (j=0; j<tree.getNodeCount(); j++)
                if (tree.getNode(j).getChildCount() == 1) {
                    dCladeCount++;
                    break;
                }
        }

        double a =  (double)dCladeCount/trace.treeCount;
        System.out.format(dCladeCount + " trees (or %2.2f%%) have sampled internal nodes.%n", a*100);
        System.out.println();
    }
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
public void printTreeHeights(){
    Tree tree;

    System.out.print("heights <- c(");
    for (int i =0; i < trace.treeCount-1; i++) {
        tree = trace.beastTrees.get(i);
        System.out.print(tree.getRoot().getHeight() + ",");
    }
    tree = trace.beastTrees.get(trace.treeCount-1);
    System.out.println(tree.getRoot().getHeight() + ")");

    System.out.print("lengths <- c(");
    for (int i =0; i < trace.treeCount-1; i++) {
        tree = trace.beastTrees.get(i);
        double length = 0;
        for (int j=0; j< tree.getNodeCount(); j++){
            length += tree.getNode(j).getLength();
        }

        System.out.print(length + ",");
    }
    tree = trace.beastTrees.get(trace.treeCount-1);
    System.out.println(tree.getRoot().getHeight() + ")");
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * @param tree
 */
public double wide(final Tree tree) {

    final int nodeCount = tree.getNodeCount();

    //make sure that there are at least two distinct non-root nodes which are not direct ancestors.
    if (nodeCount == 3 && (tree.getRoot()).isFake()) {
        return Double.NEGATIVE_INFINITY;
    }

    Node i, j, iP, jP;
    do {
        i = tree.getNode(Randomizer.nextInt(nodeCount));
    } while (i.isRoot() || (i).isDirectAncestor());

    do {
        j = tree.getNode(Randomizer.nextInt(nodeCount));
    } while (j.getNr() == i.getNr() || j.isRoot() || (j).isDirectAncestor());

    iP = i.getParent();
    jP = j.getParent();

    if ((iP != jP) && (i != jP) && (j != iP)
            && (j.getHeight() < iP.getHeight())
            && (i.getHeight() < jP.getHeight())) {
        exchangeNodes(i, j, iP, jP);

        return 0.0;
    }

    // Couldn't find valid wide move on this beast.tree!
    return Double.NEGATIVE_INFINITY;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * @param tree
 */
public double wide(final Tree tree) {

    final int nodeCount = tree.getNodeCount();

    //make sure that there are at least two distinct non-root nodes which are not direct ancestors.
    if (nodeCount == 3 && ((ZeroBranchSANode)tree.getRoot()).isFake()) {
        return Double.NEGATIVE_INFINITY;
    }

    Node i, j, iP, jP;
    do {
        i = tree.getNode(Randomizer.nextInt(nodeCount));
    } while (i.isRoot() || ((ZeroBranchSANode)i).isDirectAncestor());

    do {
        j = tree.getNode(Randomizer.nextInt(nodeCount));
    } while (j.getNr() == i.getNr() || j.isRoot() || ((ZeroBranchSANode)j).isDirectAncestor());

    iP = i.getParent();
    jP = j.getParent();

    if ((iP != jP) && (i != jP) && (j != iP)
            && (j.getHeight() < iP.getHeight())
            && (i.getHeight() < jP.getHeight())) {
        exchangeNodes(i, j, iP, jP);

        return 0.0;
    }

    // Couldn't find valid wide move on this beast.tree!
    return Double.NEGATIVE_INFINITY;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * print the number of sampled ancestor in each tree
 *
 * @param zeroBranchTrees
 */
public void countSampledAncestors(boolean zeroBranchTrees){
    Tree tree;
    int sAcount;
    int totalsAcount = 0;

    if (zeroBranchTrees) {
        //System.out.println("Sample \t Prior \t Posterior");
        for (int i =0; i < trace.treeCount-1; i++) {
            tree = trace.beastTrees.get(i);
            sAcount=0;
            for (int j=0; j<tree.getNodeCount(); j++) {
                if (((ZeroBranchSANode)tree.getNode(j)).isFake()) sAcount++;
            }
            totalsAcount += sAcount;
            //System.out.println(i + "\t" + sAcount + "\t" + Randomizer.nextDouble());
        }

        tree = trace.beastTrees.get(trace.treeCount-1);
        sAcount=0;
        for (int j=0; j<tree.getNodeCount(); j++) {
            if (((ZeroBranchSANode)tree.getNode(j)).isFake()) sAcount++;
        }
        totalsAcount += sAcount;
        //System.out.println(trace.treeCount-1 + "\t" + sAcount + "\t" + Randomizer.nextDouble());
        System.out.format("The average number of sampled ancestors per tree is %2.2f", ((double) totalsAcount / trace.treeCount));
        System.out.println();

