Examples with SiteModel beast.evolution.sitemodel.SiteModel used on opensource projects

Example 31 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project beast2 by CompEvol.

the class SiteModelInputEditor method createGammaCategoryCountEditor.

public InputEditor createGammaCategoryCountEditor() {
    SiteModel sitemodel = ((SiteModel) m_input.get());
    final Input<?> input = sitemodel.gammaCategoryCount;
    categoryCountEditor = new IntegerInputEditor(doc) {

        private static final long serialVersionUID = 1L;

        @Override
        public void validateInput() {
            super.validateInput();
            SiteModel sitemodel = (SiteModel) m_beastObject;
            if (sitemodel.gammaCategoryCount.get() < 2 && sitemodel.shapeParameterInput.get().isEstimatedInput.get()) {
                m_validateLabel.m_circleColor = Color.orange;
                m_validateLabel.setToolTipText("shape parameter is estimated, but not used");
                m_validateLabel.setVisible(true);
            }
        }
    };
    categoryCountEditor.init(input, sitemodel, -1, ExpandOption.FALSE, true);
    categoryCountEntry = categoryCountEditor.getEntry();
    categoryCountEntry.getDocument().addDocumentListener(new DocumentListener() {

        @Override
        public void removeUpdate(DocumentEvent e) {
            processEntry2();
        }

        @Override
        public void insertUpdate(DocumentEvent e) {
            processEntry2();
        }

        @Override
        public void changedUpdate(DocumentEvent e) {
            processEntry2();
        }
    });
    categoryCountEditor.validateInput();
    return categoryCountEditor;
}

Example 32 with SiteModel

use of beast.evolution.sitemodel.SiteModel 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 33 with SiteModel

use of beast.evolution.sitemodel.SiteModel 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 34 with SiteModel

use of beast.evolution.sitemodel.SiteModel 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);
}

Example 35 with SiteModel

use of beast.evolution.sitemodel.SiteModel 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);
}