Examples with MicrosatelliteSamplerTreeModel dr.evomodel.tree.MicrosatelliteSamplerTreeModel used on opensource projects

Example 1 with MicrosatelliteSamplerTreeModel

use of dr.evomodel.tree.MicrosatelliteSamplerTreeModel in project beast-mcmc by beast-dev.

the class MicrosatelliteSamplerTreeModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel tree = (TreeModel) xo.getElementFirstChild(TREE);
    Parameter internalVal = (Parameter) xo.getElementFirstChild(INTERNAL_VALUES);
    Patterns microsatellitePattern = (Patterns) xo.getElementFirstChild(EXTERNAL_VALUES);
    int[] externalValues = microsatellitePattern.getPattern(0);
    HashMap<String, Integer> taxaMap = new HashMap<String, Integer>(externalValues.length);
    boolean internalValuesProvided = false;
    if (xo.hasAttribute(USE_PROVIDED_INTERNAL_VALUES)) {
        internalValuesProvided = xo.getBooleanAttribute(USE_PROVIDED_INTERNAL_VALUES);
    }
    for (int i = 0; i < externalValues.length; i++) {
        taxaMap.put(microsatellitePattern.getTaxonId(i), i);
    }
    String modelId = xo.getAttribute("id", "treeMicrosatelliteSamplerModel");
    return new MicrosatelliteSamplerTreeModel(modelId, tree, internalVal, microsatellitePattern, externalValues, taxaMap, internalValuesProvided);
}

Example 2 with MicrosatelliteSamplerTreeModel

use of dr.evomodel.tree.MicrosatelliteSamplerTreeModel in project beast-mcmc by beast-dev.

the class RandomWalkIntegerSetSizeWeightedOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    double d = xo.getDoubleAttribute(WINDOW_SIZE);
    if (d != Math.floor(d)) {
        throw new XMLParseException("The window size of a " + RANDOM_WALK_INT_SET_SIZE_WGT_OP + " should be an integer");
    }
    double baseSetSize = xo.getDoubleAttribute(BASE_SET_SIZE);
    int windowSize = (int) d;
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    MicrosatelliteSamplerTreeModel msatSampleTreeModel = (MicrosatelliteSamplerTreeModel) xo.getChild(MicrosatelliteSamplerTreeModel.class);
    return new RandomWalkIntegerSetSizeWeightedOperator(parameter, windowSize, weight, msatSampleTreeModel, baseSetSize);
}

Example 3 with MicrosatelliteSamplerTreeModel

use of dr.evomodel.tree.MicrosatelliteSamplerTreeModel in project beast-mcmc by beast-dev.

the class MicrosatelliteFullAncestryImportanceSamplingOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    final MicrosatelliteSamplerTreeModel msatSamplerTreeModel = (MicrosatelliteSamplerTreeModel) xo.getChild(MicrosatelliteSamplerTreeModel.class);
    final MicrosatelliteModel msatModel = (MicrosatelliteModel) xo.getChild(MicrosatelliteModel.class);
    final BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    return new MicrosatelliteFullAncestryImportanceSamplingOperator(parameter, msatSamplerTreeModel, msatModel, branchRateModel, weight);
}

Example 4 with MicrosatelliteSamplerTreeModel

use of dr.evomodel.tree.MicrosatelliteSamplerTreeModel in project beast-mcmc by beast-dev.

