/*
* ALSTreeLikelihoodParser.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.treelikelihood;
import dr.evolution.alignment.PatternList;
import dr.evolution.util.Taxon;
import dr.oldevomodel.MSSD.ALSTreeLikelihood;
import dr.oldevomodel.MSSD.AbstractObservationProcess;
import dr.oldevomodel.MSSD.AnyTipObservationProcess;
import dr.oldevomodel.MSSD.SingleTipObservationProcess;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.oldevomodel.sitemodel.SiteModel;
import dr.oldevomodel.substmodel.MutationDeathModel;
import dr.evomodel.tree.TreeModel;
import dr.oldevomodelxml.treelikelihood.TreeLikelihoodParser;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
*
*/
public class ALSTreeLikelihoodParser extends AbstractXMLObjectParser {
public static final String LIKE_NAME = "alsTreeLikelihood";
public static final String INTEGRATE_GAIN_RATE = "integrateGainRate";
public static final String OBSERVATION_PROCESS = "observationProcess";
public static final String OBSERVATION_TYPE = "type";
public static final String OBSERVATION_TAXON = "taxon";
public static final String ANY_TIP = "anyTip";
public final static String IMMIGRATION_RATE = "immigrationRate";
public static final String FORCE_RESCALING = TreeLikelihoodParser.FORCE_RESCALING;
public String getParserName() {
return LIKE_NAME;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean useAmbiguities = false;
boolean storePartials = true;
if (xo.hasAttribute(TreeLikelihoodParser.USE_AMBIGUITIES)) {
useAmbiguities = xo.getBooleanAttribute(TreeLikelihoodParser.USE_AMBIGUITIES);
}
if (xo.hasAttribute(TreeLikelihoodParser.STORE_PARTIALS)) {
storePartials = xo.getBooleanAttribute(TreeLikelihoodParser.STORE_PARTIALS);
}
boolean integrateGainRate = xo.getBooleanAttribute(INTEGRATE_GAIN_RATE);
//AbstractObservationProcess observationProcess = (AbstractObservationProcess) xo.getChild(AbstractObservationProcess.class);
PatternList patternList = (PatternList) xo.getChild(PatternList.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
SiteModel siteModel = (SiteModel) xo.getChild(SiteModel.class);
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
Parameter mu = ((MutationDeathModel) siteModel.getSubstitutionModel()).getDeathParameter();
Parameter lam;
if (!integrateGainRate) {
lam = (Parameter) xo.getElementFirstChild(IMMIGRATION_RATE);
} else {
lam = new Parameter.Default("gainRate", 1.0, 0.001, 1.999);
}
AbstractObservationProcess observationProcess = null;
Logger.getLogger("dr.evolution").info("\n ---------------------------------\nCreating ALSTreeLikelihood model.");
for (int i = 0; i < xo.getChildCount(); ++i) {
Object cxo = xo.getChild(i);
if (cxo instanceof XMLObject && ((XMLObject) cxo).getName().equals(OBSERVATION_PROCESS)) {
if (((XMLObject) cxo).getStringAttribute(OBSERVATION_TYPE).equals("singleTip")) {
String taxonName = ((XMLObject) cxo).getStringAttribute(OBSERVATION_TAXON);
Taxon taxon = treeModel.getTaxon(treeModel.getTaxonIndex(taxonName));
observationProcess = new SingleTipObservationProcess(treeModel, patternList, siteModel,
branchRateModel, mu, lam, taxon);
Logger.getLogger("dr.evolution").info("All traits are assumed extant in " + taxonName);
} else { // "anyTip" observation process
observationProcess = new AnyTipObservationProcess(ANY_TIP, treeModel, patternList,
siteModel, branchRateModel, mu, lam);
Logger.getLogger("dr.evolution").info("Observed traits are assumed to be extant in at least one tip node.");
}
observationProcess.setIntegrateGainRate(integrateGainRate);
}
}
Logger.getLogger("dr.evolution").info("\tIf you publish results using Acquisition-Loss-Mutation (ALS) Model likelihood, please reference Alekseyenko, Lee and Suchard (2008) Syst. Biol 57: 772-784.\n---------------------------------\n");
boolean forceRescaling = xo.getAttribute(FORCE_RESCALING, false);
// forceRescaling = true;
return new ALSTreeLikelihood(observationProcess, patternList, treeModel, siteModel, branchRateModel,
useAmbiguities, storePartials, forceRescaling);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents the likelihood of a patternlist on a tree given the site model.";
}
public Class getReturnType() {
return ALSTreeLikelihood.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(TreeLikelihoodParser.USE_AMBIGUITIES, true),
AttributeRule.newBooleanRule(TreeLikelihoodParser.STORE_PARTIALS, true),
AttributeRule.newBooleanRule(INTEGRATE_GAIN_RATE),
AttributeRule.newBooleanRule(FORCE_RESCALING, true),
new ElementRule(IMMIGRATION_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true),
new ElementRule(PatternList.class),
new ElementRule(TreeModel.class),
new ElementRule(SiteModel.class),
new ElementRule(BranchRateModel.class, true),
new ElementRule(OBSERVATION_PROCESS,
new XMLSyntaxRule[]{AttributeRule.newStringRule(OBSERVATION_TYPE, false),
AttributeRule.newStringRule(OBSERVATION_TAXON, true)})
//new ElementRule(AbstractObservationProcess.class)
};
}