/*
* SpeciesTreeStatisticParser.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.evomodelxml.tree;
import dr.evolution.tree.Tree;
import dr.evomodel.tree.SpeciesTreeStatistic;
import dr.inference.model.Statistic;
import dr.xml.*;
/**
*/
public class SpeciesTreeStatisticParser extends AbstractXMLObjectParser {
public static final String SPECIES_TREE_STATISTIC = "speciesTreeStatistic";
public String getParserName() {
return SPECIES_TREE_STATISTIC;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String name = xo.getAttribute(Statistic.NAME, xo.getId());
Tree speciesTree = (Tree) xo.getElementFirstChild("speciesTree");
Tree popTree = (Tree) xo.getElementFirstChild("populationTree");
return new SpeciesTreeStatistic(name, speciesTree, popTree);
}
public String getParserDescription() {
return "A statistic that returns true if the given population tree is compatible with the species tree. " +
"Compatibility is defined as the compatibility of the timings of the events, so that incompatibility arises " +
"if two individuals in the population tree coalescent before their species do in the species tree.";
}
public Class getReturnType() {
return Statistic.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new StringAttributeRule("name", "A name for this statistic primarily for the purposes of logging", true),
new ElementRule("speciesTree",
new XMLSyntaxRule[]{new ElementRule(Tree.class)}),
new ElementRule("populationTree",
new XMLSyntaxRule[]{new ElementRule(Tree.class)})
};
}