Examples with SitePatterns dr.evolution.alignment.SitePatterns used on opensource projects

Example 6 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodGTR.

public void testLikelihoodGTR() {
    System.out.println("\nTest Likelihood using GTR:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    Variable<Double> rateACValue = new Parameter.Default(GTRParser.A_TO_C, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateAGValue = new Parameter.Default(GTRParser.A_TO_G, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateATValue = new Parameter.Default(GTRParser.A_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateCGValue = new Parameter.Default(GTRParser.C_TO_G, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateCTValue = new Parameter.Default(GTRParser.C_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateGTValue = new Parameter.Default(GTRParser.G_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    GTR gtr = new GTR(rateACValue, rateAGValue, rateATValue, rateCGValue, rateCTValue, rateGTValue, f);
    //siteModel
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    GammaSiteModel siteModel = new GammaSiteModel(gtr, mu, null, 4, null);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodGTR", format.format(-1969.14584), format.format(treeLikelihood.getLogLikelihood()));
}

Example 7 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodHKY85I.

public void testLikelihoodHKY85I() {
    System.out.println("\nTest Likelihood using HKY85I:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 38.564672, 0, 100);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    //siteModel
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    Parameter invar = new Parameter.Default(GammaSiteModelParser.PROPORTION_INVARIANT, 0.701211, 0, 1.0);
    GammaSiteModel siteModel = new GammaSiteModel(hky, mu, null, 4, invar);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodHKY85I", format.format(-1789.91240), format.format(treeLikelihood.getLogLikelihood()));
}

Example 8 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class NormalizedSequenceLikelihoodTest method testAllPossibleAlignments.

public void testAllPossibleAlignments() {
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    tryAllPossibleAlignments(3, patterns);
}

Example 9 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class AscertainmentCorrectedLikelihoodTest method testMissingPatterns.

public void testMissingPatterns() {
    SitePatterns patterns = new SitePatterns(alignment, null, 10, -1, 1, true);
    System.out.println("Using " + patterns.getPatternCount() + " patterns");
    double total = computeSumOfPatterns(patterns);
    System.out.println("Total of 10 missing (uncorrected) probabilities = " + total);
    assertEquals("uncorrected", 0.78287044, total, tolerance);
}

Example 10 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class AscertainmentCorrectedLikelihoodTest method testAllPatterns.

public void testAllPatterns() {
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    System.out.println("Using " + patterns.getPatternCount() + " patterns");
    double total = computeSumOfPatterns(patterns);
    System.out.println("Total of all (uncorrected) probabilities = " + total);
    assertEquals("uncorrected", 1.0, total, tolerance);
}