/*
* BirthDeathCollapseModelParser.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;
/**
* @author Graham Jones
* Date: 01/09/2013
*/
import dr.evolution.tree.Tree;
import dr.evolution.util.Units;
import dr.evomodel.alloppnet.speciation.BirthDeathCollapseModel;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
import static dr.xml.AttributeRule.newDoubleRule;
public class BirthDeathCollapseModelParser extends AbstractXMLObjectParser {
public static final String BIRTH_DEATH_COLLAPSE_MODEL = "birthDeathCollapseModel";
public static final String COLLAPSE_HEIGHT = "collapseHeight";
public static final String TREE = "speciesTree";
public static final String BIRTHDIFF_RATE = "birthMinusDeathRate";
public static final String RELATIVE_DEATH_RATE = "relativeDeathRate";
public static final String ORIGIN_HEIGHT = "originHeight";
public static final String COLLAPSE_WEIGHT = "collapseWeight";
public String getParserName() {
return BIRTH_DEATH_COLLAPSE_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
final double collH = xo.getDoubleAttribute(COLLAPSE_HEIGHT);
XMLObject cxo = xo.getChild(TREE);
final Tree tree = (Tree) cxo.getChild(Tree.class);
final Parameter birthMinusDeath = (Parameter) xo.getElementFirstChild(BIRTHDIFF_RATE);
final Parameter relativeDeathRate = (Parameter) xo.getElementFirstChild(RELATIVE_DEATH_RATE);
final Parameter originHeight = (Parameter) xo.getElementFirstChild(ORIGIN_HEIGHT);
final Parameter collapseWeight = (Parameter) xo.getElementFirstChild(COLLAPSE_WEIGHT);
final String modelName = xo.getId();
return new BirthDeathCollapseModel(modelName, tree, units,
birthMinusDeath, relativeDeathRate, originHeight, collapseWeight, collH);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public Class getReturnType() {
return BirthDeathCollapseModel.class;
}
public String getParserDescription() {
return "A speciation model aimed at species delimitation, mixing birth-death model with spike near zero for node heights.";
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(TREE, new XMLSyntaxRule[]{new ElementRule(Tree.class)}),
new ElementRule(BIRTHDIFF_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(RELATIVE_DEATH_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(ORIGIN_HEIGHT, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(COLLAPSE_WEIGHT, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
XMLUnits.SYNTAX_RULES[0],
newDoubleRule(COLLAPSE_HEIGHT),
};
}