/*
* MulTreeSequenceReassignmentParser.java
*
* Copyright (c) 2002-2017 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.evomodel.alloppnet.parsers;
import dr.evomodel.alloppnet.operators.MulTreeSequenceReassignment;
import dr.evomodel.alloppnet.speciation.MulSpeciesBindings;
import dr.evomodel.alloppnet.speciation.MulSpeciesTreeModel;
import dr.inference.operators.MCMCOperator;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
/**
*
* @author Graham Jones
* Date: 20/12/2011
*/
public class MulTreeSequenceReassignmentParser extends AbstractXMLObjectParser {
public static final String MULTREE_SEQUENCE_REASSIGNMENT = "mulTreeSequenceReassignment";
public String getParserName() {
return MULTREE_SEQUENCE_REASSIGNMENT;
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
MulSpeciesBindings mulspb = (MulSpeciesBindings) xo.getChild(MulSpeciesBindings.class);
MulSpeciesTreeModel multree = (MulSpeciesTreeModel) xo.getChild(MulSpeciesTreeModel.class);
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new MulTreeSequenceReassignment(multree, mulspb, weight);
}
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
new ElementRule(MulSpeciesBindings.class),
new ElementRule(MulSpeciesTreeModel.class)
};
}
@Override
public String getParserDescription() {
return "Operator which reassigns sequences within an allopolyploid species.";
}
@Override
public Class getReturnType() {
return MulTreeSequenceReassignment.class;
}
}