Java Node.getChild方法代码示例

import pal.tree.Node; //导入方法依赖的package包/类
/**
 * Calculates rooted support.
 * 
 * @param wTree the weighted tree instance
 * @param node the node
 * @param support the support
 * 
 * @return the fixed bit set
 */
private FixedBitSet rootedSupport(WeightedTree wTree, Node node, Map<FixedBitSet, Support> support) {
    FixedBitSet clade = new FixedBitSet(numTaxa);
    if (node.isLeaf()) {
        clade.set(idGroup.whichIdNumber(node.getIdentifier().getName()));
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node n = node.getChild(i);
            FixedBitSet childClade = rootedSupport(wTree, n, support);
            clade.union(childClade);
        }
    }

    Support s = support.get(clade);
    if (s == null) {
        s = new Support();
        support.put(clade, s);
    }
    s.add(wTree.getWeight(), TreeUtilities.safeNodeHeight(wTree.getTree(), node), node.getBranchLength());
    return clade;
}
 

import pal.tree.Node; //导入方法依赖的package包/类
/**
 * Make sure subtree below node has consistent heights, i.e. node height is higher than it's descendants
 * 
 * @param tree the tree
 * @param node the node
 * 
 * @return height of node
 */
public static double insureConsistency(Tree tree, Node node) {
    double height = TreeUtilities.safeNodeHeight(tree, node);
    if (node.isLeaf()) {
        return height;
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node n = node.getChild(i);
            final double childHeight = insureConsistency(tree, n);
            height = Math.max(height, childHeight);
        }
    }

    node.setNodeHeight(height);
    return height;
}
 

import pal.tree.Node; //导入方法依赖的package包/类
/**
 * Make sure subtree below node has consistent heights, i.e. node height is higher than it's descendants
 * 
 * @param tree the tree
 * @param node the node
 * 
 * @return height of node
 */
public static double insureConsistency(Tree tree, Node node) {
    double height = TreeUtils.safeNodeHeight(tree, node);
    if (node.isLeaf()) {
        return height;
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node n = node.getChild(i);
            final double childHeight = insureConsistency(tree, n);
            height = Math.max(height, childHeight);
        }
    }

    node.setNodeHeight(height);
    return height;
}
 

import pal.tree.Node; //导入方法依赖的package包/类
/**
 * Calculates rooted support.
 * 
 * @param wTree the weighted tree instance
 * @param node the node
 * @param support the support
 * 
 * @return the fixed bit set
 */
private FixedBitSet rootedSupport(WeightedTree wTree, Node node, Map<FixedBitSet, Support> support) {
    FixedBitSet clade = new FixedBitSet(numTaxa);
    if (node.isLeaf()) {
        clade.set(idGroup.whichIdNumber(node.getIdentifier().getName()));
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node n = node.getChild(i);
            FixedBitSet childClade = rootedSupport(wTree, n, support);
            clade.union(childClade);
        }
    }

    Support s = support.get(clade);
    if (s == null) {
        s = new Support();
        support.put(clade, s);
    }
    s.add(wTree.getWeight(), TreeUtils.safeNodeHeight(wTree.getTree(), node), node.getBranchLength());
    return clade;
}
 

import pal.tree.Node; //导入方法依赖的package包/类
/**
 * Calculates the number of branches from node to most remote tip.
 * 
 * @param node the starting node
 * 
 * @return the node distance
 */
public static int nodeDistance(final Node node) {
    if (node.isLeaf()) {
        return 0;
    }

    int d = 0;
    for (int i = 0; i < node.getChildCount(); i++) {
        Node n = node.getChild(i);
        d = Math.max(d, nodeDistance(n));
    }
    return d + 1;
}
 

import pal.tree.Node; //导入方法依赖的package包/类
private void getLeavesFromNode(Node node, Set<String> leaves) {
    if (node.isLeaf()) {
        leaves.add(node.getIdentifier().getName());
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node child = node.getChild(i);
            getLeavesFromNode(child, leaves);
        }
    }
}
 

import pal.tree.Node; //导入方法依赖的package包/类
private void simulate(SwMutSel model, Node node, byte state, int site) {

        for (int i = 0; i < node.getChildCount(); i++) {

            Node child = node.getChild(i);

            model.getPtCalculator().getTransitionProbabilities(Pt, child.getBranchLength());
            double[] Pij = Pt[state];
            byte newState = randomState(Pij);

            if (child.isLeaf()) {

                child.getSequence()[site] = newState;

            } else {

                simulate(model, child, newState, site);

            }

        }

    }
 

import pal.tree.Node; //导入方法依赖的package包/类
private double[] downTree() {
    //long start = CodeTimer.start();
    for (Node node : nodeTraversalOrder) {

        double[] conditional = new double[GeneticCode.CODON_STATES];
        for (int j : senseCodons) conditional[j] = 1.0;

        for (int j = 0; j < node.getChildCount(); j++) {
            Node child = node.getChild(j);

            double[] lowerConditional;

            if (child.isLeaf()) {
                if (GeneticCode.getInstance().isUnknownCodonState(states.get(getNodeLabel(child)))) {
                    lowerConditional = gapConditional;
                } else {
                    Arrays.fill(tipConditional, 0.0);
                    tipConditional[states.get(getNodeLabel(child))] = 1.0;
                    lowerConditional = tipConditional;
                }

