Examples with Alignment beast.evolution.alignment.Alignment used on opensource projects

Example 31 with Alignment

use of beast.evolution.alignment.Alignment in project beast2 by CompEvol.

the class TreeLikelihoodTest method testHKY85GLikelihood.

@Test
public void testHKY85GLikelihood() throws Exception {
    // Set up HKY85+G model: estimated freqs, kappa = 38.82974, 4 gamma categories, shape = 0.137064
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    HKY hky = new HKY();
    hky.initByName("kappa", "38.82974", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 4, "shape", "0.137064", "proportionInvariant", "0.0", "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    System.err.println(logP - -1789.7593576610134);
    assertEquals(logP, -1789.7593576610134, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1789.7593576610134, BEASTTestCase.PRECISION);
}

Example 32 with Alignment

use of beast.evolution.alignment.Alignment in project beast2 by CompEvol.

the class TreeLikelihoodTest method aminoacidModelTest.

void aminoacidModelTest(SubstitutionModel substModel, double expectedValue) throws Exception {
    Alignment data = BEASTTestCase.getAminoAcidAlignment();
    Tree tree = BEASTTestCase.getAminoAcidTree(data);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", substModel);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(expectedValue, logP, BEASTTestCase.PRECISION);
}

Example 33 with Alignment

use of beast.evolution.alignment.Alignment in project beast2 by CompEvol.

the class TreeLikelihoodTest method testAscertainedJC69Likelihood.

@Test
public void testAscertainedJC69Likelihood() throws Exception {
    // as testJC69Likelihood but with ascertained alignment
    Alignment data = BEASTTestCase.getAscertainedAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data, "estimate", false);
    HKY hky = new HKY();
    hky.initByName("kappa", "1.0", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    // the following number comes from Beast 1.6
    assertEquals(logP, -737.7140695360017, BEASTTestCase.PRECISION);
}

Example 34 with Alignment

use of beast.evolution.alignment.Alignment in project beast2 by CompEvol.

the class TreeLikelihoodTest method testMarginalisationOfLikelihoodNucleotide.

@Test
public void testMarginalisationOfLikelihoodNucleotide() throws Exception {
    // test summation over all patterns adds to 1 for nucleotide data
    Sequence German_ST = new Sequence("German_ST", "           AAAAAAAAAAAAAAAA CCCCCCCCCCCCCCCC GGGGGGGGGGGGGGGG TTTTTTTTTTTTTTTT");
    Sequence Dutch_List = new Sequence("Dutch_List", "          AAAACCCCGGGGTTTT AAAACCCCGGGGTTTT AAAACCCCGGGGTTTT AAAACCCCGGGGTTTT");
    Sequence English_ST = new Sequence("English_ST", "          ACGTACGTACGTACGT ACGTACGTACGTACGT ACGTACGTACGTACGT ACGTACGTACGTACGT");
    Alignment data = new Alignment();
    data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST, "dataType", "nucleotide");
    Tree tree = BEASTTestCase.getTree(data, "(English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):0.0;");
    RealParameter frequencies = new RealParameter("0.2 0.3 0.4 0.1");
    Frequencies freqs = new Frequencies();
    freqs.initByName("frequencies", frequencies);
    GeneralSubstitutionModel gsm = new GeneralSubstitutionModel();
    gsm.initByName("rates", "1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", gsm);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    likelihood.calculateLogP();
    double[] logPs = likelihood.getPatternLogLikelihoods();
    double P = 0;
    for (double d : logPs) {
        P += Math.exp(d);
    }
    assertEquals(P, 1.0, BEASTTestCase.PRECISION);
}

Example 35 with Alignment

use of beast.evolution.alignment.Alignment in project beast2 by CompEvol.

the class TreeLikelihoodTest method testK80Likelihood.

@Test
public void testK80Likelihood() throws Exception {
    // Set up K80 model: uniform freqs, kappa = 27.402591, 0 gamma categories
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data, "estimate", false);
    HKY hky = new HKY();
    hky.initByName("kappa", "27.40259", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1856.303048876734, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1856.303048876734, BEASTTestCase.PRECISION);
}