Examples with JukesCantor beast.evolution.substitutionmodel.JukesCantor used on opensource projects

Example 6 with JukesCantor

use of beast.evolution.substitutionmodel.JukesCantor in project bacter by tgvaughan.

the class ACGLikelihoodTest method testBeagleLikelihood.

@Test
public void testBeagleLikelihood() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihoodBeagle argLikelihood = new ACGLikelihoodBeagle();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    acg.setEverythingDirty(true);
    try {
        double logP = argLikelihood.calculateLogP();
        double logPtrue = argLikelihoodSlow.calculateLogP();
        double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
        // Add a single recombination event
        Node node1 = acg.getExternalNodes().get(0);
        Node node2 = node1.getParent();
        double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
        double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
        int startLocus = 100;
        int endLocus = 200;
        Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
        acg.addConversion(recomb1);
        logP = argLikelihood.calculateLogP();
        logPtrue = argLikelihoodSlow.calculateLogP();
        relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
        // Add another recombination event
        node1 = acg.getExternalNodes().get(0);
        node2 = acg.getNode(20);
        height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
        height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
        startLocus = 250;
        endLocus = 300;
        Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
        acg.addConversion(recomb2);
        logP = argLikelihood.calculateLogP();
        logPtrue = argLikelihoodSlow.calculateLogP();
        relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
    } catch (RuntimeException ex) {
        System.err.println("Beagle library not found: skipping beagle likelihood test.");
    }
}

Example 7 with JukesCantor

use of beast.evolution.substitutionmodel.JukesCantor in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodFixedData.

@Test
public void testLikelihoodFixedData() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    acg.setEverythingDirty(true);
    double logP = argLikelihood.calculateLogP();
    double logPtrue = argLikelihoodSlow.calculateLogP();
    double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add a single recombination event
    Node node1 = acg.getExternalNodes().get(0);
    Node node2 = node1.getParent();
    double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    int startLocus = 100;
    int endLocus = 200;
    Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb1);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add another recombination event
    node1 = acg.getExternalNodes().get(0);
    node2 = acg.getNode(20);
    height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    startLocus = 250;
    endLocus = 300;
    Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb2);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
}

Example 8 with JukesCantor

use of beast.evolution.substitutionmodel.JukesCantor in project beast2 by CompEvol.

the class Utils method main.

public static void main(String[] args) {
    try {
        Sequence a = new Sequence("A", "A");
        Sequence b = new Sequence("B", "A");
        Sequence c = new Sequence("C", "A");
        Sequence d = new Sequence("D", "A");
        Alignment data = new Alignment();
        data.initByName("sequence", a, "sequence", b, "sequence", c, "sequence", d, "dataType", "nucleotide");
        TreeParser tree = new TreeParser();
        tree.initByName("taxa", data, "newick", "(((A:1,B:1):1,C:2):1,D:3)", "IsLabelledNewick", true);
        JukesCantor JC = new JukesCantor();
        JC.initAndValidate();
        SiteModel siteModel = new SiteModel();
        siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", JC);
        BeagleTreeLikelihood likelihood = new BeagleTreeLikelihood();
        likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    System.out.println("Success");
    // if we got this far, exit with status 0
    System.exit(0);
}

Example 9 with JukesCantor

use of beast.evolution.substitutionmodel.JukesCantor in project beast2 by CompEvol.

the class TreeLikelihoodTest method testBeagleRNALikelihood.

/**
 * Test only effective when BEAGLE installed - otherwise it will always
 * pass since BEAGLE code will never be run.
 *
 * @throws Exception
 */
@Test
public void testBeagleRNALikelihood() throws Exception {
    Sequence seq1 = new Sequence("t1", "GUACGUACGUAC");
    Sequence seq2 = new Sequence("t2", "UACGUACGUACG");
    Sequence seq3 = new Sequence("t3", "ACGUACGUACGU");
    Alignment data = new Alignment();
    data.initByName("sequence", seq1, "sequence", seq2, "sequence", seq3, "dataType", "nucleotide");
    Tree tree = BEASTTestCase.getTree(data, "((t1:0.5,t2:0.5):0.5,t3:1.0):0.0;");
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("gammaCategoryCount", 1, "substModel", new JukesCantor());
    TreeLikelihood likelihoodNoBeagle = newTreeLikelihood();
    likelihoodNoBeagle.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logLnoBeagle = likelihoodNoBeagle.calculateLogP();
    System.setProperty("java.only", "false");
    TreeLikelihood likelihoodBeagle = new TreeLikelihood();
    likelihoodBeagle.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logLBeagle = likelihoodBeagle.calculateLogP();
    assertEquals(logLBeagle, logLnoBeagle, BEASTTestCase.PRECISION);
}

Example 10 with JukesCantor

use of beast.evolution.substitutionmodel.JukesCantor in project beast2 by CompEvol.

the class TreeLikelihoodTest method testJC69Likelihood.

@Test
public void testJC69Likelihood() throws Exception {
    // Set up JC69 model: uniform freqs, kappa = 1, 0 gamma categories
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    JukesCantor JC = new JukesCantor();
    JC.initAndValidate();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", JC);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1992.2056440317247, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1992.2056440317247, BEASTTestCase.PRECISION);
}