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

Example 21 with DefaultTreeModel

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

the class TraceCorrelationAssert method createSpecifiedTree.

protected void createSpecifiedTree(String t) throws Exception {
    // Tree.Utils.newick(tree)
    // create tree
    NewickImporter importer = new NewickImporter(t);
    Tree tree = importer.importTree(null);
    // treeModel
    treeModel = new DefaultTreeModel(tree);
}

Example 22 with DefaultTreeModel

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

the class NormalizedSequenceLikelihoodTest method createSillyTreeModel.

protected TreeModel createSillyTreeModel(int numTaxa) {
    SimpleNode[] nodes = new SimpleNode[2 * numTaxa - 1];
    for (int n = 0; n < 2 * numTaxa - 1; n++) {
        nodes[n] = new SimpleNode();
    }
    nodes[0].setTaxon(taxa[0]);
    nodes[1].setTaxon(taxa[1]);
    nodes[2].setHeight(1);
    nodes[2].addChild(nodes[0]);
    nodes[2].addChild(nodes[1]);
    SimpleNode root = nodes[2];
    if (numTaxa == 3) {
        nodes[3].setTaxon(taxa[2]);
        nodes[4].setHeight(2);
        nodes[4].addChild(nodes[2]);
        nodes[4].addChild(nodes[3]);
        root = nodes[4];
    }
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    // treeModel
    return new DefaultTreeModel(tree);
}

Example 23 with DefaultTreeModel

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

the class PartitionData method createTreeModel.

public TreeModel createTreeModel() {
    TreeModel treeModel = null;
    if (this.demographicModelIndex == 0 && this.record.isTreeSet()) {
        treeModel = new DefaultTreeModel(this.record.getTree());
    } else if ((this.demographicModelIndex > 0 && this.demographicModelIndex <= lastImplementedIndex) && this.record.isTreeSet()) {
        Taxa taxa = new Taxa(this.record.getTree().asList());
        CoalescentSimulator topologySimulator = new CoalescentSimulator();
        treeModel = new DefaultTreeModel(topologySimulator.simulateTree(taxa, createDemographicFunction()));
    } else if ((this.demographicModelIndex > 0 && this.demographicModelIndex <= lastImplementedIndex) && this.record.isTaxaSet()) {
        Taxa taxa = this.record.getTaxa();
        CoalescentSimulator topologySimulator = new CoalescentSimulator();
        treeModel = new DefaultTreeModel(topologySimulator.simulateTree(taxa, createDemographicFunction()));
    // } else if (this.demographicModelIndex == 0 && this.record.taxaSet) {
    // throw new RuntimeException("Data and demographic model incompatible for partition ");
    } else {
        throw new RuntimeException("Data and demographic model incompatible.");
    }
    return treeModel;
}

Example 24 with DefaultTreeModel

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

the class BeagleSeqSimTest method simulateCodon.

// END: simulateAminoAcid
static void simulateCodon() {
    try {
        boolean calculateLikelihood = true;
        System.out.println("Test case 6: simulate codons");
        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(Utils.UNIFORM_CODON_FREQUENCIES);
        FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
        // create substitution model
        Parameter alpha = new Parameter.Default(1, 10);
        Parameter beta = new Parameter.Default(1, 5);
        // Parameter kappa = new Parameter.Default(1, 1);
        MG94HKYCodonModel mg94 = new MG94K80CodonModel(Codons.UNIVERSAL, alpha, beta, freqModel, new CodonOptions());
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(mg94);
        // 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);
        Alignment alignment = simulator.simulate(simulateInPar, false);
        System.out.println(alignment.toString());
        if (calculateLikelihood) {
            // NewBeagleSequenceLikelihood nbtl = new
            // NewBeagleSequenceLikelihood(alignment, treeModel,
            // substitutionModel, (SiteModel) siteRateModel,
            // branchRateModel, null, false,
            // PartialsRescalingScheme.DEFAULT);
            ConvertAlignment convert = new ConvertAlignment(Nucleotides.INSTANCE, GeneticCode.UNIVERSAL, alignment);
            BeagleTreeLikelihood nbtl = new // 
            BeagleTreeLikelihood(// 
            convert, // 
            treeModel, // 
            substitutionModel, // 
            siteRateModel, // 
            branchRateModel, // 
            null, // 
            false, PartialsRescalingScheme.DEFAULT, true);
            System.out.println("likelihood = " + nbtl.getLogLikelihood());
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch
}

Example 25 with DefaultTreeModel

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

the class BeagleSeqSimTest method simulateOnePartition.

// END: simulate topology
static void simulateOnePartition() {
    try {
        MathUtils.setSeed(666);
        System.out.println("Test case 2: simulateOnePartition");
        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 Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new // 
        Partition(// 
        treeModel, // 
        substitutionModel, // 
        siteRateModel, // 
        branchRateModel, // 
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAAGTGAGG");
        partition1.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        SimpleAlignment alignment = simulator.simulate(simulateInPar, false);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}