/*
* AbstractSinglePartitionTreeLikelihood.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.evomodel.treelikelihood;
/**
* ${CLASS_NAME}
*
* @author Andrew Rambaut
* @version $Id$
*
* $HeadURL$
*
* $LastChangedBy$
* $LastChangedDate$
* $LastChangedRevision$
*/
import dr.evolution.alignment.PatternList;
import dr.evolution.datatype.DataType;
import dr.evomodel.tree.TreeModel;
public abstract class AbstractSinglePartitionTreeLikelihood extends AbstractTreeLikelihood {
public AbstractSinglePartitionTreeLikelihood(String name, PatternList patternList, TreeModel treeModel) {
super(name, treeModel);
this.patternList = patternList;
this.dataType = patternList.getDataType();
patternCount = patternList.getPatternCount();
stateCount = dataType.getStateCount();
patternWeights = patternList.getPatternWeights();
}
/**
* 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;
}
/**
* Forces a complete recalculation of the likelihood next time getLikelihood is called
*/
public void makeDirty() {
super.makeDirty();
updateAllPatterns();
}
/**
* 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;
/**
* Flags to specify which patterns are to be updated
*/
protected boolean[] updatePattern = null;
}