package dr.evomodelxml.substmodel;

import dr.evolution.datatype.MutationDeathType;
import dr.evomodel.substmodel.AbstractSubstitutionModel;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.MutationDeathModel;
import dr.inference.model.Parameter;
import dr.xml.*;

import java.util.logging.Logger;

/**
 *
 */
public class MutationDeathModelParser extends AbstractXMLObjectParser {

    public static final String MD_MODEL = "MutationDeathModel";
    public static final String MUTATION_RATE = "mutationRate";

    public String getParserName() {
        return MD_MODEL;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {
        Parameter dummyFreqParameter;
        Parameter delParam = (Parameter) xo.getChild(Parameter.class);

        Logger.getLogger("dr.evomodel").info("Creating MutationDeath substitution model.\n\tInitial death rate is "
                + delParam.getParameterValue(0));

        MutationDeathType dT = (MutationDeathType) xo.getChild(MutationDeathType.class);

        AbstractSubstitutionModel evoModel = (AbstractSubstitutionModel) xo.getChild(AbstractSubstitutionModel.class);
        if (evoModel == null) {  // Assuming pure survival model
            Logger.getLogger("dr.evomodel").info("\tSubstitutionModel not provided assuming pure death/survival model.");
            dummyFreqParameter = new Parameter.Default(new double[]{1.0, 0.0});
        } else {
            dummyFreqParameter = new Parameter.Default(dT.getStateCount());
            double freqs[] = evoModel.getFrequencyModel().getFrequencies();
            for (int i = 0; i < freqs.length; ++i) {
                dummyFreqParameter.setParameterValueQuietly(i, freqs[i]);
            }
            dummyFreqParameter.setParameterValueQuietly(dT.getStateCount() - 1, 0.0);
        }

        FrequencyModel dummyFrequencies = new FrequencyModel(dT, dummyFreqParameter);

        Parameter mutationRate;

        if (xo.hasChildNamed(MUTATION_RATE)) {
            mutationRate = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
        } else {
            mutationRate = new Parameter.Default(new double[]{1.0});
        }
        Logger.getLogger("dr.evomodel").info("\tInitial mutation rate is " + mutationRate.getParameterValue(0));

        return new MutationDeathModel(delParam, dT, evoModel, dummyFrequencies, mutationRate);
    }

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

    public String getParserDescription() {
        return "This element represents an instance of the MutationDeath model of CTMC evolution with deletions.";
    }

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

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

    private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
            new ElementRule(AbstractSubstitutionModel.class, true),
            new ElementRule(Parameter.class),
            new ElementRule(MutationDeathType.class),
            new ElementRule(MUTATION_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true)
    };

}