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

Example 1 with TwoStateCovarionModel

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

the class TwoStateCovarionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter alphaParameter;
    Parameter switchingRateParameter;
    XMLObject cxo = xo.getChild(AbstractCovarionDNAModel.FREQUENCIES);
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    // fancy new datatype courtesy of Helen
    TwoStateCovarion dataType = TwoStateCovarion.INSTANCE;
    cxo = xo.getChild(ALPHA);
    alphaParameter = (Parameter) cxo.getChild(Parameter.class);
    // alpha must be positive and less than 1.0 because the fast rate is normalized to 1.0
    alphaParameter.addBounds(new Parameter.DefaultBounds(1.0, 0.0, 1));
    cxo = xo.getChild(SWITCHING_RATE);
    switchingRateParameter = (Parameter) cxo.getChild(Parameter.class);
    if (dataType != freqModel.getDataType()) {
        throw new XMLParseException("Data type of " + getParserName() + " element does not match that of its frequencyModel.");
    }
    TwoStateCovarionModel model = new TwoStateCovarionModel(dataType, freqModel, alphaParameter, switchingRateParameter);
    System.out.println(model);
    return model;
}

Example 2 with TwoStateCovarionModel

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

the class TwoStateCovarionModelTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    frequencies = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
    alpha = new Parameter.Default(0.0);
    switchingRate = new Parameter.Default(1.0);
    FrequencyModel freqModel = new FrequencyModel(TwoStateCovarion.INSTANCE, frequencies);
    model = new TwoStateCovarionModel(TwoStateCovarion.INSTANCE, freqModel, alpha, switchingRate);
    dataType = model.getDataType();
}