            } else {
                lowerConditional = conditionals[child.getNumber()];
            }

            if (node.isRoot()) {
                conditionalAtRoot.add(new Partial(child, PhyloUtils.getNodeNumber(tree, child), Arrays.copyOf(lowerConditional, GeneticCode.CODON_STATES), child.getBranchLength()));
            }

            if (cladeModels.size() == 1) { // homogeneous model

                // TODO: A probability matrix (of sorts) already exists in TdGCodonModel...do we need to create it again?
                // cladeCalculators.get(ROOT_MODEL_NAME).getTransitionProbabilities(probMatrix, child.getBranchLength());
                // updateIntraCladeConditionals(lowerConditional, conditional, probMatrix);
                cladeCalculators.get(ROOT_MODEL_NAME).calculatePartialLikelihood(lowerConditional, conditional, child.getBranchLength());

            } else { // non-homogeneous model

                if (getNodeLabel(node).length() == 0 // the root of the tree is a parent without a label
                        || getNodeLabel(child).substring(0, 2).equals(getNodeLabel(node).substring(0, 2))) { // or we're not switching to a different model

                    cladeCalculators.get(getNodeLabel(child).substring(0, 2)).getTransitionProbabilities(probMatrix, child.getBranchLength());
                    updateIntraCladeConditionals(lowerConditional, conditional, probMatrix);

                } else { // this is a hostshift!
                    final double[][] probMatrix1 = new double[GeneticCode.CODON_STATES][GeneticCode.CODON_STATES];
                    cladeCalculators.get(getNodeLabel(node).substring(0, 2)).getTransitionProbabilities(probMatrix, child.getBranchLength() * Constants.CLADE_BRANCH_SPLIT);
                    cladeCalculators.get(getNodeLabel(child).substring(0, 2)).getTransitionProbabilities(probMatrix1, child.getBranchLength() * (1 - Constants.CLADE_BRANCH_SPLIT));
                    updateInterCladeConditionals(lowerConditional, conditional, probMatrix, probMatrix1);
                }
            }
        }

        // don't scale the root node
        if (!node.isRoot()) {
            scaleConditionals(node, conditional);
        }

        conditionals[node.getNumber()] = conditional;

    }

    return conditionals[tree.getRoot().getNumber()];
}
 

import pal.tree.Node; //导入方法依赖的package包/类
private void orderNodesInTree(Tree t) {
    for (Node n : PhyloUtils.internalNodes(t)) {

        Node n0 = n.getChild(CHILD_0);
        Set<String> child0 = Sets.newHashSet();
        getDescendants(n0, child0);

        Node n1 = n.getChild(CHILD_1);
        Set<String> child1 = Sets.newHashSet();
        getDescendants(n1, child1);

        Set<String> nodeKey = Sets.newHashSet();
        nodeKey.addAll(child0);
        nodeKey.addAll(child1);

        if (n.getChildCount() == UNROOTED_DEGREE) {
            Set<String> child2 = Sets.newHashSet();
            getDescendants(n.getChild(CHILD_2), child2);
            nodeKey.addAll(child2);
        }

        for (Set<String> s : descendantsOfNodes.keySet()) {
            if (s.equals(nodeKey)) {
                if (n.getChildCount() == UNROOTED_DEGREE) {
                    if (!n.isRoot())
                        throw new RuntimeException("ERROR: Trifurcating node isn't root. I don't know what to do!");


                    Node n2 = n.getChild(CHILD_2);

                    n.removeChild(0);
                    n.removeChild(0);
                    n.removeChild(0);

                    Set<String> originalChild0 = orderAtRoot.first;
                    Set<String> originalChild1 = orderAtRoot.second;
                    Set<String> originalChild2 = orderAtRoot.third;

                    if (originalChild0.equals(child0)) {
                        n.insertChild(n0, CHILD_0);
                    } else if (originalChild0.equals(child1)) {
                        n.insertChild(n1, CHILD_0);
                    } else {
                        n.insertChild(n2, CHILD_0);
                    }

                    if (originalChild1.equals(child0)) {
                        n.insertChild(n0, CHILD_1);
                    } else if (originalChild1.equals(child1)) {
                        n.insertChild(n1, CHILD_1);
                    } else {
                        n.insertChild(n2, CHILD_1);
                    }

                    if (originalChild2.equals(child0)) {
                        n.insertChild(n0, CHILD_2);
                    } else if (originalChild2.equals(child1)) {
                        n.insertChild(n1, CHILD_2);
                    } else {
                        n.insertChild(n2, CHILD_2);
                    }

                } else {
                    if (!child0.equals(descendantsOfNodes.get(s).first)) {
                        n.removeChild(0);
                        n.removeChild(0);

                        n.insertChild(n1, CHILD_0);
                        n.insertChild(n0, CHILD_1);
                    }
                }
            }
        }
    }
}