/*
* MsatPatternStatisticParser.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.xml.*;
import dr.evolution.alignment.Patterns;
import dr.evolution.alignment.MsatPatternStatistic;
/**
* @author Chieh-Hsi Wu
* Parser for computing the statistics of msat pattern
*/
public class MsatPatternStatisticParser extends AbstractXMLObjectParser {
public static final String MSAT_PATTERN_STATISTIC_PARSER = "msatPatternStatistic";
public static final String MODE = "mode";
public String getParserName(){
return MSAT_PATTERN_STATISTIC_PARSER;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Patterns pats = (Patterns)xo.getChild(Patterns.class);
if(xo.hasAttribute(MODE)){
return new MsatPatternStatistic(pats, xo.getStringAttribute(MODE));
}
return new MsatPatternStatistic(pats);
}
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
new ElementRule(Patterns.class),
AttributeRule.newStringRule(MODE, true)
};
}
public String getParserDescription(){
return "Returns MsatPatternStatistic object";
}
public Class getReturnType(){
return MsatPatternStatistic.class;
}
}