/*
* ParsimonyStateStatisticParser.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.evolution.tree.TreeUtils;
import dr.evolution.util.Taxa;
import dr.evolution.util.TaxonList;
import dr.evomodel.tree.ParsimonyStateStatistic;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Statistic;
import dr.xml.*;
/**
*/
public class ParsimonyStateStatisticParser extends AbstractXMLObjectParser {
public static final String PARSIMONY_STATE_STATISTIC = "parsimonyStateStatistic";
public static final String STATE = "state";
public static final String MRCA = "mrca";
public String getParserName() {
return PARSIMONY_STATE_STATISTIC;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String name = xo.getAttribute(Statistic.NAME, xo.getId());
Tree tree = (Tree) xo.getChild(Tree.class);
XMLObject cxo = xo.getChild(STATE);
TaxonList stateTaxa = (TaxonList) cxo.getChild(TaxonList.class);
cxo = xo.getChild(MRCA);
TaxonList mrcaTaxa = (TaxonList) cxo.getChild(TaxonList.class);
try {
return new ParsimonyStateStatistic(name, tree, stateTaxa, mrcaTaxa);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A statistic that has as its value the parsimony state reconstruction of a " +
"binary state defined by a set of taxa at a given MRCA of a tree";
}
public Class getReturnType() {
return ParsimonyStateStatistic.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new StringAttributeRule(Statistic.NAME, "A name for this statistic for the purposes of logging", true),
new ElementRule(TreeModel.class),
new ElementRule(STATE,
new XMLSyntaxRule[]{new ElementRule(Taxa.class)}),
new ElementRule(MRCA,
new XMLSyntaxRule[]{new ElementRule(Taxa.class)})
};
}