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// File: JCprot.h
// Created by: Julien Dutheil
// Created on: Tue May 25 16:04:36 2003
//
/*
Copyright or © or Copr. CNRS, (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 _JCPROT_H_
#define _JCPROT_H_
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
#include "ProteinSubstitutionModel.h"
#include "../AbstractSubstitutionModel.h"
#include "../FrequenciesSet/ProteinFrequenciesSet.h"
namespace bpp
{
/**
* @brief The Jukes-Cantor substitution model for proteins.
*
* All rates equal:
* \f[
* \begin{pmatrix}
* \ddots & r & \ldots & r \\
* r & \ddots & \ddots & \vdots \\
* \vdots & \ddots & \ddots & r \\
* r & \ldots & r & \ddots \\
* \end{pmatrix}
* \f]
* \f[
* \pi = diag\left(\frac{1}{20}, \ldots, \frac{1}{20}\right)
* \f]
* Normalization: \f$r\f$ is set so that \f$\sum_i Q_{i,i}\pi_i = -1\f$:
* \f[
* S = \begin{pmatrix}
* -20 & \frac{20}{19} & \ldots & \frac{20}{19} \\
* \frac{20}{19} & -20 & \ddots & \vdots \\
* \vdots & \ddots & \ddots & \frac{20}{19} \\
* \frac{20}{19} & \ldots & \frac{20}{19} & -20 \\
* \end{pmatrix}
* \f]
* The normalized generator is obtained by taking the dot product of \f$S\f$ and \f$pi\f$:
* \f[
* Q = S . \pi = \begin{pmatrix}
* -1 & \frac{1}{19} & \ldots & \frac{1}{19} \\
* \frac{1}{19} & -1 & \ddots & \vdots \\
* \vdots & \ddots & \ddots & \frac{1}{19} \\
* \frac{1}{19} & \ldots & \frac{1}{19} & -1 \\
* \end{pmatrix}
* \f]
*
* The eigen values are \f$\left(0, -\frac{20}{19}, \ldots, -\frac{20}{19}\right)\f$,
* the left eigen vectors are, by row:
* \f[
* U = \begin{pmatrix}
* \frac{1}{20} & \ldots & \frac{1}{20} & \frac{1}{20} & \frac{1}{20} \\
* -\frac{1}{20} & \ldots & -\frac{1}{20} & \frac{19}{20} & -\frac{1}{20} \\
* \vdots & \ddots & \frac{19}{20} & -\frac{1}{20} & -\frac{1}{20} \\
* -\frac{1}{20} & \ddots & \ddots & \vdots & \vdots \\
* \frac{19}{20} & -\frac{1}{20} & \ldots & -\frac{1}{20} & -\frac{1}{20} \\
* \end{pmatrix}
* \f]
* and the right eigen vectors are, by column:
* \f[
* U^-1 = \begin{pmatrix}
* 1 & 0 & \ldots & 0 & 1 \\
* \vdots & \vdots & \ddots & \ddots & 0 \\
* 1 & 0 & 1 & \ddots & \vdots \\
* 1 & 1 & 0 & \ldots & 0 \\
* 1 & -1 & -1 & \ldots & -1 \\
* \end{pmatrix}
* \f]
*
* In addition, a rate_ factor defines the mean rate of the model.
*
* The probabilities of changes are computed analytically using the formulas:
* \f[
* P_{i,j}(t) = \begin{cases}
* \frac{1}{20} + \frac{19}{20}e^{- rate\_ * \frac{20}{19}t}& \text{if $i=j$}, \\
* \frac{1}{20} - \frac{1}{20}e^{- rate\_ * \frac{20}{19}t} & \text{otherwise}.
* \end{cases}
* \f]
*
* First and second order derivatives are also computed analytically using the formulas:
* \f[
* \frac{\partial P_{i,j}(t)}{\partial t} = rate\_ * \begin{cases}
* -e^{- rate\_ * \frac{20}{19}t} & \text{if $i=j$}, \\
* \frac{1}{19}e^{- rate\_ * \frac{20}{19}t} & \text{otherwise}.
