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

Example 36 with Alignment

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

the class TreeLikelihoodTest method testHKY85Likelihood.

@Test
public void testHKY85Likelihood() throws Exception {
    // Set up HKY85 model: estimated freqs, kappa = 29.739445, 0 gamma categories
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    HKY hky = new HKY();
    hky.initByName("kappa", "29.739445", "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, -1825.2131708068507, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1825.2131708068507, BEASTTestCase.PRECISION);
}

Example 37 with Alignment

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

the class TreeLikelihoodTest method testGTRILikelihood.

@Test
public void testGTRILikelihood() throws Exception {
    // Set up GTR model: prop invariant = 0.5
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    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, "proportionInvariant", "0.5", "substModel", gsm);
    // siteModel.init("1.0", 1, null, "0.5", gsm);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1948.8417455357564, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1948.8417455357564, BEASTTestCase.PRECISION);
}

Example 38 with Alignment

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

the class TreeLikelihoodTest method testGTRGILikelihood.

@Test
public void testGTRGILikelihood() throws Exception {
    // Set up GTR model: 4 gamma categories, gamma shape = 0.5, prop invariant = 0.5
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    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", 4, "shape", "0.5", "proportionInvariant", "0.5", "substModel", gsm);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1947.5829396144961, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1947.5829396144961, BEASTTestCase.PRECISION);
}

Example 39 with Alignment

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

the class TreeLikelihoodTest method testGTRGLikelihood.

@Test
public void testGTRGLikelihood() throws Exception {
    // Set up GTR model: 4 gamma categories, gamma shape = 0.5
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    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", 4, "shape", "0.5", "substModel", gsm);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1949.0360143622, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1949.0360143622, BEASTTestCase.PRECISION);
}

Example 40 with Alignment

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

the class BEASTTestCase method getCovarionAlignment.

public static Alignment getCovarionAlignment() throws Exception {
    Alignment data = new Alignment();
    data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST, "sequence", French, "sequence", Italian, "sequence", Spanish, "dataType", "twoStateCovarion", "strip", true);
    return data;
}