/*
* BeagleTreeLikelihoodParser.java
*
* Copyright (c) 2002-2016 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.app.beagle.evomodel.treelikelihood.RestrictedPartialsSequenceLikelihood;
import dr.evolution.tree.TreeUtils;
import dr.evomodel.branchmodel.BranchModel;
import dr.evomodel.branchmodel.HomogeneousBranchModel;
import dr.evomodel.siteratemodel.GammaSiteRateModel;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evomodel.treelikelihood.AbstractTreeLikelihood;
import dr.evomodel.treelikelihood.BeagleTreeLikelihood;
import dr.evomodel.treelikelihood.PartialsRescalingScheme;
import dr.evolution.alignment.PatternList;
import dr.evolution.alignment.Patterns;
import dr.evolution.util.TaxonList;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.tree.TreeModel;
import dr.evomodel.tipstatesmodel.TipStatesModel;
import dr.inference.model.CompoundLikelihood;
import dr.inference.model.Likelihood;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* @author Andrew Rambaut
* @author Alexei Drummond
* @author Marc Suchard
* @version $Id$
*/
public class BeagleTreeLikelihoodParser extends AbstractXMLObjectParser {
public static final String BEAGLE_INSTANCE_COUNT = "beagle.instance.count";
public static final String TREE_LIKELIHOOD = "treeLikelihood";
public static final String USE_AMBIGUITIES = "useAmbiguities";
public static final String INSTANCE_COUNT = "instanceCount";
// public static final String DEVICE_NUMBER = "deviceNumber";
// public static final String PREFER_SINGLE_PRECISION = "preferSinglePrecision";
public static final String SCALING_SCHEME = "scalingScheme";
public static final String DELAY_SCALING = "delayScaling";
public static final String PARTIALS_RESTRICTION = "partialsRestriction";
public String getParserName() {
return TREE_LIKELIHOOD;
}
protected BeagleTreeLikelihood createTreeLikelihood(PatternList patternList, TreeModel treeModel,
BranchModel branchModel,
GammaSiteRateModel siteRateModel,
BranchRateModel branchRateModel,
TipStatesModel tipStatesModel,
boolean useAmbiguities, PartialsRescalingScheme scalingScheme,
boolean delayRescalingUntilUnderflow,
Map<Set<String>, Parameter> partialsRestrictions,
XMLObject xo) throws XMLParseException {
return new BeagleTreeLikelihood(
patternList,
treeModel,
branchModel,
siteRateModel,
branchRateModel,
tipStatesModel,
useAmbiguities,
scalingScheme,
delayRescalingUntilUnderflow,
partialsRestrictions
);
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean useAmbiguities = xo.getAttribute(USE_AMBIGUITIES, false);
int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
if (instanceCount < 1) {
instanceCount = 1;
}
String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
if (ic != null && ic.length() > 0) {
instanceCount = Integer.parseInt(ic);
}
PatternList patternList = (PatternList) xo.getChild(PatternList.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
GammaSiteRateModel siteRateModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
if (branchModel == null) {
SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
if (substitutionModel == null) {
substitutionModel = siteRateModel.getSubstitutionModel();
}
if (substitutionModel == null) {
throw new XMLParseException("No substitution model available for TreeLikelihood: "+xo.getId());
}
branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
}
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
// if (xo.getChild(TipStatesModel.class) != null) {
// throw new XMLParseException("Sequence Error Models are not supported under BEAGLE yet. Please use Native BEAST Likelihood.");
// }
PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
boolean delayScaling = true;
if (xo.hasAttribute(SCALING_SCHEME)) {
scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(SCALING_SCHEME));
if (scalingScheme == null)
throw new XMLParseException("Unknown scaling scheme '"+xo.getStringAttribute(SCALING_SCHEME)+"' in "+
"OldBeagleTreeLikelihood object '"+xo.getId());
}
if (xo.hasAttribute(DELAY_SCALING)) {
delayScaling = xo.getBooleanAttribute(DELAY_SCALING);
}
Map<Set<String>, Parameter> partialsRestrictions = null;
if (xo.hasChildNamed(PARTIALS_RESTRICTION)) {
XMLObject cxo = xo.getChild(PARTIALS_RESTRICTION);
TaxonList taxonList = (TaxonList) cxo.getChild(TaxonList.class);
// Parameter parameter = (Parameter) cxo.getChild(Parameter.class);
try {
TreeUtils.getLeavesForTaxa(treeModel, taxonList);
} catch (TreeUtils.MissingTaxonException e) {
throw new XMLParseException("Unable to parse taxon list: " + e.getMessage());
}
throw new XMLParseException("Restricting internal nodes is not yet implemented. Contact Marc");
}
if (instanceCount == 1 || patternList.getPatternCount() < instanceCount) {
return createTreeLikelihood(
patternList,
treeModel,
branchModel,
siteRateModel,
branchRateModel,
tipStatesModel,
useAmbiguities,
scalingScheme,
delayScaling,
partialsRestrictions,
xo
);
}
// using multiple instances of BEAGLE...
// if (!(patternList instanceof SitePatterns)) {
// throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with BEAUti-selected codon partitioning.");
// }
if (tipStatesModel != null) {
throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
}
List<Likelihood> likelihoods = new ArrayList<Likelihood>();
for (int i = 0; i < instanceCount; i++) {
Patterns subPatterns = new Patterns(patternList, i, instanceCount);
AbstractTreeLikelihood treeLikelihood = createTreeLikelihood(
subPatterns,
treeModel,
branchModel,
siteRateModel,
branchRateModel,
null,
useAmbiguities,
scalingScheme,
delayScaling,
partialsRestrictions,
xo);
treeLikelihood.setId(xo.getId() + "_" + instanceCount);
likelihoods.add(treeLikelihood);
}
return new CompoundLikelihood(likelihoods);
}
//************************************************************************
// 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 Likelihood.class;
}
public static final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(USE_AMBIGUITIES, true),
new ElementRule(PatternList.class),
new ElementRule(TreeModel.class),
new ElementRule(GammaSiteRateModel.class),
new ElementRule(BranchModel.class, true),
new ElementRule(SubstitutionModel.class, true),
new ElementRule(BranchRateModel.class, true),
new ElementRule(TipStatesModel.class, true),
AttributeRule.newStringRule(SCALING_SCHEME,true),
new ElementRule(PARTIALS_RESTRICTION, new XMLSyntaxRule[] {
new ElementRule(TaxonList.class),
new ElementRule(Parameter.class),
}, true),
new ElementRule(TipStatesModel.class, true),
new ElementRule(FrequencyModel.class, true),
};
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
}