/*
* AlloppNetworkPriorModel.java
*
* Copyright (c) 2002-2017 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.alloppnet.speciation;
import dr.evolution.util.Units;
import dr.evomodel.alloppnet.parsers.AlloppNetworkPriorModelParser;
import dr.inference.distribution.ParametricDistributionModel;
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;
/**
*
* Model for prior of an allopolyploid network.
*
* @author Graham Jones
* Date: 01/07/2011
*/
/*
*/
public class AlloppNetworkPriorModel extends AbstractModel implements Units {
private Parameter rate;
private Parameter popsf;
private ParametricDistributionModel tpmodel;
private ParametricDistributionModel rpmodel;
private ParametricDistributionModel hpmodel;
private Units.Type units;
public AlloppNetworkPriorModel(Parameter eventrate, Parameter popscalingfactor,
ParametricDistributionModel tippopmodel, ParametricDistributionModel rootpopmodel,
ParametricDistributionModel hybpopmodel, Units.Type units) {
super(AlloppNetworkPriorModelParser.ALLOPPNETWORKPRIORMODEL);
this.rate = eventrate;
this.popsf = popscalingfactor;
this.tpmodel = tippopmodel;
this.rpmodel = rootpopmodel;
this.hpmodel = hybpopmodel;
this.units = units;
addVariable(rate);
addVariable(popsf);
}
Parameter getRate() {
return rate;
}
Parameter getPopScalingFactor() {
return popsf;
}
ParametricDistributionModel getTipPopModel() {
return tpmodel;
}
ParametricDistributionModel getRootPopModel() {
return rpmodel;
}
ParametricDistributionModel getHybridPopModel() {
return hpmodel;
}
@Override
protected void handleModelChangedEvent(Model model, Object object, int index) {
if (AlloppSpeciesNetworkModel.DBUGTUNE)
System.out.println("AlloppNetworkPriorModel.handleModelChangedEvent() " + model.getId());
}
@Override
protected void handleVariableChangedEvent(Variable variable, int index,
ChangeType type) {
if (AlloppSpeciesNetworkModel.DBUGTUNE)
System.out.println("AlloppNetworkPriorModel.handleModelChangedEvent() " + variable.getId());
}
@Override
protected void storeState() {
// addVariable(rate), addVariable(popsf) deal with this
if (AlloppSpeciesNetworkModel.DBUGTUNE)
System.out.println("AlloppNetworkPriorModel.storeState()");
}
@Override
protected void restoreState() {
// addVariable(rate), addVariable(popsf) deal with this
if (AlloppSpeciesNetworkModel.DBUGTUNE)
System.out.println("AlloppNetworkPriorModel.restoreState()");
}
@Override
protected void acceptState() {
}
public Type getUnits() {
return units;
}
public void setUnits(Type units) {
// grjtodo-oneday allow units other than substitutions
}
}