Examples with Clade dr.evolution.tree.Clade used on opensource projects

Example 16 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method getChanceForNodeHeights.

public double getChanceForNodeHeights(TreeModel tree, Likelihood likelihood) {
    double prob = 0.0;
    NodeRef node = tree.getRoot();
    Clade currentClade = getClade(tree, node);
    int childcount = tree.getChildCount(node);
    for (int i = 0; i < childcount; i++) {
        NodeRef child = tree.getChild(node, i);
        if (!tree.isExternal(child)) {
        //				prob += getChanceForNodeheights(tree, child, currentClade,
        //						likelihood, prior);
        }
    }
    return prob;
}

Example 17 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method addTree.

/**
     * increments the number of occurrences for all conditional clades
     *
     * @param tree - the tree to be added
     */
public void addTree(Tree tree) {
    samples++;
    List<Clade> clades = new ArrayList<Clade>();
    List<Clade> parentClades = new ArrayList<Clade>();
    // get clades contained in the tree
    getClades(tree, tree.getRoot(), parentClades, clades);
    // add the clade containing all taxa as well so that it get counted
    clades.add(parentClades.get(parentClades.size() - 1));
    parentClades.add(clades.get(clades.size() - 1));
    int size = clades.size();
    // tree probability
    for (int i = 0; i < size; i++) {
        Clade c = clades.get(i);
        // get the bits of the clade
        Clade parent = parentClades.get(i);
        HashMap<BitSet, Clade> coFreqs;
        // increment the clade occurrences
        if (cladeProbabilities.containsKey(c.getBits())) {
            Clade tmp = cladeProbabilities.get(c.getBits());
            // tmp.addSample();
            tmp.addHeight(c.getHeight());
        // add the amount to the current occurences
        // frequency += cladeProbabilities.get(c);
        } else {
            // just to set the first value of the height value list
            // c.addSample();
            c.addHeight(c.getHeight());
            cladeProbabilities.put(c.getBits(), c);
        }
        // increment the conditional clade occurrences
        if (!parent.equals(c)) {
            if (cladeCoProbabilities.containsKey(parent.getBits())) {
                coFreqs = cladeCoProbabilities.get(parent.getBits());
            } else {
                // if it's the first time we observe the parent then we need
                // a new list for its conditional clades
                coFreqs = new HashMap<BitSet, Clade>();
                cladeCoProbabilities.put(parent.getBits(), coFreqs);
            }
            // clade
            if (coFreqs.containsKey(c.getBits())) {
                Clade tmp = coFreqs.get(c.getBits());
                tmp.addHeight(c.getHeight());
            // coFrequency += coFreqs.get(c.getBits());
            } else {
                // TODO check this code, especially if the cloning is needed
                // and not just the clade could be added
                Clade tmp = new Clade((BitSet) c.getBits().clone(), c.getHeight());
                tmp.addHeight(c.getHeight());
                coFreqs.put(c.getBits(), tmp);
            }
        }
    }
}

Example 18 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class AbstractCladeImportanceDistribution method getClades.

/**
     * Creates a list with all clades of the tree
     *
     * @param taxonMap - the lookup map for the taxon representing an index
     * @param tree     - the tree from which the clades are extracted
     * @param node     - the starting node. All clades below starting at this branch
     *                 are added
     */
protected Clade getClades(Tree tree, NodeRef node, List<Clade> parentClades, List<Clade> childClade, HashMap<String, Integer> taxonMap) {
    // create a new bit set for this clade
    BitSet bits = new BitSet();
    Clade c = null;
    // check if the node is external
    if (tree.isExternal(node)) {
        // if so, the only taxon in the clade is I
        // int index = node.getNumber();
        String taxon = tree.getTaxon(node.getNumber()).getId();
        int index = taxonMap.get(taxon);
        bits.set(index);
        c = new Clade(bits, tree.getNodeHeight(node));
    } else {
        // otherwise, call all children and add its taxon together to one
        // clade
        NodeRef childNode = tree.getChild(node, 0);
        // add just my first child to the list
        // the second child is complementary to the first
        Clade leftChild = getClades(tree, childNode, parentClades, childClade, taxonMap);
        bits.or(leftChild.getBits());
        childNode = tree.getChild(node, 1);
        // add just my first child to the list
        // the second child is complementary to the first
        Clade rightChild = getClades(tree, childNode, parentClades, childClade, taxonMap);
        bits.or(rightChild.getBits());
        c = new Clade(bits, tree.getNodeHeight(node));
        if (leftChild.getSize() >= 2) {
            parentClades.add(c);
            childClade.add(leftChild);
        }
        if (rightChild.getSize() >= 2) {
            parentClades.add(c);
            childClade.add(rightChild);
        }
    }
    return c;
}

Example 19 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class AbstractCladeImportanceDistribution method getClades.

/**
     * Creates a list with all clades of the tree
     *
     * @param tree   - the tree from which the clades are extracted
     * @param node   - the starting node. All clades below starting at this branch
     *               are added
     * @param clades - the list in which the clades are stored
     * @param bits   - a bit set to which the current bits of the clades are added
     */
public void getClades(Tree tree, NodeRef node, List<Clade> clades, BitSet bits) {
    // create a new bit set for this clade
    BitSet bits2 = new BitSet();
    // check if the node is external
    if (tree.isExternal(node)) {
        // if so, the only taxon in the clade is I
        int index = node.getNumber();
        bits2.set(index);
    } else {
        // clade
        for (int i = 0; i < tree.getChildCount(node); i++) {
            NodeRef child = tree.getChild(node, i);
            getClades(tree, child, clades, bits2);
        }
        // add my bit set to the list
        clades.add(new Clade(bits2, tree.getNodeHeight(node)));
    }
    // this is needed for adding all children clades together
    if (bits != null) {
        bits.or(bits2);
    }
}

Example 20 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class AbstractCladeImportanceDistribution method getClades.

/**
     * Creates a list with all clades of the tree
     *
     * @param tree - the tree from which the clades are extracted
     * @param node - the starting node. All clades below starting at this branch
     *             are added
     */
protected Clade getClades(Tree tree, NodeRef node, List<Clade> parentClades, List<Clade> childClade) {
    // create a new bit set for this clade
    BitSet bits = new BitSet();
    Clade c = null;
    // check if the node is external
    if (tree.isExternal(node)) {
        // if so, the only taxon in the clade is I
        int index = node.getNumber();
        bits.set(index);
        c = new Clade(bits, tree.getNodeHeight(node));
    } else {
        // otherwise, call all children and add its taxon together to one
        // clade
        NodeRef childNode = tree.getChild(node, 0);
        // add just my first child to the list
        // the second child is complementary to the first
        Clade leftChild = getClades(tree, childNode, parentClades, childClade);
        bits.or(leftChild.getBits());
        childNode = tree.getChild(node, 1);
        // add just my first child to the list
        // the second child is complementary to the first
        Clade rightChild = getClades(tree, childNode, parentClades, childClade);
        bits.or(rightChild.getBits());
        c = new Clade(bits, tree.getNodeHeight(node));
        if (leftChild.getSize() >= 2) {
            parentClades.add(c);
            childClade.add(leftChild);
        }
        if (rightChild.getSize() >= 2) {
            parentClades.add(c);
            childClade.add(rightChild);
        }
    }
    return c;
}