/*
* AbstractTreeLikelihood.java
*
* Copyright (C) 2002-2012 Alexei Drummond, Andrew Rambaut & Marc A. 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.app.beagle.evomodel.treelikelihood;
import dr.evolution.alignment.PatternList;
import dr.evolution.datatype.DataType;
import dr.evolution.tree.NodeRef;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.AbstractModelLikelihood;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
import dr.xml.Reportable;
/**
* AbstractTreeLikelihood - a base class for likelihood calculators of sites on a tree.
*
* @author Andrew Rambaut
* @author Marc Suchard
* @version $Id: AbstractTreeLikelihood.java,v 1.16 2005/06/07 16:27:39 alexei Exp $
*/
public abstract class AbstractTreeLikelihood extends AbstractModelLikelihood implements Reportable {
protected static final boolean COUNT_TOTAL_OPERATIONS = false;
public AbstractTreeLikelihood(String name, PatternList patternList,
TreeModel treeModel) {
super(name);
this.patternList = patternList;
this.dataType = patternList.getDataType();
patternCount = patternList.getPatternCount();
stateCount = dataType.getStateCount();
patternWeights = patternList.getPatternWeights();
this.treeModel = treeModel;
addModel(treeModel);
nodeCount = treeModel.getNodeCount();
updateNode = new boolean[nodeCount];
for (int i = 0; i < nodeCount; i++) {
updateNode[i] = true;
}
likelihoodKnown = false;
}
/**
* Set update flag for a node and its children
*/
protected void updateNode(NodeRef node) {
updateNode[node.getNumber()] = true;
likelihoodKnown = false;
}
/**
* Set update flag for a node and its direct children
*/
protected void updateNodeAndChildren(NodeRef node) {
updateNode[node.getNumber()] = true;
for (int i = 0; i < treeModel.getChildCount(node); i++) {
NodeRef child = treeModel.getChild(node, i);
updateNode[child.getNumber()] = true;
}
likelihoodKnown = false;
}
/**
* Set update flag for a node and all its descendents
*/
protected void updateNodeAndDescendents(NodeRef node) {
updateNode[node.getNumber()] = true;
for (int i = 0; i < treeModel.getChildCount(node); i++) {
NodeRef child = treeModel.getChild(node, i);
updateNodeAndDescendents(child);
}
likelihoodKnown = false;
}
/**
* Set update flag for all nodes
*/
protected void updateAllNodes() {
for (int i = 0; i < nodeCount; i++) {
updateNode[i] = true;
}
likelihoodKnown = false;
}
/**
* Set update flag for a pattern
*/
protected void updatePattern(int i) {
if (updatePattern != null) {
updatePattern[i] = true;
}
likelihoodKnown = false;
}
/**
* Set update flag for all patterns
*/
protected void updateAllPatterns() {
if (updatePattern != null) {
for (int i = 0; i < patternCount; i++) {
updatePattern[i] = true;
}
}
likelihoodKnown = false;
}
public final double[] getPatternWeights() {
return patternWeights;
}
// **************************************************************
// VariableListener IMPLEMENTATION
// **************************************************************
protected void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
// do nothing
}
// **************************************************************
// Model IMPLEMENTATION
// **************************************************************
protected void handleModelChangedEvent(Model model, Object object, int index) {
if (COUNT_TOTAL_OPERATIONS)
totalModelChangedCount++;
likelihoodKnown = false;
}
/**
* Stores the additional state other than model components
*/
protected void storeState() {
storedLikelihoodKnown = likelihoodKnown;
storedLogLikelihood = logLikelihood;
}
/**
* Restore the additional stored state
*/
protected void restoreState() {
likelihoodKnown = storedLikelihoodKnown;
logLikelihood = storedLogLikelihood;
}
protected void acceptState() {
} // nothing to do
// **************************************************************
// Likelihood IMPLEMENTATION
// **************************************************************
public final Model getModel() {
return this;
}
public final double getLogLikelihood() {
if (COUNT_TOTAL_OPERATIONS)
totalGetLogLikelihoodCount++;
if (!likelihoodKnown) {
if (COUNT_TOTAL_OPERATIONS)
totalcalculateLikelihoodCount++;
logLikelihood = calculateLogLikelihood();
likelihoodKnown = true;
}
return logLikelihood;
}
/**
* Forces a complete recalculation of the likelihood next time getLikelihood is called
*/
public void makeDirty() {
if (COUNT_TOTAL_OPERATIONS)
totalMakeDirtyCount++;
likelihoodKnown = false;
updateAllNodes();
updateAllPatterns();
}
protected abstract double calculateLogLikelihood();
public String getReport() {
if (hasInitialized) {
String rtnValue = getClass().getName() + "(" + getLogLikelihood() + ")";
if (COUNT_TOTAL_OPERATIONS)
rtnValue += " total operations = " + totalOperationCount +
" matrix updates = " + totalMatrixUpdateCount + " model changes = " + totalModelChangedCount +
" make dirties = " + totalMakeDirtyCount +
" calculate likelihoods = " + totalcalculateLikelihoodCount +
" get likelihoods = " + totalGetLogLikelihoodCount +
" all rate updates = " + totalRateUpdateAllCount +
" partial rate updates = " + totalRateUpdateSingleCount;
return rtnValue;
} else {
return getClass().getName() + "(uninitialized)";
}
}
// **************************************************************
// INSTANCE VARIABLES
// **************************************************************
/**
* the tree
*/
protected TreeModel treeModel = null;
/**
* the patternList
*/
protected PatternList patternList = null;
protected DataType dataType = null;
/**
* the pattern weights
*/
protected double[] patternWeights;
/**
* the number of patterns
*/
protected int patternCount;
/**
* the number of states in the data
*/
protected int stateCount;
/**
* the number of nodes in the tree
*/
protected int nodeCount;
/**
* Flags to specify which patterns are to be updated
*/
protected boolean[] updatePattern = null;
/**
* Flags to specify which nodes are to be updated
*/
protected boolean[] updateNode;
private double logLikelihood;
private double storedLogLikelihood;
protected boolean likelihoodKnown = false;
private boolean storedLikelihoodKnown = false;
protected boolean hasInitialized = false;
protected int totalOperationCount = 0;
protected int totalMatrixUpdateCount = 0;
protected int totalGetLogLikelihoodCount = 0;
protected int totalModelChangedCount = 0;
protected int totalMakeDirtyCount = 0;
protected int totalcalculateLikelihoodCount = 0;
protected int totalRateUpdateAllCount = 0;
protected int totalRateUpdateSingleCount = 0;
}