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

Example 1 with DefaultTreeModel

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

the class DataLikelihoodTester2 method createSpecifiedTree.

private static TreeModel createSpecifiedTree(String t) throws Exception {
    NewickImporter importer = new NewickImporter(t);
    Tree tree = importer.importTree(null);
    // treeModel
    return new DefaultTreeModel(tree);
}

Example 2 with DefaultTreeModel

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

the class SubtreeSlideOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean swapRates = xo.getAttribute(SWAP_RATES, false);
    boolean swapTraits = xo.getAttribute(SWAP_TRAITS, false);
    boolean scaledDirichletBranches = xo.getAttribute(DIRICHLET_BRANCHES, false);
    AdaptationMode mode = AdaptationMode.DEFAULT;
    if (xo.hasAttribute(AdaptableMCMCOperator.AUTO_OPTIMIZE)) {
        if (xo.getBooleanAttribute(AdaptableMCMCOperator.AUTO_OPTIMIZE)) {
            mode = AdaptationMode.ADAPTATION_ON;
        } else {
            mode = AdaptationMode.ADAPTATION_OFF;
        }
    }
    DefaultTreeModel treeModel = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234);
    final double size = xo.getAttribute("size", 1.0);
    if (Double.isInfinite(size) || size <= 0.0) {
        throw new XMLParseException("size attribute must be positive and not infinite. was " + size + " for tree " + treeModel.getId());
    }
    final boolean gaussian = xo.getBooleanAttribute("gaussian");
    SubtreeSlideOperator operator = new SubtreeSlideOperator(treeModel, weight, size, gaussian, swapRates, swapTraits, scaledDirichletBranches, mode, targetAcceptance);
    return operator;
}

Example 3 with DefaultTreeModel

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

the class TreeBitRandomWalkOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    DefaultTreeModel treeModel = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class);
    String trait1 = null;
    String trait2 = null;
    if (xo.hasAttribute(INDICTATOR_TRAIT))
        trait1 = xo.getStringAttribute(INDICTATOR_TRAIT);
    if (xo.hasAttribute(TRAIT2))
        trait2 = xo.getStringAttribute(TRAIT2);
    int k = xo.getAttribute("k", 1);
    boolean swapTrait2 = xo.getAttribute(SWAP_TRAIT2, true);
    return new TreeBitRandomWalkOperator(treeModel, trait1, trait2, weight, k, swapTrait2);
}

Example 4 with DefaultTreeModel

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

the class TreeBitMoveOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    DefaultTreeModel treeModel = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class);
    String trait1 = null;
    String trait2 = null;
    if (xo.hasAttribute(INDICTATOR_TRAIT))
        trait1 = xo.getStringAttribute(INDICTATOR_TRAIT);
    if (xo.hasAttribute(TRAIT2))
        trait2 = xo.getStringAttribute(TRAIT2);
    return new TreeBitMoveOperator(treeModel, trait1, trait2, weight);
}

Example 5 with DefaultTreeModel

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

the class BeagleSeqSimTest method simulateAminoAcid.

// END: simulateThreePartitions
static void simulateAminoAcid() {
    try {
        System.out.println("Test case 4: simulateAminoAcid");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        DefaultTreeModel treeModel = new DefaultTreeModel(tree);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05 });
        FrequencyModel freqModel = new FrequencyModel(AminoAcids.INSTANCE, freqs);
        // create substitution model
        EmpiricalRateMatrix rateMatrix = Blosum62.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
        // create partition
        Partition partition1 = new // 
        Partition(// 
        treeModel, // 
        substitutionModel, // 
        siteRateModel, // 
        branchRateModel, // 
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch
}