the class MsatSamplingTreeLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    //taxa
    ArrayList<Taxon> taxonList3 = new ArrayList<Taxon>();
    Collections.addAll(taxonList3, new Taxon("Taxon1"), new Taxon("Taxon2"), new Taxon("Taxon3"), new Taxon("Taxon4"), new Taxon("Taxon5"), new Taxon("Taxon6"), new Taxon("Taxon7"));
    Taxa taxa3 = new Taxa(taxonList3);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 6);
    Patterns msatPatterns = new Patterns(msat, taxa3);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 3, 2, 4, 5, 1 });
    //create tree
    NewickImporter importer = new NewickImporter("(((Taxon1:0.3,Taxon2:0.3):0.6,Taxon3:0.9):0.9,((Taxon4:0.5,Taxon5:0.5):0.3,(Taxon6:0.7,Taxon7:0.7):0.1):1.0);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel eu1 = new AsymmetricQuadraticModel(msat, null);
    //create msatSamplerTreeModel
    Parameter internalVal = new Parameter.Default(new double[] { 2, 3, 4, 2, 1, 5 });
    int[] externalValues = msatPatterns.getPattern(0);
    HashMap<String, Integer> taxaMap = new HashMap<String, Integer>(externalValues.length);
    boolean internalValuesProvided = true;
    for (int i = 0; i < externalValues.length; i++) {
        taxaMap.put(msatPatterns.getTaxonId(i), i);
    }
    MicrosatelliteSamplerTreeModel msatTreeModel = new MicrosatelliteSamplerTreeModel("JUnitTestEx", treeModel, internalVal, msatPatterns, externalValues, taxaMap, internalValuesProvided);
    //create msatSamplerTreeLikelihood
    BranchRateModel branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    eu1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, eu1, branchRateModel);
    //eu2
    TwoPhaseModel eu2 = new TwoPhaseModel(msat, null, eu1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    eu2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, eu2, branchRateModel);
    //ec1
    LinearBiasModel ec1 = new LinearBiasModel(msat, null, eu1, new Parameter.Default(0.48), new Parameter.Default(0.0), false, false, false);
    ec1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, ec1, branchRateModel);
    //ec2
    TwoPhaseModel ec2 = new TwoPhaseModel(msat, null, ec1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    ec2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, ec2, branchRateModel);
    //el1
    LinearBiasModel el1 = new LinearBiasModel(msat, null, eu1, new Parameter.Default(0.2), new Parameter.Default(-0.018), true, false, false);
    el1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, el1, branchRateModel);
    AsymmetricQuadraticModel pu1 = new AsymmetricQuadraticModel(msat, null, new Parameter.Default(1.0), new Parameter.Default(0.015), new Parameter.Default(0.0), new Parameter.Default(1.0), new Parameter.Default(0.015), new Parameter.Default(0.0), false);
    pu1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pu1, branchRateModel);
    //ec2
    TwoPhaseModel pu2 = new TwoPhaseModel(msat, null, pu1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    pu2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pu2, branchRateModel);
    //ec1
    LinearBiasModel pc1 = new LinearBiasModel(msat, null, pu1, new Parameter.Default(0.48), new Parameter.Default(0.0), false, false, false);
    pc1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pc1, branchRateModel);
}

Example 5 with MicrosatelliteSamplerTreeModel

use of dr.evomodel.tree.MicrosatelliteSamplerTreeModel in project beast-mcmc by beast-dev.

the class MicrosatelliteSamplerTreeLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    MicrosatelliteSamplerTreeModel mstModel = (MicrosatelliteSamplerTreeModel) xo.getChild(MicrosatelliteSamplerTreeModel.class);
    MicrosatelliteModel microsatelliteModel = (MicrosatelliteModel) xo.getChild(MicrosatelliteModel.class);
    BranchRateModel branchRateModel;
    Object cxo = xo.getChild(BranchRateModel.class);
    if (xo.getChild(BranchRateModel.class) != null) {
        branchRateModel = (BranchRateModel) cxo;
        System.out.println("BranchRateModel provided to MicrosatelliteSamplerTreeLikelihood");
    } else if (xo.hasChildNamed(MUTATION_RATE)) {
        Parameter muRate = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
        branchRateModel = new StrictClockBranchRates(muRate);
        System.out.println("mutation rate provided to MicrosatelliteSamplerTreeLikelihood");
    } else {
        branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    }
    return new MicrosatelliteSamplerTreeLikelihood(mstModel, microsatelliteModel, branchRateModel);
}