CTMCScalePriorParser.java

package dr.evomodelxml.MSSD;

import dr.evomodel.MSSD.CTMCScalePrior;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.xml.*;

import java.util.logging.Logger;

/**
 *
 */
public class CTMCScalePriorParser extends AbstractXMLObjectParser {
    public static final String MODEL_NAME = "ctmcScalePrior";
    public static final String SCALEPARAMETER = "ctmcScale";
    
    public String getParserName() {
        return MODEL_NAME;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
        Parameter ctmcScale = (Parameter) xo.getElementFirstChild(SCALEPARAMETER);

        Logger.getLogger("dr.evolution").info("\n ---------------------------------\nCreating ctmcScalePrior model.");
        Logger.getLogger("dr.evolution").info("\tIf you publish results using this prior, please reference:");
        Logger.getLogger("dr.evolution").info("\t\t 1. Ferreira and Suchard (2008) for the conditional reference prior on CTMC scale parameter prior;");

        return new CTMCScalePrior(MODEL_NAME, ctmcScale, treeModel);
    }

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

    public String getParserDescription() {
        return "This element represents the prior for CTMC scale parameter.";
    }

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

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

    private final XMLSyntaxRule[] rules = {
            new ElementRule(TreeModel.class),
            new ElementRule(SCALEPARAMETER, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
    };
}