Examples with Node beast.evolution.tree.Node used on opensource projects

Example 21 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class SimulatedAlignment method getTransitionProbabilities.

// traverse
/**
 * get transition probability matrix for particular rate category *
 */
void getTransitionProbabilities(Tree tree, Node node, int rateCategory, double[] probs) {
    Node parent = node.getParent();
    double branchRate = (m_branchRateModel == null ? 1.0 : m_branchRateModel.getRateForBranch(node));
    branchRate *= m_siteModel.getRateForCategory(rateCategory, node);
    // Get the operational time of the branch
    // final double branchTime = branchRate * (parent.getHeight() - node.getHeight());
    // if (branchTime < 0.0) {
    // throw new RuntimeException("Negative branch length: " + branchTime);
    // }
    // double branchLength = m_siteModel.getRateForCategory(rateCategory) * branchTime;
    // // TODO Hack until SiteRateModel issue is resolved
    // if (m_siteModel.getSubstitutionModel() instanceof SubstitutionEpochModel) {
    // ((SubstitutionEpochModel)m_siteModel.getSubstitutionModel()).getTransitionProbabilities(tree.getNodeHeight(node),
    // tree.getNodeHeight(parent),branchLength, probs);
    // return;
    // }
    // m_siteModel.getSubstitutionModel().getTransitionProbabilities(branchLength, probs);
    m_siteModel.getSubstitutionModel().getTransitionProbabilities(node, parent.getHeight(), node.getHeight(), branchRate, probs);
}

Example 22 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class SimulatedAlignment method simulate.

// intArray2Sequence
/**
 * perform the actual sequence generation
 *
 * @return alignment containing randomly generated sequences for the nodes in the
 *         leaves of the tree
 */
public void simulate() {
    Node root = m_tree.getRoot();
    double[] categoryProbs = m_siteModel.getCategoryProportions(root);
    int[] category = new int[m_sequenceLength];
    for (int i = 0; i < m_sequenceLength; i++) {
        category[i] = Randomizer.randomChoicePDF(categoryProbs);
    }
    double[] frequencies = m_siteModel.getSubstitutionModel().getFrequencies();
    int[] seq = new int[m_sequenceLength];
    for (int i = 0; i < m_sequenceLength; i++) {
        seq[i] = Randomizer.randomChoicePDF(frequencies);
    }
    // alignment.setDataType(m_siteModel.getFrequencyModel().getDataType());
    traverse(root, seq, category);
}

Example 23 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class CladeSystem method addClades.

private BitSet addClades(Node node, boolean includeTips) {
    BitSet bits = new BitSet();
    if (node.isLeaf()) {
        int index = getTaxonIndex(node);
        bits.set(2 * index);
        if (includeTips) {
            addClade(bits);
        }
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node node1 = node.getChild(i);
            bits.or(addClades(node1, includeTips));
        }
        for (int i = 1; i < bits.length(); i = i + 2) {
            bits.set(i, false);
        }
        if (node.isFake()) {
            int index = getTaxonIndex(node.getDirectAncestorChild());
            bits.set(2 * index + 1);
        }
        addClade(bits);
    }
    return bits;
}

Example 24 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class CladeSystem method getTreeCladeCodes.

int getTreeCladeCodes(Node node, BitSet[] codes) {
    final int inode = node.getNr();
    codes[inode].clear();
    if (node.isLeaf()) {
        // getTaxonIndex(node);
        int index = getTaxonIndex(node);
        codes[inode].set(index);
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            final Node child = node.getChild(i);
            final int childIndex = getTreeCladeCodes(child, codes);
            codes[inode].or(codes[childIndex]);
        }
    }
    return inode;
}

Example 25 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class CladeSystem method collectAttributes.

private BitSet collectAttributes(Node node, Set<String> attributeNames) {
    BitSet bits = new BitSet();
    if (node.isLeaf()) {
        int index = getTaxonIndex(node);
        if (index < 0) {
            throw new IllegalArgumentException("Taxon, " + node.getID() + ", not found in target tree");
        }
        bits.set(2 * index);
    } else {
        for (int i = 0; i < node.getChildCount(); i++) {
            Node node1 = node.getChild(i);
            bits.or(collectAttributes(node1, attributeNames));
        }
        for (int i = 1; i < bits.length(); i = i + 2) {
            bits.set(i, false);
        }
        if (node.isFake()) {
            int index = getTaxonIndex(node.getDirectAncestorChild());
            bits.set(2 * index + 1);
        }
    }
    collectAttributesForClade(bits, node, attributeNames);
    return bits;
}