* \end{cases}
* \f]
* \f[
* \frac{\partial^2 P_{i,j}(t)}{\partial t^2} = rate\_^2 * \begin{cases}
* \frac{20}{19}e^{- rate\_ * \frac{20}{19}t} & \text{if $i=j$}, \\
* -\frac{20}{361}e^{- rate\_ * \frac{20}{19}t} & \text{otherwise}.
* \end{cases}
* \f]
*
* Reference:
* - Jukes TH and Cantor CR (1969), Evolution_ of proteins molecules_, 121-123, in Mammalian_ protein metabolism_.
*/
class JCprot:
public virtual ProteinSubstitutionModel,
public AbstractReversibleSubstitutionModel
{
private:
mutable double exp_;
mutable RowMatrix<double> p_;
ProteinFrequenciesSet* freqSet_;
public:
/**
* @brief Build a simple JC69 model, with original equilibrium frequencies.
*
* @param alpha A proteic alphabet.
*/
JCprot(const ProteicAlphabet* alpha);
/**
* @brief Build a JC69 model with special equilibrium frequencies.
*
* @param alpha A proteic alphabet.
* @param freqSet A pointer toward a protein frequencies set, which will be owned by this instance.
* @param initFreqs Tell if the frequency set should be initialized with the original JTT92 values.
* Otherwise, the values of the set will be used.
*/
JCprot(const ProteicAlphabet* alpha, ProteinFrequenciesSet* freqSet, bool initFreqs = false);
JCprot(const JCprot& model) :
AbstractParameterAliasable(model),
AbstractSubstitutionModel(model),
AbstractReversibleSubstitutionModel(model),
exp_(model.exp_),
p_(model.p_),
freqSet_(dynamic_cast<ProteinFrequenciesSet*>(model.freqSet_->clone()))
{}
JCprot& operator=(const JCprot& model)
{
AbstractParameterAliasable::operator=(model);
AbstractSubstitutionModel::operator=(model);
AbstractReversibleSubstitutionModel::operator=(model);
exp_ = model.exp_;
p_ = model.p_;
if (freqSet_) delete freqSet_;
freqSet_ = dynamic_cast<ProteinFrequenciesSet*>(model.freqSet_->clone());
return *this;
}
virtual ~JCprot() { delete freqSet_; }
#ifndef NO_VIRTUAL_COV
JCprot*
#else
Clonable*
#endif
clone() const { return new JCprot(*this); }
public:
double Pij_t (int i, int j, double d) const;
double dPij_dt (int i, int j, double d) const;
double d2Pij_dt2(int i, int j, double d) const;
const Matrix<double>& getPij_t (double d) const;
const Matrix<double>& getdPij_dt (double d) const;
const Matrix<double>& getd2Pij_dt2(double d) const;
std::string getName() const
{
if (freqSet_->getNamespace().find("+F.")!=std::string::npos)
return "JC69+F";
else
return "JC69";
}
void fireParameterChanged(const ParameterList& parameters)
{
freqSet_->matchParametersValues(parameters);
freq_ = freqSet_->getFrequencies();
AbstractReversibleSubstitutionModel::fireParameterChanged(parameters);
}
void setFrequenciesSet(const ProteinFrequenciesSet& freqSet)
{
delete freqSet_;
freqSet_ = dynamic_cast<ProteinFrequenciesSet*>(freqSet.clone());
resetParameters_();
addParameters_(freqSet_->getParameters());
}
const FrequenciesSet* getFrequenciesSet() const { return freqSet_; }
void setFreqFromData(const SequenceContainer& data);
protected:
/**
* In the case of the model of Jukes & Cantor, this method is useless since
* the generator is fixed! No matrice can be changed... This method is only
* used in the constructor of the class.
*/
void updateMatrices();
};
} //end of namespace bpp.
#endif //_JCPROT_H_
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