/*
* RandomBranchModel.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.branchmodel;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.math.random.MersenneTwister;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.codon.GY94CodonModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evolution.datatype.Codons;
import dr.evolution.datatype.DataType;
import dr.evolution.tree.NodeRef;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.AbstractModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
import dr.inference.model.Variable.ChangeType;
import dr.math.MathUtils;
/**
* @author Filip Bielejec
* @version $Id$
*
*/
@SuppressWarnings("serial")
public class RandomBranchModel extends AbstractModel implements BranchModel {
public static final String RANDOM_BRANCH_MODEL = "randomBranchModel";
private final TreeModel treeModel;
private GY94CodonModel baseSubstitutionModel;
private LinkedList<SubstitutionModel> substitutionModels;
private LinkedHashMap<NodeRef, Integer> branchAssignmentMap;
// TODO: parse distribution model for e_i
// TODO: parse substitution model (hardcoded now)
// TODO: parse parameter that follows trend (hardcoded now)
private double rate;
private static MersenneTwister random;
public RandomBranchModel(TreeModel treeModel, //
GY94CodonModel baseSubstitutionModel, //
double rate, //
boolean hasSeed,
long seed
) {
super(RANDOM_BRANCH_MODEL);
this.treeModel = treeModel;
this.baseSubstitutionModel = baseSubstitutionModel;
this.rate = rate;
if( hasSeed) {
// use fixed seed for e_i
random = new MersenneTwister(
seed);
} else {
//use BEAST seed
random = new MersenneTwister( MathUtils.nextLong() );
}//END: seed check
setup();
}// END: Constructor
private void setup() {
DataType dataType = baseSubstitutionModel.getDataType();
FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel();
Parameter kappaParameter = new Parameter.Default("kappa", 1,
baseSubstitutionModel.getKappa());
substitutionModels = new LinkedList<SubstitutionModel>();
branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>();
int branchClass = 0;
for (NodeRef node : treeModel.getNodes()) {
if (!treeModel.isRoot(node)) {
double nodeHeight = treeModel.getNodeHeight(node);
double parentHeight = treeModel.getNodeHeight(treeModel
.getParent(node));
double time = 0.5 * (parentHeight + nodeHeight);
double baseOmega = baseSubstitutionModel.getOmega();
double fixed = baseOmega * time;
double epsilon = (Math.log(1-random.nextDouble()) / (-rate) ); //Math.exp((random.nextGaussian() * stdev + mean));
double value = fixed + epsilon;
Parameter omegaParameter = new Parameter.Default("omega", 1,
value);
GY94CodonModel gy94 = new GY94CodonModel((Codons) dataType,
omegaParameter, kappaParameter, freqModel);
substitutionModels.add(gy94);
branchAssignmentMap.put(node, branchClass);
branchClass++;
}//END: root check
}// END: nodes loop
}// END: setup
@Override
public Mapping getBranchModelMapping(NodeRef branch) {
final int branchClass = branchAssignmentMap.get(branch);
return new Mapping() {
public int[] getOrder() {
return new int[] { branchClass };
}
public double[] getWeights() {
return new double[] { 1.0 };
}
};
}
@Override
public List<SubstitutionModel> getSubstitutionModels() {
return substitutionModels;
}
@Override
public SubstitutionModel getRootSubstitutionModel() {
// int rootClass = branchAssignmentMap.get(treeModel.getRoot());
// return substitutionModels.get(rootClass);
throw new RuntimeException("Not implemented!");
}
@Override
public FrequencyModel getRootFrequencyModel() {
return getRootSubstitutionModel().getFrequencyModel();
}
@Override
public boolean requiresMatrixConvolution() {
return false;
}
@Override
protected void handleModelChangedEvent(Model model, Object object, int index) {
fireModelChanged();
}
@Override
protected void handleVariableChangedEvent(Variable variable, int index,
ChangeType type) {
}
@Override
protected void storeState() {
}
@Override
protected void restoreState() {
}
@Override
protected void acceptState() {
}
}// END: class