/*
* BranchModel.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 dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evolution.tree.NodeRef;
import dr.inference.model.Model;
import java.util.List;
/**
* This is an interface which provides a mapping of substitution models to branches.
*
* @author Andrew Rambaut
* @author Filip Bielejec
* @author Marc A. Suchard
* @version $Id$
*/
public interface BranchModel extends Model {
/**
* Returns a mapping of substitution models to the given branch. The Mapping
* contains a list of substitution models in order from tipward to rootward
* and a set of relative weights for each (may be times or proportions).
*
* @param branch the branch
* @return a Mapping object
*/
Mapping getBranchModelMapping(final NodeRef branch);
/**
* Gets the list of substitution models in order they will be referred to
* by the indices returned by the mappings.
* @return the list of substitution models
*/
List<SubstitutionModel> getSubstitutionModels();
/**
* Gets the substitution model that will be applied at the root.
* @return the substitution model
*/
SubstitutionModel getRootSubstitutionModel();
/**
* Gets the frequency model that will be applied at the root.
* @return the substitution model
*/
FrequencyModel getRootFrequencyModel();
/**
* Is this model going to require convolution of matrices along any branches (essentially
* are the mappings ever going to return more than one substitution model.
* @return does it?
*/
boolean requiresMatrixConvolution();
interface Mapping {
int[] getOrder();
double[] getWeights();
}
Mapping DEFAULT = new Mapping() {
public int[] getOrder() {
return new int[] { 0 };
}
public double[] getWeights() {
return new double[] { 1.0 };
}
};
}