CompositeDataTypeParser.java

/*
 * CompositeDataTypeParser.java
 *
 * Copyright (c) 2002-2015 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.evoxml;

import dr.evolution.datatype.DataType;
import dr.evolution.datatype.GeneralDataType;
import dr.util.Identifiable;
import dr.xml.*;

import java.util.ArrayList;
import java.util.List;

/**
 * @author Andrew Rambaut
 * @author Marc Suchard
 *
 * @version $Id: GeneralDataTypeParser.java,v 1.2 2005/05/24 20:25:59 rambaut Exp $
 */
public class CompositeDataTypeParser extends AbstractXMLObjectParser {

    /**
     * Name of data type. For XML and human reading of data type.
     */
    public static final String COMPOSITE_DATA_TYPE = "compositeDataType";

    public static final String COMPOSITE_STATE_SEPARATOR = "-";


    public String getParserName() { return COMPOSITE_DATA_TYPE; }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        List<String> states = new ArrayList<String>();

        List<DataType> dataTypes = new ArrayList<DataType>();

        for (int i =0; i < xo.getChildCount(); i++) {
           if (xo.getChild(i) instanceof DataType)  {
               dataTypes.add((DataType)xo.getChild(i));
           } else {
                throw new XMLParseException("illegal element in " + getParserName() + " element");
            }
        }

        if (dataTypes.size() != 2) {
            throw new XMLParseException("CompositeDataType requires exactly 2 component DataTypes");
        }

        DataType dt1 = dataTypes.get(0);
        DataType dt2 = dataTypes.get(1);

        List<String> jointStates = new ArrayList<String>();

        for (int state1 = 0; state1 < dt1.getStateCount(); state1++) {
            String code1  = dt1.getCode(state1);
            for (int state2 = 0; state2 < dt2.getStateCount(); state2++) {
                String code2  = dt2.getCode(state2);
                jointStates.add(code1 + COMPOSITE_STATE_SEPARATOR + code2);
            }
        }

        if (states.size() == 0) {
            throw new XMLParseException("No state elements defined in " + getParserName() + " element");
        } else if (states.size() < 2 ) {
            throw new XMLParseException("Fewer than two state elements defined in " + getParserName() + " element");
        }

        GeneralDataType dataType = new GeneralDataType(states);

        return dataType;
    }

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

    public String getParserDescription() {
        return "Defines a composite DataType consisting of multiple data types";
    }

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

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

    private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
            new ElementRule(DataType.class, 2, 2),
    };
}