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// File: ProteinFrequenciesSet.h
// Created by: Bastien Boussau
// Julien Dutheil
// Created on: Tue Aug 21 2007
//
/*
Copyright or (c) 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 _PROTEINFREQUENCIESSET_H_
#define _PROTEINFREQUENCIESSET_H_
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
#include "FrequenciesSet.h"
namespace bpp
{
/**
* @brief Parametrize a set of state frequencies for proteins.
*/
class ProteinFrequenciesSet :
public virtual FrequenciesSet
{
public:
#ifndef NO_VIRTUAL_COV
ProteinFrequenciesSet* clone() const = 0;
const ProteicAlphabet* getAlphabet() const = 0;
#endif
};
/**
* @brief Protein FrequenciesSet using 19 independent parameters to modelize the 20 frequencies.
*
* The parameters are called @f$ \theta_{i \in 1..19} @f$, and are initialized so that all frequencies are equal to 0.005, that is
* @f[ \theta_i = \frac{0.05}{0.956{i-1}},\quad i = 1..19 @f] or according to a user-specified vector of initial values.
*/
class FullProteinFrequenciesSet :
public virtual ProteinFrequenciesSet,
public FullFrequenciesSet
{
public:
FullProteinFrequenciesSet(const ProteicAlphabet* alphabet, bool allowNullFreqs = false, const std::string& name = "Full") :
FullFrequenciesSet(alphabet, allowNullFreqs, name) {}
FullProteinFrequenciesSet(const ProteicAlphabet* alphabet, const std::vector<double>& initFreqs, bool allowNullFreqs = false, const std::string& name = "Full") :
FullFrequenciesSet(alphabet, initFreqs, allowNullFreqs, name) {}
#ifndef NO_VIRTUAL_COV
FullProteinFrequenciesSet*
#else
Clonable*
#endif
clone() const { return new FullProteinFrequenciesSet(*this); }
public:
#ifndef NO_VIRTUAL_COV
const ProteicAlphabet* getAlphabet() const
{
return dynamic_cast<const ProteicAlphabet*>(AbstractFrequenciesSet::getAlphabet());
}
#endif
};
/**
* @brief FrequenciesSet useful for homogeneous and stationary models, protein implementation
*
* This set contains no parameter.
*/
class FixedProteinFrequenciesSet :
public virtual ProteinFrequenciesSet,
public FixedFrequenciesSet
{
public:
FixedProteinFrequenciesSet(const ProteicAlphabet* alphabet, const std::vector<double>& initFreqs, const std::string& name = "Fixed") :
FixedFrequenciesSet(alphabet, initFreqs, name) {}
/**
* @brief Construction with uniform frequencies on the letters of
* the alphabet.
*/
FixedProteinFrequenciesSet(const ProteicAlphabet* alphabet, const std::string& name = "Fixed") :
FixedFrequenciesSet(alphabet, alphabet->getSize(), name) {}
#ifndef NO_VIRTUAL_COV
FixedProteinFrequenciesSet*
#else
FixedFrequenciesSet*
#endif
clone() const { return new FixedProteinFrequenciesSet(*this); }
#ifndef NO_VIRTUAL_COV
const ProteicAlphabet* getAlphabet() const
{
return dynamic_cast<const ProteicAlphabet*>(AbstractFrequenciesSet::getAlphabet());
}
#endif
};
} // end of namespace bpp.
#endif // _PROTEINFREQUENCIESSET_H_
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