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

Example 91 with Alignment

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

the class BEASTTestCase method getBinaryAlignment.

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

Example 92 with Alignment

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

the class UncertainAlignmentTest method getAlignment.

public static Alignment getAlignment() throws Exception {
    // The sequences now denote the most likely annotation
    Sequence seq1 = new Sequence("seq1", "ATT");
    Sequence seq2 = new Sequence("seq2", "ATC");
    Sequence seq3 = new Sequence("seq3", "GCC");
    Alignment data = new Alignment();
    data.initByName("sequence", seq1, "sequence", seq2, "sequence", seq3, "dataType", "nucleotide");
    return data;
}

Example 93 with Alignment

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

the class TreeLikelihoodTest method testJC69LikelihoodWithUncertainCharacters.

@Test
public void testJC69LikelihoodWithUncertainCharacters() throws Exception {
    Alignment data = UncertainAlignmentTest.getAlignment();
    Alignment data2 = UncertainAlignmentTest.getUncertainAlignment();
    double[] logL, logL_uncertain;
    System.out.println("\nTree A:");
    Tree tree = UncertainAlignmentTest.getTreeA(data2);
    logL = testJC69Likelihood(data, tree);
    logL_uncertain = testJC69Likelihood(data2, tree);
    double x1 = -11.853202336328778;
    double x2 = -12.069603116476458;
    assertEquals(logL[0], x1, BEASTTestCase.PRECISION);
    assertEquals(logL[1], x1, BEASTTestCase.PRECISION);
    assertEquals(logL_uncertain[0], x1, BEASTTestCase.PRECISION);
    assertEquals(logL_uncertain[1], x2, BEASTTestCase.PRECISION);
    System.out.println("\nTree B:");
    tree = UncertainAlignmentTest.getTreeB(data2);
    logL = testJC69Likelihood(data, tree);
    logL_uncertain = testJC69Likelihood(data2, tree);
    double x3 = -12.421114302827698;
    double x4 = -11.62105662310513;
    assertEquals(logL[0], x3, BEASTTestCase.PRECISION);
    assertEquals(logL[1], x3, BEASTTestCase.PRECISION);
    assertEquals(logL_uncertain[0], x3, BEASTTestCase.PRECISION);
    assertEquals(logL_uncertain[1], x4, BEASTTestCase.PRECISION);
    System.out.println("\nTesting alignment doubling:");
    Alignment data3 = UncertainAlignmentTest.getUncertainAlignmentDoubled();
    logL_uncertain = testJC69Likelihood(data3, tree);
    assertEquals(logL_uncertain[0], 2 * x3, BEASTTestCase.PRECISION);
    assertEquals(logL_uncertain[1], 2 * x4, BEASTTestCase.PRECISION);
}

Example 94 with Alignment

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

the class TreeLikelihoodTest method testHKY85GILikelihood.

@Test
public void testHKY85GILikelihood() throws Exception {
    // Set up HKY85+G+I model: estimated freqs, kappa = 39.464538, 4 gamma categories, shape = 0.587649, prop invariant = 0.486548
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    HKY hky = new HKY();
    hky.initByName("kappa", "39.464538", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 4, "shape", "0.587649", "proportionInvariant", "0.486548", "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1789.639227747059, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1789.639227747059, BEASTTestCase.PRECISION);
}

Example 95 with Alignment

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

the class TreeLikelihoodTest method testMarginalisationOfLikelihoodBinary.

@Test
public void testMarginalisationOfLikelihoodBinary() throws Exception {
    // test summation over all patterns adds to 1 for binary data
    Sequence German_ST = new Sequence("German_ST", "           10110010");
    Sequence Dutch_List = new Sequence("Dutch_List", "          11010100");
    Sequence English_ST = new Sequence("English_ST", "          11101000");
    Alignment data = new Alignment();
    data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST, "dataType", "binary");
    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("0.683 0.317");
    Frequencies freqs = new Frequencies();
    freqs.initByName("frequencies", frequencies);
    GeneralSubstitutionModel covarion = new GeneralSubstitutionModel();
    covarion.initByName("frequencies", freqs, "rates", new RealParameter("1.0 1.0"));
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", covarion);
    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);
}