LogRandomWalkOperatorParser.java

package dr.inferencexml.operators;

import dr.inference.model.Parameter;
import dr.inference.operators.CoercableMCMCOperator;
import dr.inference.operators.CoercionMode;
import dr.inference.operators.LogRandomWalkOperator;
import dr.inference.operators.MCMCOperator;
import dr.xml.*;

/**
 */
public class LogRandomWalkOperatorParser extends AbstractXMLObjectParser {

    public static final String LOGRANDOMWALK_OPERATOR = "logRandomWalkOperator";
    // Use same attributes as scale operator to help users
    public static final String SCALE_ALL = ScaleOperatorParser.SCALE_ALL;
    public static final String SCALE_ALL_IND = ScaleOperatorParser.SCALE_ALL_IND;
    public static final String WINDOW_SIZE = "window";

    public String getParserName() {
        return LOGRANDOMWALK_OPERATOR;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        CoercionMode mode = CoercionMode.parseMode(xo);

        final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
        final double size = xo.getDoubleAttribute(WINDOW_SIZE);
        final boolean scaleAll = xo.getAttribute(SCALE_ALL, false);
        final boolean scaleAllInd = xo.getAttribute(SCALE_ALL_IND, false);

        if( size <= 0.0 ) {
            throw new XMLParseException("size must be positive");
        }

        final Parameter parameter = (Parameter) xo.getChild(Parameter.class);

        return new LogRandomWalkOperator(parameter, size, mode, weight, scaleAll, scaleAllInd);
    }

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

    public String getParserDescription() {
        return "This element returns a scale operator on a given parameter.";
    }

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

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

    private final XMLSyntaxRule[] rules = {
            AttributeRule.newDoubleRule(WINDOW_SIZE),
            AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
            AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true),

            AttributeRule.newBooleanRule(SCALE_ALL, true),
            AttributeRule.newBooleanRule(SCALE_ALL_IND, true),

            new ElementRule(Parameter.class),
    };

}