/*
* MixtureModelBranchRatesParser.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.MixtureModelBranchRates;
import dr.evomodel.tree.TreeModel;
import dr.inference.distribution.ParametricDistributionModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
import java.util.ArrayList;
/**
* @author Wai Lok Sibon Li
*/
public class MixtureModelBranchRatesParser extends AbstractXMLObjectParser {
public static final String MIXTURE_MODEL_BRANCH_RATES = "mixtureModelBranchRates";
public static final String DISTRIBUTION = "distribution";
public static final String RATE_CATEGORY_QUANTILES = "rateCategoryQuantiles";
public static final String SINGLE_ROOT_RATE = "singleRootRate";
public static final String NORMALIZE = "normalize";
public static final String NORMALIZE_BRANCH_RATE_TO = "normalizeBranchRateTo";
public static final String DISTRIBUTION_INDEX = "distributionIndex";
public static final String USE_QUANTILE = "useQuantilesForRates";
//public static final String NORMALIZED_MEAN = "normalizedMean";
public String getParserName() {
return MIXTURE_MODEL_BRANCH_RATES;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
ArrayList<ParametricDistributionModel> modelsList = new ArrayList<ParametricDistributionModel>();
final boolean normalize = xo.getAttribute(NORMALIZE, false);
final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_BRANCH_RATE_TO, Double.NaN);
final boolean useQuantilesForRates = xo.getAttribute(USE_QUANTILE, true);
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
//while (xo.hasChildNamed(DISTRIBUTION)) {
for (int i = 0; i < xo.getChildCount(); i++) {
Object child = xo.getChild(i);
if( child instanceof XMLObject ) {
if( ((XMLObject) child).getName().equals(DISTRIBUTION) ) {
XMLObject childXML = (XMLObject) child;
modelsList.add((ParametricDistributionModel) childXML.getChild(0));
}
}
}
//Parameter rateCategoryParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORIES);
ParametricDistributionModel[] models = modelsList.toArray(new ParametricDistributionModel[modelsList.size()]);
Parameter rateCategoryQuantilesParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORY_QUANTILES);
Parameter distributionIndexParameter = (Parameter) xo.getElementFirstChild(DISTRIBUTION_INDEX);
Logger.getLogger("dr.evomodel").info("Using random discretized relaxed clock model with a mixture distribution.");
for(int i=0; i<models.length; i++) {
Logger.getLogger("dr.evomodel").info(" parametric model " + (i+1) +" = " + models[i].getModelName());
}
//Logger.getLogger("dr.evomodel").info(" rate categories = " + rateCategoryParameter.getDimension());
Logger.getLogger("dr.evomodel").info(" rate categories = " + rateCategoryQuantilesParameter.getDimension());
if(normalize) {
Logger.getLogger("dr.evomodel").info(" mean rate is normalized to " + normalizeBranchRateTo);
}
if (xo.hasAttribute(SINGLE_ROOT_RATE)) {
//singleRootRate = xo.getBooleanAttribute(SINGLE_ROOT_RATE);
Logger.getLogger("dr.evomodel").warning(" WARNING: single root rate is not implemented!");
}
if(!useQuantilesForRates) {
Logger.getLogger("dr.evomodel").info("Rates are set to not being drawn using quantiles. Thus they are not drawn from any particular distribution.");
}
/* if (xo.hasAttribute(NORMALIZED_MEAN)) {
dbr.setNormalizedMean(xo.getDoubleAttribute(NORMALIZED_MEAN));
}*/
return new MixtureModelBranchRates(tree, rateCategoryQuantilesParameter, models, distributionIndexParameter, useQuantilesForRates, normalize, normalizeBranchRateTo);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return
"This element returns a random discretized relaxed clock model." +
"The branch rates are drawn from a continuous parametric distribution.";
}
public Class getReturnType() {
return MixtureModelBranchRates.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(SINGLE_ROOT_RATE, true, "Whether only a single rate should be used for the two children branches of the root"),
//AttributeRule.newDoubleRule(NORMALIZED_MEAN, true, "The mean rate to constrain branch rates to once branch lengths are taken into account"),
//AttributeRule.newIntegerRule(OVERSAMPLING, true, "The integer factor for oversampling the distribution model (1 means no oversampling)"),
AttributeRule.newBooleanRule(NORMALIZE, true, "Whether the mean rate has to be normalized to a particular value"),
AttributeRule.newDoubleRule(NORMALIZE_BRANCH_RATE_TO, true, "The mean rate to normalize to, if normalizing"),
AttributeRule.newBooleanRule(USE_QUANTILE, true, "Whether or not to use quantiles to represent rates. If false then rates are not drawn " +
"specifically from any of the distributions"),
new ElementRule(TreeModel.class),
//new ElementRule(DISTRIBUTION, ParametricDistributionModel.class, "The distribution model for rates among branches", false),
/* Can have an infinite number of rate distribution models */
new ElementRule(DISTRIBUTION, ParametricDistributionModel.class, "The distribution model for rates among branches", 1, Integer.MAX_VALUE),
new ElementRule(DISTRIBUTION_INDEX, Parameter.class, "Operator that switches between the distributions of the branch rate distribution model", false),
/*new ElementRule(RATE_CATEGORIES, Parameter.class, "The rate categories parameter", false), */
new ElementRule(RATE_CATEGORY_QUANTILES, Parameter.class, "The quantiles for", false),
};
}