/*
* TDistributionModelParser.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.inferencexml.distribution;
import dr.inference.distribution.TDistributionModel;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Reads a normal distribution model from a DOM Document element.
*/
public class TDistributionModelParser extends AbstractXMLObjectParser {
public static final String T_DISTRIBUTION_MODEL = "tDistributionModel";
public static final String LOCATION = "location";
public static final String SCALE = "scale";
public static final String DF = "df";
public String getParserName() {
return T_DISTRIBUTION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter locationParam;
Parameter scaleParam;
Parameter dfParam;
XMLObject cxo = xo.getChild(LOCATION);
if (cxo.getChild(0) instanceof Parameter) {
locationParam = (Parameter) cxo.getChild(Parameter.class);
} else {
locationParam = new Parameter.Default(cxo.getDoubleChild(0));
}
cxo = xo.getChild(SCALE);
if (cxo.getChild(0) instanceof Parameter) {
scaleParam = (Parameter) cxo.getChild(Parameter.class);
} else {
scaleParam = new Parameter.Default(cxo.getDoubleChild(0));
}
cxo = xo.getChild(DF);
if (cxo.getChild(0) instanceof Parameter) {
dfParam = (Parameter) cxo.getChild(Parameter.class);
} else {
dfParam = new Parameter.Default(cxo.getDoubleChild(0));
}
return new TDistributionModel(locationParam, scaleParam, dfParam);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(LOCATION,
new XMLSyntaxRule[]{
new XORRule(
new ElementRule(Parameter.class),
new ElementRule(Double.class)
)}
),
new ElementRule(SCALE,
new XMLSyntaxRule[]{
new XORRule(
new ElementRule(Parameter.class),
new ElementRule(Double.class)
)}
),
new ElementRule(DF,
new XMLSyntaxRule[]{
new XORRule(
new ElementRule(Parameter.class),
new ElementRule(Double.class)
)}
)
};
public String getParserDescription() {
return "Describes a normal distribution with a given mean and standard deviation " +
"that can be used in a distributionLikelihood element";
}
public Class getReturnType() {
return TDistributionModel.class;
}
}