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

Example 11 with Clade

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

the class AbstractImportanceDistributionOperator method createTree.

private double createTree(NodeRef node, Clade c) throws InvalidTreeException {
    double prob = 0.0;
    if (c.getSize() == 2) {
        // this clade only contains two tips
        // the split between them is trivial
        int leftTipIndex = c.getBits().nextSetBit(0);
        int rightTipIndex = c.getBits().nextSetBit(leftTipIndex + 1);
        NodeRef leftTip = externalNodes.get(leftTipIndex);
        NodeRef rightTip = externalNodes.get(rightTipIndex);
        removeChildren(node);
        NodeRef leftParent = tree.getParent(leftTip);
        if (leftParent != null)
            tree.removeChild(leftParent, leftTip);
        NodeRef rightParent = tree.getParent(rightTip);
        if (rightParent != null)
            tree.removeChild(rightParent, rightTip);
        tree.addChild(node, leftTip);
        tree.addChild(node, rightTip);
    } else {
        Clade[] clades = new Clade[2];
        prob = splitClade(c, clades);
        NodeRef leftChild, rightChild;
        if (clades[0].getSize() == 1) {
            int tipIndex = clades[0].getBits().nextSetBit(0);
            leftChild = externalNodes.get(tipIndex);
        } else {
            leftChild = internalNodes.poll();
            // TODO set the node height for the new node
            tree.setNodeHeight(leftChild, tree.getNodeHeight(node) * 0.5);
            prob += createTree(leftChild, clades[0]);
        }
        if (clades[1].getSize() == 1) {
            int tipIndex = clades[1].getBits().nextSetBit(0);
            rightChild = externalNodes.get(tipIndex);
        } else {
            rightChild = internalNodes.poll();
            // TODO set the node height for the new node
            tree.setNodeHeight(rightChild, tree.getNodeHeight(node) * 0.5);
            prob += createTree(rightChild, clades[1]);
        }
        removeChildren(node);
        NodeRef leftParent = tree.getParent(leftChild);
        if (leftParent != null)
            tree.removeChild(leftParent, leftChild);
        NodeRef rightParent = tree.getParent(rightChild);
        if (rightParent != null)
            tree.removeChild(rightParent, rightChild);
        tree.addChild(node, leftChild);
        tree.addChild(node, rightChild);
    }
    return prob;
}

Example 12 with Clade

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

the class AbstractImportanceDistributionOperator method assignCladeHeights.

/**
     * Creates a list with all clades of the tree
     *
     * @param node   - the starting node. All clades below starting at this branch
     *               are added
     * @param clades - the list in which the clades are stored
     */
private void assignCladeHeights(NodeRef node, HashMap<Clade, Double> 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);
            assignCladeHeights(child, clades, bits2);
        }
        Clade c = new Clade(bits2, tree.getNodeHeight(node));
        if (clades.containsKey(c)) {
            tree.setNodeHeight(node, clades.get(c));
            clades.remove(c);
        }
    }
    // this is needed for adding all children clades together
    if (bits != null) {
        bits.or(bits2);
    }
}

Example 13 with Clade

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

the class AbstractImportanceDistributionOperator method doImportanceDistributionOperation.

protected double doImportanceDistributionOperation(Likelihood likelihood) {
    final NodeRef root = tree.getRoot();
    BitSet all = new BitSet();
    all.set(0, (tree.getNodeCount() + 1) / 2);
    Clade rootClade = new Clade(all, tree.getNodeHeight(root));
    internalNodes.clear();
    fillInternalNodes(root);
    // remove the root
    internalNodes.poll();
    externalNodes.clear();
    fillExternalNodes(root);
    double prob;
    double back = probabilityEstimater.getTreeProbability(tree);
    try {
        tree.beginTreeEdit();
        List<Clade> originalClades = new ArrayList<Clade>();
        extractClades(tree, tree.getRoot(), originalClades, null);
        double[] originalNodeHeights = getAbsoluteNodeHeights(originalClades);
        Arrays.sort(originalNodeHeights);
        back += getChanceForNodeHeights(originalNodeHeights);
        prob = createTree(root, rootClade);
        assignDummyHeights(root);
        //			assignCladeHeights(tree.getRoot(), originalClades, null);
        //			double[] originalNodeHeights = getAbsoluteNodeHeights(originalClades);
        //			Arrays.sort(originalNodeHeights);
        //			prob += setMissingNodeHeights(tree.getChild(tree.getRoot(),0));
        //			prob += setMissingNodeHeights(tree.getChild(tree.getRoot(),1));
        prob += setNodeHeights(originalNodeHeights);
        //			List<Clade> newClades = new ArrayList<Clade>();
        //			extractClades(tree, tree.getRoot(), newClades, null);
        tree.endTreeEdit();
        tree.checkTreeIsValid();
    } catch (InvalidTreeException e) {
        throw new RuntimeException(e.getMessage());
    }
    tree.pushTreeChangedEvent(root);
    return back - prob;
}

Example 14 with Clade

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

the class ConditionalCladeFrequency method setNodeHeights.

public double setNodeHeights(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 += setNodeHeights(tree, child, currentClade, likelihood,
        //						prior);
        }
    }
    return prob;
}

Example 15 with Clade

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

the class ConditionalCladeFrequency method getTreeProbability.

/**
     * Calculates the probability of a given tree.
     *
     * @param tree - the tree to be analyzed
     * @return estimated posterior probability in log
     */
public double getTreeProbability(Tree tree, HashMap<String, Integer> taxonMap) {
    double prob = 0.0;
    List<Clade> clades = new ArrayList<Clade>();
    List<Clade> parentClades = new ArrayList<Clade>();
    // get clades contained in the tree
    getNonComplementaryClades(tree, tree.getRoot(), parentClades, clades, taxonMap);
    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);
        // set the occurrences to epsilon
        double tmp = EPSILON;
        double parentOccurrences = 0.0;
        BitSet parentBits = parent.getBits();
        if (cladeProbabilities.containsKey(parentBits)) {
            // if we observed this clade in the trace, add the
            // occurrences
            // to epsilon
            parentOccurrences += cladeProbabilities.get(parentBits).getSampleCount();
        }
        if (cladeCoProbabilities.containsKey(parentBits)) {
            // if we observed the parent clade
            HashMap<BitSet, Clade> conditionalProbs = cladeCoProbabilities.get(parentBits);
            BitSet bits = c.getBits();
            if (conditionalProbs.containsKey(bits)) {
                // if we observed this conditional clade in the trace,
                // add
                // the occurrences to epsilon
                tmp += conditionalProbs.get(bits).getSampleCount();
            }
        }
        // add epsilon for each clade
        final double splits = Math.pow(2, parent.getSize() - 1) - 1;
        parentOccurrences += EPSILON * splits;
        // multiply the conditional clade probability to the tree
        // probability
        prob += Math.log(tmp / parentOccurrences);
    }
    return prob;
}