/*
* SVSComplexSubstitutionModel.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.substmodel;
import dr.inference.model.*;
import dr.evolution.datatype.DataType;
import java.util.ArrayList;
import java.util.List;
/**
* @author Marc Suchard
*/
public class SVSComplexSubstitutionModel extends ComplexSubstitutionModel implements Likelihood,
BayesianStochasticSearchVariableSelection {
public SVSComplexSubstitutionModel(String name, DataType dataType, FrequencyModel freqModel,
Parameter ratesParameter, Parameter indicatorsParameter) {
super(name, dataType, freqModel, ratesParameter);
if (indicatorsParameter == null) {
this.indicatorsParameter = new Parameter.Default(ratesParameter.getDimension(), 1.0);
} else {
this.indicatorsParameter = indicatorsParameter;
addVariable(indicatorsParameter);
}
setupIndicatorDimensionNames(-1);
}
@Override
protected void setupRelativeRates(double[] rates) {
for (int i = 0; i < rates.length; i++) {
rates[i] = ratesParameter.getParameterValue(i) * indicatorsParameter.getParameterValue(i);
}
}
protected void setupIndicatorDimensionNames(int relativeTo) {
List<String> indicatorNames = new ArrayList<String>();
String indicatorPrefix = indicatorsParameter.getParameterName();
for (int i = 0; i < dataType.getStateCount(); ++i) {
for (int j = i + 1; j < dataType.getStateCount(); ++j) {
indicatorNames.add(getDimensionString(i, j, indicatorPrefix));
}
}
for (int j = 0; j < dataType.getStateCount(); ++j) {
for (int i = j + 1; i < dataType.getStateCount(); ++i) {
indicatorNames.add(getDimensionString(i, j, indicatorPrefix));
}
}
String[] tmp = new String[0];
indicatorsParameter.setDimensionNames(indicatorNames.toArray(tmp));
}
public Parameter getIndicators() {
return indicatorsParameter;
}
public boolean validState() {
return !updateMatrix ||
BayesianStochasticSearchVariableSelection.Utils.connectedAndWellConditioned(probability,this);
}
protected void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
if (variable == ratesParameter && indicatorsParameter.getParameterValue(index) == 0)
return; // Does not affect likelihood
super.handleVariableChangedEvent(variable,index,type);
}
public Model getModel() {
return this;
}
/**
* Forces a complete recalculation of the likelihood next time getLikelihood is called
*/
public void makeDirty() {
updateMatrix = true;
}
/**
* @return A detailed name of likelihood for debugging.
*/
// public String prettyName() {
// return "SVSComplexSubstitutionModel-connectedness";
// }
@Override
public boolean isUsed() {
return super.isUsed() && isUsed;
}
public void setUsed() {
isUsed = true;
}
private boolean isUsed = false;
private double[] probability = null;
private final Parameter indicatorsParameter;
}