Examples with VariableSkylineLikelihood dr.evomodel.coalescent.VariableSkylineLikelihood used on opensource projects

Example 1 with VariableSkylineLikelihood

use of dr.evomodel.coalescent.VariableSkylineLikelihood in project beast-mcmc by beast-dev.

the class VariableSkylineLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(POPULATION_SIZES);
    Parameter param = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(INDICATOR_PARAMETER);
    Parameter param2 = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(CoalescentLikelihoodParser.POPULATION_TREE);
    TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
    VariableSkylineLikelihood.Type type = VariableSkylineLikelihood.Type.STEPWISE;
    if (xo.hasAttribute(TYPE)) {
        final String s = xo.getStringAttribute(TYPE);
        if (s.equalsIgnoreCase(STEPWISE)) {
            type = VariableSkylineLikelihood.Type.STEPWISE;
        } else if (s.equalsIgnoreCase(LINEAR)) {
            type = VariableSkylineLikelihood.Type.LINEAR;
        } else if (s.equalsIgnoreCase(EXPONENTIAL)) {
            type = VariableSkylineLikelihood.Type.EXPONENTIAL;
        } else {
            throw new XMLParseException("Unknown Bayesian Skyline type: " + s);
        }
    }
    boolean logSpace = xo.getBooleanAttribute(LOG_SPACE);
    Logger.getLogger("dr.evomodel").info("Variable skyline plot: " + type.toString() + " control points");
    return new VariableSkylineLikelihood(treeModel, param, param2, type, logSpace);
}