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// File: UniformizationSubstitutionCount.h
// Created by: Julien Dutheil
// Created on: Sat Mar 19 13:54 2011
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 16, 2004, 2005, 2006)
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 _UNIFORMIZATIONSUBSTITUTIONCOUNT_H_
#define _UNIFORMIZATIONSUBSTITUTIONCOUNT_H_
#include "SubstitutionCount.h"
#include <Bpp/Numeric/Matrix/Matrix.h>
namespace bpp
{
/**
* @brief Analytical substitution count using the uniformization method.
*
* The codes is adapted from the original R code by Paula Tataru and Asger Hobolth.
*
* @author Julien Dutheil
*/
class UniformizationSubstitutionCount:
public AbstractSubstitutionCount
{
private:
const SubstitutionModel* model_;
unsigned int nbStates_;
std::vector< RowMatrix<double> > bMatrices_;
mutable std::vector< RowMatrix<double> > power_;
mutable std::vector < std::vector< RowMatrix<double> > > s_;
double miu_;
mutable std::vector< RowMatrix<double> > counts_;
mutable double currentLength_;
public:
UniformizationSubstitutionCount(const SubstitutionModel* model, SubstitutionRegister* reg);
UniformizationSubstitutionCount(const UniformizationSubstitutionCount& usc) :
AbstractSubstitutionCount(usc), model_(usc.model_),
nbStates_(usc.nbStates_),
bMatrices_(usc.bMatrices_),
power_(usc.power_),
s_(usc.s_),
miu_(usc.miu_),
counts_(usc.counts_),
currentLength_(usc.currentLength_)
{}
UniformizationSubstitutionCount& operator=(const UniformizationSubstitutionCount& usc)
{
AbstractSubstitutionCount::operator=(usc);
model_ = usc.model_;
nbStates_ = usc.nbStates_;
bMatrices_ = usc.bMatrices_;
power_ = usc.power_;
s_ = usc.s_;
miu_ = usc.miu_;
counts_ = usc.counts_;
currentLength_ = usc.currentLength_;
return *this;
}
virtual ~UniformizationSubstitutionCount() {}
public:
double getNumberOfSubstitutions(unsigned int initialState, unsigned int finalState, double length, unsigned int type = 1) const;
Matrix<double>* getAllNumbersOfSubstitutions(double length, unsigned int type = 1) const;
std::vector<double> getNumberOfSubstitutionsForEachType(unsigned int initialState, unsigned int finalState, double length) const;
void setSubstitutionModel(const SubstitutionModel* model);
protected:
void computeCounts_(double length) const;
};
} //end of namespace bpp.
#endif // _UNIFORMIZATIONSUBSTITUTIONCOUNT_H_
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