/*
* SpeciationModel.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.speciation;
import dr.evolution.tree.Tree;
import dr.evolution.util.Taxon;
import dr.evolution.util.Units;
import dr.inference.model.AbstractModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
import java.util.Set;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
*/
public abstract class SpeciationModel extends AbstractModel implements Units {
/**
* Units in which population size is measured.
*/
private Units.Type units;
public SpeciationModel(String name, Type units) {
super(name);
setUnits(units);
}
public abstract double calculateTreeLogLikelihood(Tree tree);
public abstract double calculateTreeLogLikelihood(Tree tree, Set<Taxon> exclude);
// True if Yule.
//
// Not abstract - non supporting derived classes do not need to override anything
public boolean isYule() {
return false;
}
// Likelihood for the speciation model conditional on monophyly and calibration densities in
// 'calibration'.
//
// The likelihood enforces the monophyly, so there is no need to specify it again in the XML.
//
public double calculateTreeLogLikelihood(Tree tree, CalibrationPoints calibration) {
return Double.NEGATIVE_INFINITY;
}
protected void handleModelChangedEvent(Model model, Object object, int index) {
// no intermediates need to be recalculated...
}
protected void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
// no intermediates need to be recalculated...
}
protected void storeState() {
} // no additional state needs storing
protected void restoreState() {
} // no additional state needs restoring
protected void acceptState() {
} // no additional state needs accepting
/**
* sets units of measurement.
*
* @param u units
*/
public void setUnits(Units.Type u) {
units = u;
}
/**
* returns units of measurement.
*/
public Units.Type getUnits() {
return units;
}
}