Java Node.getLeft方法代码示例

import beast.evolution.tree.Node; //导入方法依赖的package包/类
private SetMultimap<Integer, Node> getConnectingNodes(Node speciesTreeNode, MinimumDouble tipwardFreedom) {
    final Node leftChildNode = speciesTreeNode.getLeft();
    final Node rightChildNode = speciesTreeNode.getRight();
    final int leftChildNodeNumber = leftChildNode.getNr();
    final int rightChildNodeNumber = rightChildNode.getNr();
    final Set<String> leftChildDescendants = findDescendants(leftChildNode, leftChildNodeNumber);
    final Set<String> rightChildDescendants = findDescendants(rightChildNode, rightChildNodeNumber);

    final SetMultimap<Integer, Node> allConnectingNodes = 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> jConnectingNodes = new HashSet<Node>();
        findConnectingNodes(geneTreeRootNode, jConnectingNodes, leftChildDescendants, rightChildDescendants, tipwardFreedom);
        allConnectingNodes.putAll(j, jConnectingNodes);
        geneTree.startEditing(null); // hack to stop beast.core.State.Trie memory leak
    }

    return allConnectingNodes;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
protected Set<String> findDescendants(Node speciesTreeNode, int speciesTreeNodeNumber) {
    final Multimap<Integer, String> numberTipMap = speciesTreeInput.get().getNumberTipMap();
    final Set<String> descendantNames = new HashSet<>();

    if (speciesTreeNode.isLeaf()) {
        descendantNames.addAll(numberTipMap.get(speciesTreeNodeNumber));
    } else {
        final Node leftChild = speciesTreeNode.getLeft();
        final Node rightChild = speciesTreeNode.getRight();
        final int leftChildNumber = leftChild.getNr();
        final int rightChildNumber = rightChild.getNr();

        descendantNames.addAll(findDescendants(leftChild, leftChildNumber));
        descendantNames.addAll(findDescendants(rightChild, rightChildNumber));
    }

    return descendantNames;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
private boolean findGraftBranches(Node geneTreeNode, Set<Node> graftNodes, Set<String> branchDescendants) {
    if (geneTreeNode.isLeaf()) {
        final String descendantName = geneTreeNode.getID();
        return branchDescendants.contains(descendantName);
    }

    final Node leftChild = geneTreeNode.getLeft();
    final Node rightChild = geneTreeNode.getRight();
    final boolean leftOverlaps = findGraftBranches(leftChild, graftNodes, branchDescendants);
    final boolean rightOverlaps = findGraftBranches(rightChild, graftNodes, branchDescendants);

    // subtree defined by a child node overlaps species subtree defined by branch
    if (leftOverlaps || rightOverlaps) {
        if (leftOverlaps) {
            graftNodes.add(leftChild);
        }

        if (rightOverlaps) {
            graftNodes.add(rightChild);
        }

        return true;
    }

    return false;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
private SetMultimap<Integer, Node> getConnectingNodes(Node speciesTreeNode, MinimumDouble tipwardFreedom, MinimumDouble rootwardFreedom) {
    final Node leftChildNode = speciesTreeNode.getLeft();
    final Node rightChildNode = speciesTreeNode.getRight();
    final int leftChildNodeNumber = leftChildNode.getNr();
    final int rightChildNodeNumber = rightChildNode.getNr();
    final Set<String> leftChildDescendants = findDescendants(leftChildNode, leftChildNodeNumber);
    final Set<String> rightChildDescendants = findDescendants(rightChildNode, rightChildNodeNumber);

    final SetMultimap<Integer, Node> allConnectingNodes = 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> jConnectingNodes = new HashSet<Node>();
        findConnectingNodes(geneTreeRootNode, jConnectingNodes, leftChildDescendants, rightChildDescendants, tipwardFreedom, rootwardFreedom);
        allConnectingNodes.putAll(j, jConnectingNodes);
        geneTree.startEditing(null); // hack to stop beast.core.State.Trie memory leak
    }

    return allConnectingNodes;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
 * recursively walk through the tree top down, and add sequence to alignment whenever
 * a leave node is reached.
 *
 * @param node           reference to the current node, for which we visit all children
 * @param parentSequence randomly generated sequence of the parent node
 * @param category       array of categories for each of the sites
 * @param alignment
 */
void traverse(Node node, int[] parentSequence, int[] category) {
    for (int childIndex = 0; childIndex < 2; childIndex++) {
        Node child = (childIndex == 0 ? node.getLeft() : node.getRight());
        for (int i = 0; i < m_categoryCount; i++) {
            getTransitionProbabilities(m_tree, child, i, m_probabilities[i]);
        }

