/*
* AbstractBranchRateModel.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.branchratemodel;
import dr.evolution.tree.*;
import dr.inference.model.*;
/**
* An abstract base class for BranchRateModels to help implement some of the interfaces
* @author Andrew Rambaut
* @version $Id:$
*/
public abstract class AbstractBranchRateModel extends AbstractModelLikelihood implements BranchRateModel {
/**
* @param name Model Name
*/
public AbstractBranchRateModel(String name) {
super(name);
}
public String getTraitName() {
return BranchRateModel.RATE;
}
public Intent getIntent() {
return Intent.BRANCH;
}
public TreeTrait getTreeTrait(final String key) {
return this;
}
public TreeTrait[] getTreeTraits() {
return new TreeTrait[] { this };
}
public Class getTraitClass() {
return Double.class;
}
public boolean getLoggable() {
return true;
}
public Double getTrait(final Tree tree, final NodeRef node) {
return getBranchRate(tree, node);
}
public String getTraitString(final Tree tree, final NodeRef node) {
return Double.toString(getBranchRate(tree, node));
}
public Model getModel() {
return this;
}
public double getLogLikelihood() {
return 0;
}
public void makeDirty() {
// Do nothing
}
}