    }

}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
/**
 * extract coalescent times and tip information into array times from tree.
 */
private static void collectTimes(Tree tree, double[] times, int[] childCounts) {

    for (int i = 0; i < tree.getNodeCount(); i++) {
        NodeRef node = tree.getNode(i);
        times[i] = tree.getNodeHeight(node);
        childCounts[i] = tree.getChildCount(node);
    }
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
public AbstractCoalescentLikelihood(
        String name,
        Tree tree,
        TaxonList includeSubtree,
        List<TaxonList> excludeSubtrees) throws Tree.MissingTaxonException {

    super(name);

    this.tree = tree;

    if (includeSubtree != null) {
        includedLeafSet = Tree.Utils.getLeavesForTaxa(tree, includeSubtree);
    } else {
        includedLeafSet = null;
    }

    if (excludeSubtrees != null) {
        excludedLeafSets = new Set[excludeSubtrees.size()];
        for (int i = 0; i < excludeSubtrees.size(); i++) {
            excludedLeafSets[i] = Tree.Utils.getLeavesForTaxa(tree, excludeSubtrees.get(i));
        }
    } else {
        excludedLeafSets = new Set[0];
    }

    if (tree instanceof TreeModel) {
        addModel((TreeModel) tree);
    }

    intervals = new Intervals(tree.getNodeCount());
    storedIntervals = new Intervals(tree.getNodeCount());
    eventsKnown = false;

    addStatistic(new DeltaStatistic());

    likelihoodKnown = false;
}
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
public double narrow(final Tree tree) {

        final int nodeCount = tree.getNodeCount();

        //make sure that there are at least two distinct non-root nodes which are not direct ancestors.
        if (nodeCount == 3 && (tree.getRoot()).isFake()) {
            return Double.NEGATIVE_INFINITY;
        }

        Node i;
        do {
            i = tree.getNode(Randomizer.nextInt(nodeCount));
        } while (i.isRoot() || i.getParent().isRoot() || (i).isDirectAncestor());

        final Node iParent = i.getParent();
        final Node iGrandParent = iParent.getParent();
        Node iUncle = iGrandParent.getLeft();
        if (iUncle.getNr() == iParent.getNr()) {
            iUncle = iGrandParent.getRight();
            //assert (iUncle.getNr() != iParent.getNr());
        }
        //assert iUncle == getOtherChild(iGrandParent, iParent);

        //assert i.getHeight() <= iGrandParent.getHeight();

        if (iUncle.getHeight() < iParent.getHeight()) {
            exchangeNodes(i, iUncle, iParent, iGrandParent);
            return 0.0;
        } else {
            // Couldn't find valid narrow move on this beast.tree!!
            return Double.NEGATIVE_INFINITY;
        }

//        final int nInternalNodes = tree.getInternalNodeCount();  //TODO look if I can implement this more efficient code for SA trees
//        final int leafNodeCount = tree.getLeafNodeCount();
//        // make sure that the tree has at least two internal nodes
//        if (nInternalNodes <= 1 ) {
//            return Double.NEGATIVE_INFINITY;
//        }
//
//        //choose one of internal nodes that has at least one non-leaf node
//        //(there is always at least one such node as long as the tree has at least 2 internal nodes)
//        Node iGrandParent;
//        do  {
//            iGrandParent = tree.getNode(leafNodeCount + Randomizer.nextInt(nInternalNodes));
//        } while (iGrandParent.getLeft().isLeaf() && iGrandParent.getRight().isLeaf());
//
//        Node iParent = iGrandParent.getLeft();
//        Node iUncle = iGrandParent.getRight();
//        if (iParent.getHeight() < iUncle.getHeight()) {
//            iParent = iGrandParent.getRight();
//            iUncle = iGrandParent.getLeft();
//        }
//
//        if( iParent.isLeaf() ) {
//            return Double.NEGATIVE_INFINITY;
//        }
//
//        final Node i;
//
//        if (iParent.isFake()) {
//            if (iParent.getLeft().isDirectAncestor()) {
//                i = iParent.getRight();
//            }  else i = iParent.getLeft();
//        }  else {
//            i = (Randomizer.nextBoolean() ? iParent.getLeft() : iParent.getRight());
//        }
//
//        exchangeNodes(i, iUncle, iParent, iGrandParent);
//
//        return 0.0;

    }
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
public double narrow(final Tree tree) {

        final int nodeCount = tree.getNodeCount();

        //make sure that there are at least two distinct non-root nodes which are not direct ancestors.
        if (nodeCount == 3 && ((ZeroBranchSANode)tree.getRoot()).isFake()) {
            return Double.NEGATIVE_INFINITY;
        }