        int[] seq = new int[m_sequenceLength];
        double[] cProb = new double[m_stateCount];
        for (int i = 0; i < m_sequenceLength; i++) {
            System.arraycopy(m_probabilities[category[i]], parentSequence[i] * m_stateCount, cProb, 0, m_stateCount);
            seq[i] = Randomizer.randomChoicePDF(cProb);
        }

        if (child.isLeaf()) {
            sequenceInput.setValue(intArray2Sequence(seq, child), this);
        } else {
            traverse(child, seq, category);
        }
    }
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
 * recursively walk through the tree top down, and add sequence to alignment whenever
 * a leave node is reached.
 *
 * @param node           reference to the current node, for which we visit all children
 * @param parentSequence randomly generated sequence of the parent node
 * @param category       array of categories for each of the sites
 * @param alignment
 * @
 */
void traverse(Node node, int[] parentSequence, int[] category, Alignment alignment)  {
    for (int childIndex = 0; childIndex < 2; childIndex++) {
        Node child = (childIndex == 0 ? node.getLeft() : node.getRight());
        for (int i = 0; i < m_categoryCount; i++) {
            getTransitionProbabilities(m_tree, child, i, m_probabilities[i]);
        }

        int[] seq = new int[m_sequenceLength];
        double[] cProb = new double[m_stateCount];
        for (int i = 0; i < m_sequenceLength; i++) {
            System.arraycopy(m_probabilities[category[i]], parentSequence[i] * m_stateCount, cProb, 0, m_stateCount);
            seq[i] = Randomizer.randomChoicePDF(cProb);
        }

        if (child.isLeaf()) {
            alignment.sequenceInput.setValue(intArray2Sequence(seq, child), alignment);
        } else {
            traverse(child, seq, category, alignment);
        }
    }
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
 * Extract the sampled tree by discarding all the nodes that have -1 number simultaneously suppress single
 * child nodes (nodes with only one child numbered by non-negative number)
 * @param node
 */
public void removeSingleChildNodes(Node node) {
    if (!node.isLeaf()) {
        Node left = node.getLeft();
        Node right = node.getRight();

        removeSingleChildNodes(left);
        removeSingleChildNodes(right);
        for (Node child:node.getChildren()) {
            if (child.getNr() == -1) {
                node.removeChild(child);
            }
        }
        if (node.getChildCount() == 1 && node.getParent() != null) {
            Node parent = node.getParent();
            Node newChild =  node.getLeft();
            parent.removeChild(node);
            parent.addChild(newChild);
            newChild.setParent(parent);
            //node.setParent(null);
        }
    }
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
 * randomly changes left and right children in every internal node *
 */
private void reorder(final Node node) {
    if (!node.isLeaf()) {
        if (Randomizer.nextBoolean()) {
            final Node tmp = node.getLeft();
            node.setLeft(node.getRight());
            node.setRight(tmp);
        }
        reorder(node.getLeft());
        reorder(node.getRight());
    }
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
private boolean findMovedPairs(Node geneTreeNode, Map<Node, Node> movedNodes, Set<String> chosenDescendants, double lowerHeight, double upperHeight) {
    if (geneTreeNode.isLeaf()) {
        final String descendantName = geneTreeNode.getID();
        // returns true if this leaf is a descendant of the chosen species
        return chosenDescendants.contains(descendantName);
    }

    final Node leftChild = geneTreeNode.getLeft();
    final Node rightChild = geneTreeNode.getRight();

    // left child descendants are exclusively descendants of the chosen species tree node
    final boolean leftExclusive = findMovedPairs(leftChild, movedNodes, chosenDescendants, lowerHeight, upperHeight);
    // right child descendants are exclusively descendants of the chosen species tree node
    final boolean rightExclusive = findMovedPairs(rightChild, movedNodes, chosenDescendants, lowerHeight, upperHeight);

    final double nodeHeight = geneTreeNode.getHeight();
    if (nodeHeight >= lowerHeight && nodeHeight < upperHeight) {
        if (leftExclusive ^ rightExclusive) {
            if (leftExclusive) { // leave right child attached to original parent
                movedNodes.put(geneTreeNode, rightChild);
            } else { // leaf left child attached to original parent
                movedNodes.put(geneTreeNode, leftChild);
            }
        }
    }

