package dr.inferencexml.operators;

import dr.inference.model.Parameter;
import dr.inference.model.Statistic;
import dr.inference.operators.BitSwapOperator;
import dr.inference.operators.MCMCOperator;
import dr.inferencexml.distribution.MixedDistributionLikelihoodParser;
import dr.xml.*;

/**
 *
 */
public class BitSwapOperatorParser extends AbstractXMLObjectParser {

    public static final String BIT_SWAP_OPERATOR = "bitSwapOperator";
    public static final String RADIUS = "radius";

    private static final String DATA = MixedDistributionLikelihoodParser.DATA;
    private static final String INDICATORS = MixedDistributionLikelihoodParser.INDICATORS;

    public String getParserName() {
        return BIT_SWAP_OPERATOR;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
        Parameter data = (Parameter) ((XMLObject) xo.getChild(DATA)).getChild(Parameter.class);
        Parameter indicators = (Parameter) ((XMLObject) xo.getChild(INDICATORS)).getChild(Parameter.class);
        int radius = -1;

        if (xo.hasAttribute(RADIUS)) {
            double rd = xo.getDoubleAttribute(RADIUS);

            if (rd > 0) {
                if (rd < 1) {
                    rd = Math.round(rd * indicators.getDimension());
                }
                radius = (int) Math.round(rd);
                if (!(radius >= 1 && radius < indicators.getDimension() - 1)) {
                    radius = -1;
                }
            }
            if (radius < 1) {
                throw new XMLParseException("invalid radius " + rd);
            }
        }

        return new BitSwapOperator(data, indicators, radius, weight);
    }

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

    public String getParserDescription() {
        return "This element returns a bit-swap operator on a given parameter and data.";
    }

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

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

    private final XMLSyntaxRule[] rules = {
            AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
            AttributeRule.newDoubleRule(RADIUS),
            new ElementRule(DATA, new XMLSyntaxRule[]{new ElementRule(Statistic.class)}),
            new ElementRule(INDICATORS, new XMLSyntaxRule[]{new ElementRule(Statistic.class)}),
    };
}

@@ -2464,16 +2464,22 @@
 e(RADIUS
+, true
 ),%0D%0A    

Make radius optional, as originally intended