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

Example 11 with SubstitutionModel

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

the class GammaSiteModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getElementFirstChild(SUBSTITUTION_MODEL);
    String msg = "";
    Parameter muParam = null;
    if (xo.hasChildNamed(SUBSTITUTION_RATE)) {
        muParam = (Parameter) xo.getElementFirstChild(SUBSTITUTION_RATE);
        msg += "\n  with initial substitution rate = " + muParam.getParameterValue(0);
    } else if (xo.hasChildNamed(MUTATION_RATE)) {
        muParam = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
        msg += "\n  with initial substitution rate = " + muParam.getParameterValue(0);
    } else if (xo.hasChildNamed(RELATIVE_RATE)) {
        muParam = (Parameter) xo.getElementFirstChild(RELATIVE_RATE);
        msg += "\n  with initial relative rate = " + muParam.getParameterValue(0);
    }
    Parameter shapeParam = null;
    int catCount = 4;
    if (xo.hasChildNamed(GAMMA_SHAPE)) {
        final XMLObject cxo = xo.getChild(GAMMA_SHAPE);
        catCount = cxo.getIntegerAttribute(GAMMA_CATEGORIES);
        shapeParam = (Parameter) cxo.getChild(Parameter.class);
        msg += "\n  " + catCount + " category discrete gamma with initial shape = " + shapeParam.getParameterValue(0);
    }
    Parameter invarParam = null;
    if (xo.hasChildNamed(PROPORTION_INVARIANT)) {
        invarParam = (Parameter) xo.getElementFirstChild(PROPORTION_INVARIANT);
        msg += "\n  initial proportion of invariant sites = " + invarParam.getParameterValue(0);
    }
    Logger.getLogger("dr.evomodel").info("Creating site model." + (msg.length() > 0 ? msg : ""));
    return new GammaSiteModel(substitutionModel, muParam, shapeParam, catCount, invarParam);
}

Example 12 with SubstitutionModel

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

the class SampleStateModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(MUTATION_RATE);
    Parameter muParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(PROPORTIONS);
    Parameter proportionParameter = (Parameter) cxo.getChild(Parameter.class);
    Vector<Object> subModels = new Vector<Object>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof SubstitutionModel) {
            subModels.addElement(xo.getChild(i));
        }
    }
    return new SampleStateModel(muParam, proportionParameter, subModels);
}