/*
* MultiPartitionDataLikelihoodParser.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.treedatalikelihood;
import dr.evolution.alignment.PatternList;
import dr.evolution.alignment.Patterns;
import dr.evomodel.branchmodel.BranchModel;
import dr.evomodel.branchmodel.HomogeneousBranchModel;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.branchratemodel.DefaultBranchRateModel;
import dr.evomodel.siteratemodel.GammaSiteRateModel;
import dr.evomodel.siteratemodel.SiteRateModel;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evomodel.tipstatesmodel.TipStatesModel;
import dr.evomodel.tree.TreeModel;
import dr.evomodel.treedatalikelihood.DataLikelihoodDelegate;
import dr.evomodel.treedatalikelihood.MultiPartitionDataLikelihoodDelegate;
import dr.evomodel.treedatalikelihood.TreeDataLikelihood;
import dr.evomodel.treelikelihood.PartialsRescalingScheme;
import dr.xml.*;
import java.util.ArrayList;
import java.util.List;
/**
* @author Guy Baele
* @version $Id$
*/
public class MultiPartitionDataLikelihoodParser extends AbstractXMLObjectParser {
public static final boolean DEBUG = false;
public static final String BEAGLE_INSTANCE_COUNT = "beagle.instance.count";
//TODO: eventually change String to parse back to treeDataLikelihood
public static final String TREE_DATA_LIKELIHOOD = "newTreeDataLikelihood";
public static final String USE_AMBIGUITIES = "useAmbiguities";
public static final String INSTANCE_COUNT = "instanceCount";
public static final String SCALING_SCHEME = "scalingScheme";
public static final String DELAY_SCALING = "delayScaling";
public String getParserName() {
return TREE_DATA_LIKELIHOOD;
}
protected TreeDataLikelihood createTreeDataLikelihood(List<PatternList> patternLists,
TreeModel treeModel,
List<BranchModel> branchModels,
List<SiteRateModel> siteRateModels,
BranchRateModel branchRateModel,
TipStatesModel tipStatesModel,
boolean useAmbiguities,
PartialsRescalingScheme scalingScheme,
boolean delayRescalingUntilUnderflow,
XMLObject xo) throws XMLParseException {
if (tipStatesModel != null) {
throw new XMLParseException("Tip State Error models are not supported yet with TreeDataLikelihood");
}
// DataLikelihoodDelegate dataLikelihoodDelegate = new BeagleDataLikelihoodDelegate(
// treeModel,
// patternLists.get(0),
// branchModel,
// siteRateModel,
// useAmbiguities,
// scalingScheme,
// delayRescalingUntilUnderflow);
DataLikelihoodDelegate dataLikelihoodDelegate = new MultiPartitionDataLikelihoodDelegate(
treeModel,
patternLists,
branchModels,
siteRateModels,
useAmbiguities,
scalingScheme,
delayRescalingUntilUnderflow);
return new TreeDataLikelihood(
dataLikelihoodDelegate,
treeModel,
branchRateModel);
}
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);
}
if (DEBUG) {
System.out.println("instanceCount: " + instanceCount);
}
List<PatternList> patternLists = xo.getAllChildren(PatternList.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
List<SiteRateModel> siteRateModels = xo.getAllChildren(SiteRateModel.class);
FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
List<BranchModel> branchModels = xo.getAllChildren(BranchModel.class);
if (branchModels == null) {
if (DEBUG) {
System.out.println("branchModels == null");
}
branchModels = new ArrayList<BranchModel>();
List<SubstitutionModel> substitutionModels = xo.getAllChildren(SubstitutionModel.class);
if (substitutionModels == null) {
if (DEBUG) {
System.out.println("substitutionModels == null");
}
for (SiteRateModel siteRateModel : siteRateModels) {
SubstitutionModel substitutionModel = ((GammaSiteRateModel)siteRateModel).getSubstitutionModel();
if (substitutionModel == null) {
throw new XMLParseException("No substitution model available for TreeDataLikelihood: "+xo.getId());
}
branchModels.add(new HomogeneousBranchModel(substitutionModel, rootFreqModel));
}
}
if (DEBUG) {
System.out.println("branchModels size: " + branchModels.size());
}
for (BranchModel branchModel : branchModels) {
System.out.println(" " + branchModel.getId() + " " + branchModel.getModelName());
}
}
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
if (branchRateModel == null) {
branchRateModel = new DefaultBranchRateModel();
}
if (DEBUG) {
System.out.println("BranchRateModel: " + branchRateModel.getId());
}
TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
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);
}
if (instanceCount == 1) {
if (DEBUG) {
System.out.println("instanceCount == 1");
}
return createTreeDataLikelihood(
patternLists,
treeModel,
branchModels,
siteRateModels,
branchRateModel,
tipStatesModel,
useAmbiguities,
scalingScheme,
delayScaling,
xo
);
}
// using multiple instances of BEAGLE...
if (tipStatesModel != null) {
throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
}
List<PatternList> patternInstanceLists = new ArrayList<PatternList>();
for (int j = 0; j < patternLists.size(); j++) {
for (int i = 0; i < instanceCount; i++) {
patternInstanceLists.add(new Patterns(patternLists.get(j), i, instanceCount));
}
}
return createTreeDataLikelihood(
patternLists,
treeModel,
branchModels,
siteRateModels,
branchRateModel,
null,
useAmbiguities,
scalingScheme,
delayScaling,
xo);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents the likelihood of data on a tree given the site model.";
}
public Class getReturnType() {
return TreeDataLikelihood.class;
}
public static final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(USE_AMBIGUITIES, true),
//TODO: remove hard-coded maximum of 3 partitions
new ElementRule(PatternList.class,0,2),
new ElementRule(TreeModel.class),
//TODO: remove hard-coded maximum of 3 partitions
new ElementRule(SiteRateModel.class,0,2),
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(TipStatesModel.class, true),
new ElementRule(FrequencyModel.class, true),
};
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
}