/*
* RateEpochBranchRateModelParser.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.branchratemodel;
import dr.evomodel.branchratemodel.ContinuousEpochBranchRateModel;
import dr.evomodel.branchratemodel.RateEpochBranchRateModel;
import dr.evomodelxml.tree.TreeModelParser;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.logging.Logger;
/**
*/
public class RateEpochBranchRateModelParser extends AbstractXMLObjectParser {
public static final String RATE_EPOCH_BRANCH_RATES = "rateEpochBranchRates";
public static final String RATE = "rate";
public static final String EPOCH = "epoch";
public static final String TRANSITION_TIME = "transitionTime";
public static final String CONTINUOUS_NORMALIZATION = "continuousNormalization";
public String getParserName() {
return RATE_EPOCH_BRANCH_RATES;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Logger.getLogger("dr.evomodel").info("\nUsing multi-epoch rate model.");
List<Epoch> epochs = new ArrayList<Epoch>();
for (int i = 0; i < xo.getChildCount(); i++) {
XMLObject xoc = (XMLObject) xo.getChild(i);
if (xoc.getName().equals(EPOCH)) {
double t = xoc.getAttribute(TRANSITION_TIME, 0.0);
Parameter p = (Parameter) xoc.getChild(Parameter.class);
Parameter tt = null;
if (xoc.hasChildNamed(TRANSITION_TIME)) {
tt = (Parameter) xoc.getElementFirstChild(TRANSITION_TIME);
}
epochs.add(new Epoch(t, p, tt));
}
}
Parameter ancestralRateParameter = (Parameter) xo.getElementFirstChild(RATE);
Collections.sort(epochs);
Parameter[] rateParameters = new Parameter[epochs.size() + 1];
Parameter[] timeParameters = new Parameter[epochs.size()];
int i = 0;
for (Epoch epoch : epochs) {
rateParameters[i] = epoch.rateParameter;
if (epoch.timeParameter != null) {
timeParameters[i] = epoch.timeParameter;
} else {
timeParameters[i] = new Parameter.Default(1);
timeParameters[i].setParameterValue(0, epoch.transitionTime);
}
i++;
}
rateParameters[i] = ancestralRateParameter;
if (xo.hasAttribute(CONTINUOUS_NORMALIZATION) && xo.getBooleanAttribute(CONTINUOUS_NORMALIZATION)) {
Parameter rootHeight = (Parameter) xo.getChild(TreeModelParser.ROOT_HEIGHT).getChild(Parameter.class);
return new ContinuousEpochBranchRateModel(timeParameters, rateParameters, rootHeight);
}
return new RateEpochBranchRateModel(timeParameters, rateParameters);
}
class Epoch implements Comparable {
private final double transitionTime;
private final Parameter rateParameter;
private final Parameter timeParameter;
public Epoch(double transitionTime, Parameter rateParameter, Parameter timeParameter) {
this.transitionTime = transitionTime;
this.rateParameter = rateParameter;
this.timeParameter = timeParameter;
}
public int compareTo(Object o) {
return Double.compare(transitionTime, ((Epoch) o).transitionTime);
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element provides a multiple epoch molecular clock model. " +
"All branches (or portions of them) have the same rate of molecular " +
"evolution within a given epoch. If parameters are used to sample " +
"transition times, these must be kept in ascending order by judicious " +
"use of bounds or priors.";
}
public Class getReturnType() {
return RateEpochBranchRateModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(EPOCH,
new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(TRANSITION_TIME, true, "The time of transition between this epoch and the previous one"),
new ElementRule(Parameter.class, "The evolutionary rate parameter for this epoch"),
new ElementRule(TRANSITION_TIME, Parameter.class, "The transition time parameter for this epoch", true)
}, "An epoch that lasts until transitionTime",
1, Integer.MAX_VALUE
),
new ElementRule(RATE, Parameter.class, "The ancestral molecular evolutionary rate parameter", false),
AttributeRule.newBooleanRule(CONTINUOUS_NORMALIZATION, true, "Special rate normalization for a Brownian diffusion process"),
new ElementRule(TreeModelParser.ROOT_HEIGHT,
new XMLSyntaxRule[]{
new ElementRule(Parameter.class, "The tree root height")
}, "Parameterization may require the root height", 0, 1)
};
}