Examples with LikelihoodCore beast.evolution.likelihood.LikelihoodCore used on opensource projects

Example 1 with LikelihoodCore

use of beast.evolution.likelihood.LikelihoodCore in project bacter by tgvaughan.

the class ACGLikelihood method traverseNoRecurse.

/**
 * Traverse a marginal tree, computing partial likelihoods on the way.
 * This version avoids potentially-expensive recursive function calls.
 *
 * @param root Tree node
 * @param region region
 */
void traverseNoRecurse(MarginalNode root, Region region) {
    computePostOrder(root);
    LikelihoodCore lhc = likelihoodCores.get(region);
    for (MarginalNode node : postOrderNodes) {
        if (!node.isRoot()) {
            lhc.setNodeMatrixForUpdate(node.getNr());
            boolean cfEdge = node.cfNodeNr >= 0 && !acg.getNode(node.cfNodeNr).isRoot() && acg.getNode(node.cfNodeNr).getParent().getNr() == ((MarginalNode) node.getParent()).cfNodeNr;
            if (!cfEdge) {
                cacheMisses += 1;
                for (int i = 0; i < siteModel.getCategoryCount(); i++) {
                    double jointBranchRate = siteModel.getRateForCategory(i, node) * branchRateModel.getRateForBranch(node);
                    double parentHeight = node.getParent().getHeight();
                    double nodeHeight = node.getHeight();
                    substitutionModel.getTransitionProbabilities(node, parentHeight, nodeHeight, jointBranchRate, probabilities);
                    lhc.setNodeMatrix(node.getNr(), i, probabilities);
                }
            } else {
                cacheHits += 1;
                for (int i = 0; i < siteModel.getCategoryCount(); i++) {
                    lhc.setNodeMatrix(node.getNr(), i, cfTransitionProbs[node.cfNodeNr][i]);
                }
            }
        }
        if (!node.isLeaf()) {
            // LikelihoodCore only supports binary trees.
            List<Node> children = node.getChildren();
            lhc.setNodePartialsForUpdate(node.getNr());
            lhc.setNodeStatesForUpdate(node.getNr());
            lhc.calculatePartials(children.get(0).getNr(), children.get(1).getNr(), node.getNr());
            if (node.isRoot()) {
                double[] frequencies = substitutionModel.getFrequencies();
                double[] proportions = siteModel.getCategoryProportions(node);
                lhc.integratePartials(node.getNr(), proportions, rootPartials.get(region));
                for (int idx : constantPatterns.get(region)) {
                    rootPartials.get(region)[idx] += siteModel.getProportionInvariant();
                }
                lhc.calculateLogLikelihoods(rootPartials.get(region), frequencies, patternLogLikelihoods.get(region));
            }
        }
    }
}

Example 2 with LikelihoodCore

use of beast.evolution.likelihood.LikelihoodCore in project bacter by tgvaughan.

the class ACGLikelihood method calculateLogP.

@Override
public double calculateLogP() {
    while (true) {
        doLogPCalculation();
        if (logP > Double.NEGATIVE_INFINITY || scaleFactor >= maxScaleFactor)
            return logP;
        scaleFactor *= scaleFactorMultiplier;
        Log.warning.println("Turning on scaling to prevent numeric instability. Scale factor: " + scaleFactor);
        for (LikelihoodCore core : likelihoodCores.values()) core.setUseScaling(scaleFactor);
        requiresRecalculation();
    }
}

Example 3 with LikelihoodCore

use of beast.evolution.likelihood.LikelihoodCore in project bacter by tgvaughan.

the class ACGLikelihood method updateCores.

/**
 * Initialize likelihood cores.
 */
private void updateCores() {
    List<Region> regionList = acg.getRegions(locus);
    likelihoodCores.keySet().retainAll(regionList);
    for (Region region : regionList) {
        if (likelihoodCores.containsKey(region))
            continue;
        LikelihoodCore likelihoodCore;
        if (nStates == 4)
            likelihoodCore = new BeerLikelihoodCore4();
        else
            likelihoodCore = new BeerLikelihoodCore(nStates);
        likelihoodCores.put(region, likelihoodCore);
        likelihoodCore.initialize(acg.getNodeCount(), patterns.get(region).elementSet().size(), siteModel.getCategoryCount(), true, useAmbiguitiesInput.get());
        if (scaleFactor > 1.0)
            likelihoodCore.setUseScaling(scaleFactor);
        if (useAmbiguitiesInput.get())
            setPartials(likelihoodCore, patterns.get(region));
        else
            setStates(likelihoodCore, patterns.get(region));
        int intNodeCount = acg.getNodeCount() / 2;
        for (int i = 0; i < intNodeCount; i++) likelihoodCore.createNodePartials(intNodeCount + 1 + i);
    }
}