/*
* EmpiricalPiecewiseModelParser.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.evomodelxml.coalescent;
import dr.evolution.util.Units;
import dr.evomodel.coalescent.EmpiricalPiecewiseModel;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Parses an element from an DOM document into a PiecewisePopulation.
*/
public class EmpiricalPiecewiseModelParser extends AbstractXMLObjectParser {
public static final String EMPIRICAL_PIECEWISE = "empiricalPiecewise";
public static final String INTERVAL_WIDTHS = "intervalWidths";
public static final String POPULATION_SIZES = "populationSizes";
public static final String TAU = "generationLength";
public static final String THRESHOLD = "threshold";
public static final String LAG = "lag";
public String getParserName() {
return EMPIRICAL_PIECEWISE;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
XMLObject cxo = xo.getChild(INTERVAL_WIDTHS);
double[] intervalWidths = cxo.getDoubleArrayAttribute("values");
cxo = xo.getChild(POPULATION_SIZES);
Parameter popSizes = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(TAU);
Parameter scaleParam = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(THRESHOLD);
Parameter bParam = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(LAG);
Parameter offsetParam = (Parameter) cxo.getChild(Parameter.class);
return new EmpiricalPiecewiseModel(intervalWidths, popSizes, scaleParam, bParam, offsetParam, units);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents a piecewise population model";
}
public Class getReturnType() {
return EmpiricalPiecewiseModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(INTERVAL_WIDTHS,
new XMLSyntaxRule[]{AttributeRule.newDoubleArrayRule("values", false),}),
XMLUnits.SYNTAX_RULES[0],
new ElementRule(POPULATION_SIZES,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"The effective population sizes of each interval."),
new ElementRule(TAU,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"The scale factor."),
new ElementRule(THRESHOLD,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"The threshold before counts occur."),
new ElementRule(LAG,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"The lag between actual population sizes and genetic diversity.")
};
}