/*
* EpochTreeLikelihood.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.oldevomodel.treelikelihood;
import dr.evolution.alignment.PatternList;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.oldevomodel.sitemodel.SiteModel;
import dr.oldevomodel.substmodel.SubstitutionEpochModel;
import dr.evomodel.tipstatesmodel.TipStatesModel;
import dr.evomodel.tree.TreeModel;
import dr.oldevomodelxml.treelikelihood.TreeLikelihoodParser;
import dr.inference.model.Likelihood;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Marc A. Suchard
*/
@Deprecated // Switching to BEAGLE
public class EpochTreeLikelihood extends TreeLikelihood {
public static final String LIKE_NAME = "epochTreeLikelihood";
public EpochTreeLikelihood(PatternList patternList,
TreeModel treeModel,
SiteModel siteModel,
BranchRateModel branchRateModel,
TipStatesModel tipStatesModel,
boolean useAmbiguities,
boolean allowMissingTaxa,
boolean storePartials,
boolean forceJavaCore) {
super(patternList, treeModel, siteModel, branchRateModel, tipStatesModel,useAmbiguities,allowMissingTaxa,storePartials,forceJavaCore, false);
}
/**
* Traverse the tree calculating partial likelihoods.
*
* @return whether the partials for this node were recalculated.
*/
protected boolean traverse(Tree tree, NodeRef node) {
boolean update = false;
int nodeNum = node.getNumber();
NodeRef parent = tree.getParent(node);
// First update the transition probability matrix(ices) for this branch
if (parent != null && updateNode[nodeNum]) {
final double branchRate = branchRateModel.getBranchRate(tree, node);
// Get the operational time of the branch
final double parentNodeHeight = tree.getNodeHeight(parent);
final double nodeHeight = tree.getNodeHeight(node);
final double branchTime = branchRate * (parentNodeHeight - nodeHeight);
if (branchTime < 0.0) {
throw new RuntimeException("Negative branch length: " + branchTime);
}
likelihoodCore.setNodeMatrixForUpdate(nodeNum);
for (int i = 0; i < categoryCount; i++) {
double branchLength = siteModel.getRateForCategory(i) * branchTime;
((SubstitutionEpochModel)siteModel.getSubstitutionModel()).getTransitionProbabilities(nodeHeight, parentNodeHeight,branchLength, probabilities);
likelihoodCore.setNodeMatrix(nodeNum, i, probabilities);
}
update = true;
}
// If the node is internal, update the partial likelihoods.
if (!tree.isExternal(node)) {
// Traverse down the two child nodes
NodeRef child1 = tree.getChild(node, 0);
final boolean update1 = traverse(tree, child1);
NodeRef child2 = tree.getChild(node, 1);
final boolean update2 = traverse(tree, child2);
// If either child node was updated then update this node too
if (update1 || update2) {
final int childNum1 = child1.getNumber();
final int childNum2 = child2.getNumber();
likelihoodCore.setNodePartialsForUpdate(nodeNum);
if (integrateAcrossCategories) {
likelihoodCore.calculatePartials(childNum1, childNum2, nodeNum);
} else {
likelihoodCore.calculatePartials(childNum1, childNum2, nodeNum, siteCategories);
}
if (parent == null) {
// No parent this is the root of the tree -
// calculate the pattern likelihoods
double[] frequencies = frequencyModel.getFrequencies();
double[] partials = getRootPartials();
likelihoodCore.calculateLogLikelihoods(partials, frequencies, patternLogLikelihoods);
}
update = true;
}
}
return update;
}
/**
* The XML parser
*/
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return LIKE_NAME;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean useAmbiguities = xo.getAttribute(TreeLikelihoodParser.USE_AMBIGUITIES, false);
boolean allowMissingTaxa = xo.getAttribute(TreeLikelihoodParser.ALLOW_MISSING_TAXA, false);
boolean storePartials = xo.getAttribute(TreeLikelihoodParser.STORE_PARTIALS, true);
boolean forceJavaCore = xo.getAttribute(TreeLikelihoodParser.FORCE_JAVA_CORE, false);
PatternList patternList = (PatternList) xo.getChild(PatternList.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
SiteModel siteModel = (SiteModel) xo.getChild(SiteModel.class);
if (! (siteModel.getSubstitutionModel() instanceof SubstitutionEpochModel)) {
throw new XMLParseException("EpochTreeLikelihood only currently works with a SubstitutionEpochModel");
}
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
Logger.getLogger("dr.evolution").info("\n ---------------------------------\nCreating EpochTreeLikelihood model.");
Logger.getLogger("dr.evolution").info("\tIf you publish results using substitution epoch likelihood, please reference" +
" Shapiro and Suchard (in preparation).\n---------------------------------\n");
return new EpochTreeLikelihood(
patternList,
treeModel,
siteModel,
branchRateModel,
tipStatesModel,
useAmbiguities, allowMissingTaxa, storePartials, forceJavaCore);
}
//************************************************************************
// 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 XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(TreeLikelihoodParser.USE_AMBIGUITIES, true),
AttributeRule.newBooleanRule(TreeLikelihoodParser.ALLOW_MISSING_TAXA, true),
AttributeRule.newBooleanRule(TreeLikelihoodParser.STORE_PARTIALS, true),
AttributeRule.newBooleanRule(TreeLikelihoodParser.FORCE_JAVA_CORE, true),
new ElementRule(PatternList.class),
new ElementRule(TreeModel.class),
new ElementRule(SiteModel.class),
new ElementRule(BranchRateModel.class, true),
new ElementRule(TipStatesModel.class, true)
};
};
}