package dr.evomodelxml.sitemodel;

import dr.xml.*;
import dr.evomodel.sitemodel.GammaSiteBMA;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;

/**
 * @author Chieh-Hsi Wu
 *
 * Parser for Gamma site BMA.
 *
 */
public class GammaSiteBMAParser extends AbstractXMLObjectParser {

    public static final String SUBSTITUTION_MODEL = "substitutionModel";
    public static final String MUTATION_RATE = "mutationRate";
    public static final String LOG_GAMMA_SHAPE = "logGammaShape";
    public static final String GAMMA_CATEGORIES = "gammaCategories";
    public static final String LOGIT_PROPORTION_INVARIANT = "logitProportionInvariant";
    public static final String MODEL_CHOOSE = "modelChoose";
    public static final String GAMMA_SITE_BMA = "gammaSiteBMA";

    public String getParserName() {
        return GAMMA_SITE_BMA;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {
        SubstitutionModel substitutionModel = (SubstitutionModel) xo.getElementFirstChild(SUBSTITUTION_MODEL);

        Parameter muParam = (Parameter) xo.getElementFirstChild(MUTATION_RATE);

        Parameter logitInvar = (Parameter) xo.getElementFirstChild(LOGIT_PROPORTION_INVARIANT);

        final XMLObject cxo = xo.getChild(LOG_GAMMA_SHAPE);
        Parameter logShape = (Parameter) cxo.getChild(Parameter.class);

        int catCount = cxo.getIntegerAttribute(GAMMA_CATEGORIES);

        Variable<Integer> modelChoose = (Variable<Integer>) xo.getElementFirstChild(MODEL_CHOOSE);

        return new GammaSiteBMA(substitutionModel, muParam, logitInvar, logShape, catCount, modelChoose);
    }

    public String getParserDescription() {
        return "A SiteModel that does BMA for a gamma distributed rates across sites";
    }

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

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

    private final XMLSyntaxRule[] rules = {
            new ElementRule(SUBSTITUTION_MODEL, new XMLSyntaxRule[]{
                    new ElementRule(SubstitutionModel.class)
            }),
            new ElementRule(MUTATION_RATE, new XMLSyntaxRule[]{
                    new ElementRule(Parameter.class)
            }),
            new ElementRule(LOG_GAMMA_SHAPE, new XMLSyntaxRule[]{
                    AttributeRule.newIntegerRule(GAMMA_CATEGORIES),
                    new ElementRule(Parameter.class)
            }),
            new ElementRule(LOGIT_PROPORTION_INVARIANT, new XMLSyntaxRule[]{
                    new ElementRule(Parameter.class)
            }),
            new ElementRule(MODEL_CHOOSE, new XMLSyntaxRule[]{
                    new ElementRule(Variable.class)
            })
    };

}