/* * 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), }; }