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

Example 16 with DefaultTreeModel

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

the class FNPRTest method testDoOperation.

/**
 * Test method for {@link SimpleMCMCOperator#doOperation()}.
 * @throws ImportException
 * @throws IOException
 */
public void testDoOperation() throws IOException, ImportException {
    // if you pick A you can reattach it to 3 new branches
    // if you pick B you can reattach it to 3 new branches
    // if you pick {A,B} you can reattach it to 2 new branches
    // if you pick C you can reattach it to 2 new branches
    // if you pick {A,B,C} you can reattach it to 1 new branch
    // if you pick D you can reattach it to 1 new branch
    // total: 1/12 for every new tree
    System.out.println("Test 1: Forward");
    // String treeMatch = "(((A,C),D),(B,E));";
    String treeMatch = "(((A,C),D),(E,B));";
    int count = 0;
    int reps = 100000;
    HashMap<String, Boolean> trees = new HashMap<String, Boolean>();
    for (int i = 0; i < reps; i++) {
        DefaultTreeModel treeModel = new DefaultTreeModel("treeModel", tree5);
        FNPR operator = new FNPR(treeModel, 1);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        // System.out.println(tree);
        if (!trees.containsKey(tree)) {
            trees.put(tree, true);
        }
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    System.out.println("Number of trees found:\t" + trees.size());
    Set<String> keys = trees.keySet();
    for (String s : keys) {
        System.out.println(s);
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 1.0 / 12.0);
    assertExpectation(1.0 / 12.0, p_1, reps);
}

Example 17 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel 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 DefaultTreeModel(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 18 with DefaultTreeModel

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

the class MsatFullLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    // taxa
    ArrayList<Taxon> taxonList1 = new ArrayList<Taxon>();
    Collections.addAll(taxonList1, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"));
    Taxa taxa1 = new Taxa(taxonList1);
    // msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa1);
    // pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2 });
    // create tree
    NewickImporter importer = new NewickImporter("(taxon1:7.5,(taxon2:5.3,taxon3:5.3):2.2);");
    Tree tree = importer.importTree(null);
    // treeModel
    TreeModel treeModel = new DefaultTreeModel(tree);
    // msatsubstModel
    AsymmetricQuadraticModel aqm1 = new AsymmetricQuadraticModel(msat, null);
    // siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm1);
    // treeLikelihood
    treeLikelihood1 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
    setUpExample2();
    setUpExample3();
}

Example 19 with DefaultTreeModel

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

the class MsatFullLikelihoodTest method setUpExample2.

private void setUpExample2() throws Exception {
    // taxa
    ArrayList<Taxon> taxonList2 = new ArrayList<Taxon>();
    Collections.addAll(taxonList2, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"));
    Taxa taxa2 = new Taxa(taxonList2);
    // msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa2);
    // pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2, 1, 2 });
    // create tree
    NewickImporter importer = new NewickImporter("(((taxon1:1.5,taxon2:1.5):1.5,(taxon3:2.1,taxon4:2.1):0.9):0.7,taxon5:3.7);");
    Tree tree = importer.importTree(null);
    // treeModel
    TreeModel treeModel = new DefaultTreeModel(tree);
    // msatsubstModel
    AsymmetricQuadraticModel aqm2 = new AsymmetricQuadraticModel(msat, null);
    // siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm2);
    // treeLikelihood
    treeLikelihood2 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}

Example 20 with DefaultTreeModel

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

the class TraceCorrelationAssert method createPrimateTreeModel.

// ************************** data ****************************
protected TreeModel createPrimateTreeModel() {
    SimpleNode[] nodes = new SimpleNode[10];
    for (int n = 0; n < 10; n++) {
        nodes[n] = new SimpleNode();
    }
    // nodes[0].setHeight(0);
    // human
    nodes[0].setTaxon(taxa[0]);
    // chimp
    nodes[1].setTaxon(taxa[1]);
    // bonobo
    nodes[2].setTaxon(taxa[2]);
    nodes[3].setHeight(0.010772);
    nodes[3].addChild(nodes[1]);
    nodes[3].addChild(nodes[2]);
    nodes[4].setHeight(0.024003);
    nodes[4].addChild(nodes[0]);
    nodes[4].addChild(nodes[3]);
    // gorilla
    nodes[5].setTaxon(taxa[3]);
    nodes[6].setHeight(0.036038);
    nodes[6].addChild(nodes[4]);
    nodes[6].addChild(nodes[5]);
    // orangutan
    nodes[7].setTaxon(taxa[4]);
    nodes[8].setHeight(0.069125);
    nodes[8].addChild(nodes[6]);
    nodes[8].addChild(nodes[7]);
    // siamang
    nodes[9].setTaxon(taxa[5]);
    SimpleNode root = new SimpleNode();
    root.setHeight(0.099582);
    root.addChild(nodes[8]);
    root.addChild(nodes[9]);
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    // treeModel
    return new DefaultTreeModel(tree);
}