        Node i;
        do {
            i = tree.getNode(Randomizer.nextInt(nodeCount));
        } while (i.isRoot() || i.getParent().isRoot() || ((ZeroBranchSANode)i).isDirectAncestor());

        final Node iParent = i.getParent();
        final Node iGrandParent = iParent.getParent();
        Node iUncle = iGrandParent.getLeft();
        if (iUncle.getNr() == iParent.getNr()) {
            iUncle = iGrandParent.getRight();
            //assert (iUncle.getNr() != iParent.getNr());
        }
        //assert iUncle == getOtherChild(iGrandParent, iParent);

        //assert i.getHeight() <= iGrandParent.getHeight();

        if (iUncle.getHeight() < iParent.getHeight()) {
            exchangeNodes(i, iUncle, iParent, iGrandParent);
            return 0.0;
        } else {
            // Couldn't find valid narrow move on this beast.tree!!
            return Double.NEGATIVE_INFINITY;
        }

//        final int nInternalNodes = tree.getInternalNodeCount();  //TODO look if I can implement this more efficient code for SA trees
//        final int leafNodeCount = tree.getLeafNodeCount();
//        // make sure that the tree has at least two internal nodes
//        if (nInternalNodes <= 1 ) {
//            return Double.NEGATIVE_INFINITY;
//        }
//
//        //choose one of internal nodes that has at least one non-leaf node
//        //(there is always at least one such node as long as the tree has at least 2 internal nodes)
//        Node iGrandParent;
//        do  {
//            iGrandParent = tree.getNode(leafNodeCount + Randomizer.nextInt(nInternalNodes));
//        } while (iGrandParent.getLeft().isLeaf() && iGrandParent.getRight().isLeaf());
//
//        Node iParent = iGrandParent.getLeft();
//        Node iUncle = iGrandParent.getRight();
//        if (iParent.getHeight() < iUncle.getHeight()) {
//            iParent = iGrandParent.getRight();
//            iUncle = iGrandParent.getLeft();
//        }
//
//        if( iParent.isLeaf() ) {
//            return Double.NEGATIVE_INFINITY;
//        }
//
//        final Node i;
//
//        if (iParent.isFake()) {
//            if (iParent.getLeft().isDirectAncestor()) {
//                i = iParent.getRight();
//            }  else i = iParent.getLeft();
//        }  else {
//            i = (Randomizer.nextBoolean() ? iParent.getLeft() : iParent.getRight());
//        }
//
//        exchangeNodes(i, iUncle, iParent, iGrandParent);
//
//        return 0.0;

    }
 

import beast.evolution.tree.Tree; //导入方法依赖的package包/类
public static void main (String[] arg) throws Exception{


        Node root = new Node();
        root.setNr(4);
        root.setHeight(2.0);
        Node left = new Node();
        left.setNr(3);
        left.setHeight(1.0);
        root.setLeft(left);
        left.setParent(root);
        Node right = new Node();
        right.setNr(2);
        right.setHeight(2.0);
        root.setRight(right);
        right.setParent(root);
        Node leftLeft = new Node();
        leftLeft.setNr(0);
        leftLeft.setHeight(0.0);
        left.setLeft(leftLeft);
        leftLeft.setParent(left);
        Node leftRight = new Node();
        leftRight.setNr(1);
        leftRight.setHeight(1.0);
        left.setRight(leftRight);
        leftRight.setParent(left);
        Tree tree = new Tree(root);

        System.out.println("The tree is " + tree.getRoot().toShortNewick(false));


        SATreeComparingAnalysis analysis = new SATreeComparingAnalysis();
        //process tree. consider Fake SA trees
        ArrayList<Integer> dAPattern = new ArrayList<Integer>();
        for (int i=tree.getLeafNodeCount(); i< tree.getNodeCount(); i++){
            if (((ZeroBranchSANode)tree.getNode(i)).isFake()) {
                int descendantsCount = tree.getNode(i).getLeafNodeCount() - 1;
                if (descendantsCount > 0) {
                    for(int j=dAPattern.size(); j<descendantsCount; j++){
                        dAPattern.add(0);
                    }
                    int tmp = dAPattern.get(descendantsCount-1);
                    tmp++;
                    dAPattern.set(descendantsCount - 1, tmp);
                }
            }
        }

        SATreeComparingAnalysis.TreeSummary treeSummary = analysis.new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - ((ZeroBranchSATree)tree).getDirectAncestorNodeCount(), dAPattern);

        System.out.println(treeSummary.dAPattern.toString());
        ArrayList<Integer> a = new ArrayList<Integer> (Arrays.asList(new Integer[]{1, 1}));
        System.out.println(treeSummary.dAPattern.equals(a));
    }