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// File: HomogeneousTreeLikelihood.h
// Created by: Julien Dutheil
// Created on: Tue Oct 9 16:03 2007
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _HOMOGENEOUSTREELIKELIHOOD_H_
#define _HOMOGENEOUSTREELIKELIHOOD_H_
#include "TreeLikelihood.h"
#include "../Model/SubstitutionModel.h"
namespace bpp
{
/**
* @brief Specialization of the TreeLikelihood interface for the Homogeneous case.
*
* Homogeneous models assume a unique substitution model along the tree.
* This interface further assumes that the substitution model is the same for all sites.
* For likelihood functions with different model per sites, see SitePartitionHomogeneousTreeLikelihood.
*
* @see SubstitutionModel, SitePartitionHomogeneousTreeLikelihood.
*/
class HomogeneousTreeLikelihood :
public virtual TreeLikelihood
{
public:
#ifndef NO_VIRTUAL_COV
HomogeneousTreeLikelihood* clone() const = 0;
#endif
public:
const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
{
return getSubstitutionModel();
}
SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
{
return getSubstitutionModel();
}
/**
* @return The substitution model attached to this instance.
*/
virtual const SubstitutionModel* getSubstitutionModel() const = 0;
/**
* @return The substitution model attached to this instance.
*/
virtual SubstitutionModel* getSubstitutionModel() = 0;
/**
* @return Set the substitution model for this instance.
* @throw Exception If the model could not be set (for instance, because of a wrong alphabet type).
*/
virtual void setSubstitutionModel(SubstitutionModel* model) throw (Exception) = 0;
};
} //end of namespace bpp.
#endif //_HOMOGENEOUSTREELIKELIHOOD_H_
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