/*
* RandomDiscretizedBranchRatesParser.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.RandomDiscretizedBranchRates;
import dr.evomodel.tree.TreeModel;
import dr.inference.distribution.ParametricDistributionModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Wai Lok Sibon Li
*/
public class RandomDiscretizedBranchRatesParser extends AbstractXMLObjectParser {
public static final String RANDOM_DISCRETIZED_BRANCH_RATES = "randomDiscretizedBranchRates";
public static final String DISTRIBUTION = "distribution";
//public static final String RATE_CATEGORIES = "rateCategories";
public static final String RATE_CATEGORY_QUANTILES = "rateCategoryQuantiles";
public static final String SINGLE_ROOT_RATE = "singleRootRate";
//public static final String OVERSAMPLING = "overSampling";
public static final String NORMALIZE = "normalize";
public static final String NORMALIZE_BRANCH_RATE_TO = "normalizeBranchRateTo";
//public static final String NORMALIZED_MEAN = "normalizedMean";
public String getParserName() {
return RANDOM_DISCRETIZED_BRANCH_RATES;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
// throw new RuntimeException("randomDiscretizedBranchRates has been renamed to continuousBranchRates (all of the " +
// "parameters have been kept the same). Please make changes to the XML before rerunning. ");
System.err.println("randomDiscretizedBranchRates has been renamed to continuousBranchRates (all of the " +
"parameters have been kept the same). Please make changes to the XML before rerunning. ");
System.exit(1);
return null;
//final int overSampling = xo.getAttribute(OVERSAMPLING, 1);
// final boolean normalize = xo.getAttribute(NORMALIZE, false);
// final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_BRANCH_RATE_TO, Double.NaN);
//
// TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
// ParametricDistributionModel distributionModel = (ParametricDistributionModel) xo.getElementFirstChild(DISTRIBUTION);
//
// //Parameter rateCategoryParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORIES);
//
// Parameter rateCategoryQuantilesParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORY_QUANTILES);
//
// Logger.getLogger("dr.evomodel").info("Using random discretized relaxed clock model.");
// //Logger.getLogger("dr.evomodel").info(" over sampling = " + overSampling);
// Logger.getLogger("dr.evomodel").info(" parametric model = " + distributionModel.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 (xo.hasAttribute(NORMALIZED_MEAN)) {
// dbr.setNormalizedMean(xo.getDoubleAttribute(NORMALIZED_MEAN));
// }*/
//
// return new RandomDiscretizedBranchRates(tree, /*rateCategoryParameter, */rateCategoryQuantilesParameter, distributionModel, /*overSampling,*/ 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 null; //RandomDiscretizedBranchRates.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"),
new ElementRule(TreeModel.class),
new ElementRule(DISTRIBUTION, ParametricDistributionModel.class, "The distribution model for rates among branches", false),
/*new ElementRule(RATE_CATEGORIES, Parameter.class, "The rate categories parameter", false), */
new ElementRule(RATE_CATEGORY_QUANTILES, Parameter.class, "The quantiles for", false),
};
}