package dr.evomodelxml.speciation;

import dr.evomodel.speciation.PopsIOSpeciesBindings;
import dr.evomodel.speciation.PopsIOSpeciesTreeModel;
import dr.xml.*;

/**
 * User: Graham
 * Date: 10/05/12
 */


public class PopsIOSpeciesTreeModelParser extends AbstractXMLObjectParser {
    public static final String PIO_SPECIES_TREE = "pioSpeciesTree";
    public static final String PIO_POPULATIONS_PRIOR = "pioPopulationsPrior";
    public static final String PIO_PRIOR_COMPONENT = "pioPriorComponent";
    public static final String WEIGHT = "weight";
    public static final String ALPHA = "alpha";
    public static final String BETA = "beta";

    @Override
    public Object parseXMLObject(XMLObject xo) throws XMLParseException {
        System.out.println("PopsIOSpeciesTreeModelParser");
        PopsIOSpeciesBindings piosb = (PopsIOSpeciesBindings) xo.getChild(PopsIOSpeciesBindings.class);

        final XMLObject pioppxo = xo.getChild(PIO_POPULATIONS_PRIOR);
        final int nComponents = pioppxo.getChildCount();
        PopsIOSpeciesTreeModel.PriorComponent [] components = new PopsIOSpeciesTreeModel.PriorComponent[nComponents];

        for (int nc = 0; nc < nComponents; ++nc) {
            Object child = pioppxo.getChild(nc);
            assert ((XMLObject) child).getName().equals(PIO_PRIOR_COMPONENT);
            double weight = ((XMLObject) child).getDoubleAttribute(WEIGHT);
            double alpha = ((XMLObject) child).getDoubleAttribute(ALPHA);
            double beta = ((XMLObject) child).getDoubleAttribute(BETA);
            components[nc] = new PopsIOSpeciesTreeModel.PriorComponent(weight, alpha, beta);
        }


        PopsIOSpeciesTreeModel piostm = new PopsIOSpeciesTreeModel(piosb, components);
        return piostm;
    }


    private XMLSyntaxRule[] priorComponentSyntax() {
        return new XMLSyntaxRule[]{
                AttributeRule.newDoubleRule(WEIGHT),
                AttributeRule.newDoubleRule(ALPHA),
                AttributeRule.newDoubleRule(BETA)
        };
    }

    private XMLSyntaxRule[] popPriorSyntax() {
        return new XMLSyntaxRule[]{
             new ElementRule(PIO_PRIOR_COMPONENT, priorComponentSyntax(), 1, Integer.MAX_VALUE)
        };
    }

    @Override
    public XMLSyntaxRule[] getSyntaxRules() {
        return new XMLSyntaxRule[]{
              new ElementRule(PopsIOSpeciesBindings.class),
              new ElementRule(PIO_POPULATIONS_PRIOR, popPriorSyntax())
        };
    }

    @Override
    public String getParserDescription() {
        return "Species tree with population size parameters on branches integrated out analytically";  //To change body of implemented methods use File | Settings | File Templates.
    }

    @Override
    public Class getReturnType() {
        return PopsIOSpeciesTreeModel.class;
    }

    public String getParserName() {
        return PIO_SPECIES_TREE;
    }
}