Examples with DataType dr.evolution.datatype.DataType used on opensource projects

Example 66 with DataType

use of dr.evolution.datatype.DataType in project beast-mcmc by beast-dev.

the class TimeIrreversibleTest method testComplexSubstitutionModel.

private double[] testComplexSubstitutionModel(Original test, double[] rates) {
    System.out.println("\n*** Complex Substitution Model Test: " + test + " ***");
    Parameter ratesP = new Parameter.Default(rates);
    DataType dataType = test.getDataType();
    FrequencyModel freqModel = new FrequencyModel(dataType, new Parameter.Default(test.getFrequencies()));
    ComplexSubstitutionModel substModel = new ComplexSubstitutionModel("Complex Substitution Model Test", dataType, freqModel, ratesP);
    double logL = substModel.getLogLikelihood();
    System.out.println("Prior = " + logL);
    double[] finiteTimeProbs = null;
    if (!Double.isInfinite(logL)) {
        finiteTimeProbs = new double[substModel.getDataType().getStateCount() * substModel.getDataType().getStateCount()];
        substModel.getTransitionProbabilities(time, finiteTimeProbs);
        System.out.println("Probs = ");
        printRateMatrix(finiteTimeProbs, substModel.getDataType().getStateCount());
    }
    // assertEquals(1, 1, 1e-10);
    return finiteTimeProbs;
}