    // returns true if all descendants of this gene tree node are also descendants of the chosen species tree node
    return leftExclusive && rightExclusive;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
 * @param parent the parent
 * @param child  the child that you want the sister of
 * @return the other child of the given parent.
 */
protected Node getOtherChild(final Node parent, final Node child) {
    if (parent.getLeft().getNr() == child.getNr()) {
        return parent.getRight();
    } else {
        return parent.getLeft();
    }
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
 *
 * @param node
 * @return all sampled ancestor clades descendant from node
 */
public ArrayList<String> extractAllSAClades(Node node) {
    ArrayList<String> tmp = new ArrayList<String>();

    if (node.isLeaf())
        tmp.add(extractSAClade(node));
    if (node.getLeft() != null)
        tmp.addAll(extractAllSAClades(node.getLeft()));
    if (node.getRight() != null)
        tmp.addAll(extractAllSAClades(node.getRight()));

    return tmp;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
public static void convertToFakeSATree(Node node, int[] nextNr) {
    if (!node.isLeaf()) {
        convertToFakeSATree(node.getLeft(), nextNr);
        if (node.getRight() != null) {
            convertToFakeSATree(node.getRight(), nextNr);
        }
    }
    if (node.getChildCount() == 1) {
        Node parent = new Node();
        parent.setHeight(node.getHeight());
        Node child = node.getLeft();
        parent.setLeft(child);
        child.setParent(parent);
        node.removeChild(child);
        parent.setRight(node);
        parent.setNr(nextNr[0]);
        nextNr[0]++;
        if (!node.isRoot()) {
            Node grandparent = node.getParent();

            if (grandparent.getLeft().getNr() == node.getNr()) {
                grandparent.setLeft(parent);
            }  else {
                grandparent.setRight(parent);
            }
            parent.setParent(grandparent);
        }  else {
            node.getTree().setRoot(parent);
        }
        node.setParent(parent);
    }
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
private ArrayList<Integer> listNodesUnder(Node node) {

        ArrayList<Integer> tmp = new ArrayList<Integer>();
        if (node.getChildCount() < 2)
            tmp.add(node.getNr()+1);
        if (node.getLeft() != null)
            tmp.addAll(listNodesUnder(node.getLeft()));
        if (node.getRight() != null)
            tmp.addAll(listNodesUnder(node.getRight()));
        return tmp;
    }
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
public ArrayList<String> extractAllDClades(Node node, boolean zeroBranchTrees) {
    ArrayList<String> tmp = new ArrayList<String>();

    if ((!zeroBranchTrees && node.getChildCount() < 2) || (zeroBranchTrees && node.isLeaf()))
        tmp.add(extractDClade(node, zeroBranchTrees));
    if (node.getLeft() != null)
        tmp.addAll(extractAllDClades(node.getLeft(), zeroBranchTrees));
    if (node.getRight() != null)
        tmp.addAll(extractAllDClades(node.getRight(), zeroBranchTrees));

    return tmp;
}
 

import beast.evolution.tree.Node; //导入方法依赖的package包/类
public void removeFossils(Node node, Tree tree, ArrayList<Node> removedNodes) {
    if (node.isLeaf()) {
        if (!extantTaxa.contains(node.getID())) {
            node.getParent().removeChild(node);
            node.setParent(null);
            removedNodes.add(node);
        }
    }  else {
        Node left = node.getLeft();
        Node right = node.getRight();
        removeFossils(left, tree, removedNodes);
        removeFossils(right, tree, removedNodes);


        if (node.isLeaf()) {
            node.getParent().removeChild(node);
            node.setParent(null);
            removedNodes.add(node);
        }
        if (node.getChildCount() == 1) {
            Node child = node.getChild(0);
            if (node.getParent() != null) {
                Node grandParent = node.getParent();
                grandParent.removeChild(node);
                grandParent.addChild(child);
                child.setParent(grandParent);
                node.setParent(null);
            }
            else {
                child.setParent(null);
                tree.setRootOnly(child);
            }
            removedNodes.add(node);
        }

    }
}