/*
* MulTreeNodeSlideParser.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.MulTreeNodeSlide;
import dr.evomodel.alloppnet.speciation.MulSpeciesBindings;
import dr.evomodel.alloppnet.speciation.MulSpeciesTreeModel;
import dr.inference.operators.MCMCOperator;
import dr.xml.*;
/**
*
* @author Graham Jones
* Date: 20/12/2011
*/
public class MulTreeNodeSlideParser extends AbstractXMLObjectParser {
public static final String MULTREE_NODE_REHEIGHT = "mulTreeNodeReHeight";
public String getParserName() {
return MULTREE_NODE_REHEIGHT;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
MulSpeciesBindings species = (MulSpeciesBindings) xo.getChild(MulSpeciesBindings.class);
MulSpeciesTreeModel tree = (MulSpeciesTreeModel) xo.getChild(MulSpeciesTreeModel.class);
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
// final double range = xo.getAttribute("range", 1.0);
// if( range <= 0 || range > 1.0 ) {
// throw new XMLParseException("range out of range");
// }
//final boolean oo = xo.getAttribute("outgroup", false);
return new MulTreeNodeSlide(tree, species /*, range*//*, oo*/, weight);
}
public String getParserDescription() {
return "Specialized Species tree operator, transform tree without breaking embedding of gene trees.";
}
public Class getReturnType() {
return MulTreeNodeSlide.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
// AttributeRule.newDoubleRule("range", true),
// AttributeRule.newBooleanRule("outgroup", true),
new ElementRule(MulSpeciesBindings.class),
new ElementRule(MulSpeciesTreeModel.class)
};
}
}