/*
 * AlloppSpeciesBindingsIndividualParser.java
 *
 * Copyright (c) 2002-2017 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.evomodel.alloppnet.parsers;



import dr.evolution.util.Taxon;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;


/**
 * Parses an individual from a possibly-allopolyploid species. 
 * 
 * @author Graham Jones
 *         Date: 18/04/2011
 */


/*
 * 
 * Parses an individual (which is a list of taxa) from a 
 * possibly-allopolyploid species. Part of parsing a AlloppSpeciesBindings.
 * 
 */

public class AlloppSpeciesBindingsIndividualParser extends
		AbstractXMLObjectParser {
	public static final String INDIVIDUAL = "individual";

	public String getParserName() {
		return INDIVIDUAL;
	}

	@Override
	public Object parseXMLObject(XMLObject xo) throws XMLParseException {
        Taxon[] taxa = new Taxon[xo.getChildCount()];
        for (int nt = 0; nt < taxa.length; ++nt) {
            taxa[nt] = (Taxon) xo.getChild(nt);
        }
        return new AlloppSpeciesBindings.Individual(xo.getId(), taxa);
	}

	@Override
	public XMLSyntaxRule[] getSyntaxRules() {
        return new XMLSyntaxRule[]{
                new ElementRule(Taxon.class, 1, Integer.MAX_VALUE)
        };
    }
	

	@Override
	public String getParserDescription() {
		return "Individual specimen from a species, possibly containing multiple genomes.";
	}

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

}