ModelSpecificPseudoPriorLikelihoodParser.java

package dr.inferencexml.distribution;

import dr.xml.AbstractXMLObjectParser;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
import dr.inference.distribution.DistributionLikelihood;
import dr.inference.distribution.ModelSpecificPseudoPriorLikelihood;
import dr.inference.model.Parameter;
import dr.math.distributions.Distribution;

/**
 * @author Chieh-Hsi Wu
 */
public class ModelSpecificPseudoPriorLikelihoodParser  extends AbstractXMLObjectParser {
    public static final String MODEL_SPECIFIC_PSEUDO_PRIOR = "modelSpecificPseudoPrior";
    public static final String PRIOR = "priorLik";
    public static final String PSEUDO_PRIOR = "pseudoPriorLik";
    public static final String MODELS = "models";
    public static final String MODEL_INDICATOR = "modelIndicator";
    public static final String SELECTED_VARIABLE = "selectedVariable";


    public String getParserName() {
        return MODEL_SPECIFIC_PSEUDO_PRIOR;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {
        DistributionLikelihood priorLikelihood = (DistributionLikelihood)xo.getElementFirstChild(PRIOR);
        DistributionLikelihood pseudoPriorLikelihood = (DistributionLikelihood)xo.getElementFirstChild(PSEUDO_PRIOR);
        Distribution prior = priorLikelihood.getDistribution();
        Distribution pseudoPrior = pseudoPriorLikelihood.getDistribution();
        Parameter modelIndicator = (Parameter)xo.getElementFirstChild(MODEL_INDICATOR);
        int[] models = xo.getIntegerArrayAttribute(MODELS);
        Parameter selectedVariable = (Parameter)xo.getElementFirstChild(SELECTED_VARIABLE);


        ModelSpecificPseudoPriorLikelihood likelihood =
                new ModelSpecificPseudoPriorLikelihood(
                        prior,
                        pseudoPrior,
                        modelIndicator,
                        models
                );
        likelihood.addData(selectedVariable);
        

        return likelihood;
    }

    //************************************************************************
    // AbstractXMLObjectParser implementation
    //************************************************************************

    public XMLSyntaxRule[] getSyntaxRules() {
        return rules;
    }

    private final XMLSyntaxRule[] rules = {

    };

    public String getParserDescription() {
        return "Calculates the likelihood of some data given some parametric or empirical distribution.";
    }

    public Class getReturnType() {
        return ModelSpecificPseudoPriorLikelihood.class;
    }
}