/*
* GammaSiteModelParser.java
*
* Copyright (c) 2002-2016 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.siteratemodel;
import java.util.logging.Logger;
import dr.evomodel.siteratemodel.GammaSiteRateModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.oldevomodel.sitemodel.SiteModel;
import dr.inference.model.Parameter;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
import dr.xml.XORRule;
/**
* @author Andrew Rambaut
* @author Alexei Drummond
* @version $Id$
*/
public class GammaSiteModelParser extends AbstractXMLObjectParser {
public static final String SITE_MODEL = SiteModel.SITE_MODEL;
public static final String SUBSTITUTION_MODEL = "substitutionModel";
public static final String BRANCH_SUBSTITUTION_MODEL = "branchSubstitutionModel";
public static final String MUTATION_RATE = "mutationRate";
public static final String SUBSTITUTION_RATE = "substitutionRate";
public static final String RELATIVE_RATE = "relativeRate";
public static final String WEIGHT = "weight";
public static final String GAMMA_SHAPE = "gammaShape";
public static final String GAMMA_CATEGORIES = "gammaCategories";
public static final String PROPORTION_INVARIANT = "proportionInvariant";
public String getParserName() {
return SITE_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String msg = "";
SubstitutionModel substitutionModel = null;
double muWeight = 1.0;
Parameter muParam = null;
if (xo.hasChildNamed(SUBSTITUTION_RATE)) {
muParam = (Parameter) xo.getElementFirstChild(SUBSTITUTION_RATE);
msg += "\n with initial substitution rate = " + muParam.getParameterValue(0);
} else if (xo.hasChildNamed(MUTATION_RATE)) {
muParam = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
msg += "\n with initial substitution rate = " + muParam.getParameterValue(0);
} else if (xo.hasChildNamed(RELATIVE_RATE)) {
XMLObject cxo = xo.getChild(RELATIVE_RATE);
muParam = (Parameter) cxo.getChild(Parameter.class);
msg += "\n with initial relative rate = " + muParam.getParameterValue(0);
if (cxo.hasAttribute(WEIGHT)) {
muWeight = cxo.getDoubleAttribute(WEIGHT);
msg += " with weight: " + muWeight;
}
}
Parameter shapeParam = null;
int catCount = 4;
if (xo.hasChildNamed(GAMMA_SHAPE)) {
XMLObject cxo = xo.getChild(GAMMA_SHAPE);
catCount = cxo.getIntegerAttribute(GAMMA_CATEGORIES);
shapeParam = (Parameter) cxo.getChild(Parameter.class);
msg += "\n " + catCount + " category discrete gamma with initial shape = " + shapeParam.getParameterValue(0);
}
Parameter invarParam = null;
if (xo.hasChildNamed(PROPORTION_INVARIANT)) {
invarParam = (Parameter) xo.getElementFirstChild(PROPORTION_INVARIANT);
msg += "\n initial proportion of invariant sites = " + invarParam.getParameterValue(0);
}
if (msg.length() > 0) {
Logger.getLogger("dr.evomodel").info("\nCreating site rate model: " + msg);
} else {
Logger.getLogger("dr.evomodel").info("\nCreating site rate model.");
}
GammaSiteRateModel siteRateModel = new GammaSiteRateModel(SITE_MODEL, muParam, muWeight, shapeParam, catCount, invarParam);
if (xo.hasChildNamed(SUBSTITUTION_MODEL)) {
// System.err.println("Doing the substitution model stuff");
// set this to pass it along to the OldTreeLikelihoodParser...
substitutionModel = (SubstitutionModel) xo.getElementFirstChild(SUBSTITUTION_MODEL);
siteRateModel.setSubstitutionModel(substitutionModel);
}
return siteRateModel;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A SiteModel that has a gamma distributed rates across sites";
}
public Class<GammaSiteRateModel> getReturnType() {
return GammaSiteRateModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(SUBSTITUTION_MODEL, new XMLSyntaxRule[]{
new ElementRule(SubstitutionModel.class)
}, true),
new XORRule(
new XORRule(
new ElementRule(SUBSTITUTION_RATE, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(MUTATION_RATE, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
})
),
new ElementRule(RELATIVE_RATE, new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(WEIGHT, true),
new ElementRule(Parameter.class)
}), true
),
new ElementRule(GAMMA_SHAPE, new XMLSyntaxRule[]{
AttributeRule.newIntegerRule(GAMMA_CATEGORIES, true),
new ElementRule(Parameter.class)
}, true),
new ElementRule(PROPORTION_INVARIANT, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}, true)
};
}//END: class