Examples with GeneralF81Model dr.oldevomodel.substmodel.GeneralF81Model used on opensource projects

Example 1 with GeneralF81Model

use of dr.oldevomodel.substmodel.GeneralF81Model in project beast-mcmc by beast-dev.

the class GeneralF81ModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FREQUENCIES)) {
        XMLObject cxo = xo.getChild(FREQUENCIES);
        freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    }
    Logger.getLogger("dr.evomodel").info("  General F81 Model from frequencyModel '" + freqModel.getId() + "' (stateCount=" + freqModel.getFrequencyCount() + ")");
    return new GeneralF81Model(freqModel);
}

Example 2 with GeneralF81Model

use of dr.oldevomodel.substmodel.GeneralF81Model in project beast-mcmc by beast-dev.

the class GeneralF81Test method testGF81.

public void testGF81() {
    for (Instance test : all) {
        double[] pi = test.getPi();
        //            Parameter freqs = new Parameter.Default(pi);
        GeneralDataType gdt = new GeneralDataType(new String[] { "1", "2", "3", "4" });
        FrequencyModel f = new FrequencyModel(gdt, pi);
        GeneralF81Model generalF81Model = new GeneralF81Model(f);
        double distance = test.getDistance();
        double[] mat = new double[4 * 4];
        generalF81Model.getTransitionProbabilities(distance, mat);
        final double[] result = test.getExpectedResult();
        for (int k = 0; k < mat.length; ++k) {
            assertEquals(mat[k], result[k], 1e-10);
        // System.out.print(" " + (mat[k] - result[k]));
        }
    }
}