AlloppSpeciesBindingsIndividualParser.java

package dr.evomodelxml.speciation;



import dr.evolution.util.Taxon;
import dr.evomodel.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;
	}

}