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bpp::L95 Class Referenceabstract

The no-strand bias substitution model for nucleotides, from Lobry 1995. The point of this model is that the substitution rate from a nucleotide N towards another M is the same as the rate from the complement of N towards the complement of M. Note that this model is not reversible. More...

#include <Bpp/Phyl/Model/Nucleotide/L95.h>

+ Inheritance diagram for bpp::L95:
+ Collaboration diagram for bpp::L95:

Public Member Functions

 L95 (const NucleicAlphabet *alphabet, double alpha=0.5, double beta=0.5, double gamma=0.5, double kappa=1., double theta=0.5)
 
virtual ~L95 ()
 
L95clone () const
 
std::string getName () const
 Get the name of the model. More...
 
void updateMatrices ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
void setFreq (std::map< int, double > &)
 This method is redefined to actualize the corresponding parameters theta too. More...
 
virtual size_t getNumberOfStates () const
 Get the number of states. More...
 
virtual const std::vector< int > & getAlphabetChars () const =0
 
virtual int getAlphabetChar (size_t i) const =0
 Get the char in the alphabet corresponding to a given state in the model. More...
 
virtual std::vector< size_t > getModelStates (int i) const =0
 Get the state in the model corresponding to a particular char in the alphabet. More...
 
virtual double freq (size_t i) const =0
 
virtual double Qij (size_t i, size_t j) const =0
 
virtual double Pij_t (size_t i, size_t j, double t) const =0
 
virtual double dPij_dt (size_t i, size_t j, double t) const =0
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const =0
 
virtual const VdoublegetFrequencies () const =0
 
virtual const Matrix< double > & getGenerator () const =0
 
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
 
virtual double Sij (size_t i, size_t j) const =0
 
virtual const Matrix< double > & getPij_t (double t) const =0
 
virtual const Matrix< double > & getdPij_dt (double t) const =0
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
 
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed. More...
 
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed. More...
 
virtual const VdoublegetEigenValues () const =0
 
virtual const VdoublegetIEigenValues () const =0
 
virtual bool isDiagonalizable () const =0
 
virtual bool isNonSingular () const =0
 
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
 
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
 
virtual const AlphabetgetAlphabet () const =0
 
virtual double getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
 
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...
 
virtual void setScale (double scale)=0
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector. More...
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
virtual const FrequenciesSetgetFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 
virtual size_t getNumberOfIndependentParameters () const =0
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual const ParameterListgetIndependentParameters () const =0
 
virtual std::vector< std::string > getAlias (const std::string &name) const =0
 
const AlphabetgetAlphabet () const
 
const std::vector< int > & getAlphabetChars () const
 
int getAlphabetChar (size_t i) const
 Get the char in the alphabet corresponding to a given state in the model. More...
 
std::vector< size_t > getModelStates (int i) const
 Get the state in the model corresponding to a particular char in the alphabet. More...
 
virtual const VdoublegetFrequencies () const
 
const Matrix< double > & getGenerator () const
 
const Matrix< double > & getExchangeabilityMatrix () const
 
double Sij (size_t i, size_t j) const
 
virtual const Matrix< double > & getPij_t (double t) const
 
virtual const Matrix< double > & getdPij_dt (double t) const
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const
 
const VdoublegetEigenValues () const
 
const VdoublegetIEigenValues () const
 
bool isDiagonalizable () const
 
bool isNonSingular () const
 
const Matrix< double > & getRowLeftEigenVectors () const
 
const Matrix< double > & getColumnRightEigenVectors () const
 
virtual double freq (size_t i) const
 
virtual double Qij (size_t i, size_t j) const
 
virtual double Pij_t (size_t i, size_t j, double t) const
 
virtual double dPij_dt (size_t i, size_t j, double t) const
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const
 
double getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed. More...
 
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed. More...
 
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. More...
 
void addRateParameter ()
 
double getScale () const
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...
 
void setScale (double scale)
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector. More...
 
virtual double getRate () const
 Get the rate. More...
 
virtual void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
size_t getNumberOfIndependentParameters () const
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
const ParameterListgetIndependentParameters () const
 
std::vector< std::string > getAlias (const std::string &name) const
 
void setNamespace (const std::string &prefix)
 
bool hasParameter (const std::string &name) const
 
const ParameterListgetParameters () const
 
const ParametergetParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const
 
void setAllParametersValues (const ParameterList &parameters)
 
void setParameterValue (const std::string &name, double value)
 
void setParametersValues (const ParameterList &parameters)
 
bool matchParametersValues (const ParameterList &parameters)
 
size_t getNumberOfParameters () const
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 

Protected Member Functions

void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void resetParameters_ ()
 
ParametergetParameter_ (const std::string &name)
 
ParametergetParameter_ (size_t index)
 
const ParametergetParameter_ (size_t index) const
 
ParametergetParameterWithNamespace_ (const std::string &name)
 
const ParametergetParameterWithNamespace_ (const std::string &name) const
 
ParameterListgetParameters_ ()
 

Protected Attributes

const Alphabetalphabet_
 The alphabet relevant to this model. More...
 
size_t size_
 The size of the generator, i.e. the number of states. More...
 
double rate_
 The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...
 
std::vector< int > chars_
 The list of supported chars. More...
 
RowMatrix< double > generator_
 The generator matrix $Q$ of the model. More...
 
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies. More...
 
RowMatrix< double > exchangeability_
 The exchangeability matrix $S$ of the model, defined as $ S_{ij}=\frac{Q_{ij}}{\pi_j}$. When the model is reversible, this matrix is symetric. More...
 
RowMatrix< double > pijt_
 These ones are for bookkeeping: More...
 
RowMatrix< double > dpijt_
 
RowMatrix< double > d2pijt_
 
bool eigenDecompose_
 Tell if the eigen decomposition should be performed. More...
 
Vdouble eigenValues_
 The vector of eigen values. More...
 
Vdouble iEigenValues_
 The vector of the imaginary part of the eigen values. More...
 
bool isDiagonalizable_
 boolean value for diagonalizability in R of the generator_ More...
 
RowMatrix< double > rightEigenVectors_
 The $U^-1$ matrix made of right eigen vectors (by column). More...
 
bool isNonSingular_
 boolean value for non-singularity of rightEigenVectors_ More...
 
RowMatrix< double > leftEigenVectors_
 The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More...
 
std::vector< RowMatrix< double > > vPowGen_
 vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More...
 
RowMatrix< double > tmpMat_
 For computational issues. More...
 

Private Attributes

double alpha_
 
double beta_
 
double gamma_
 
double kappa_
 
double theta_
 

Detailed Description

The no-strand bias substitution model for nucleotides, from Lobry 1995. The point of this model is that the substitution rate from a nucleotide N towards another M is the same as the rate from the complement of N towards the complement of M. Note that this model is not reversible.

After normalization, this model contains 5 parameters:

\[ Q = \frac 1{2*\kappa*\theta*(1-\theta)+\gamma+\theta-2*\theta*\gamma} \begin{pmatrix} \cdots & \kappa.\beta.\theta & \kappa.(1-\beta).\theta & \gamma \\ \kappa.\alpha.(1-\theta) & \cdots & 1-\gamma & \kappa.(1-\alpha).(1-\theta) \\ \kappa.(1-\alpha).(1-\theta) & 1-\gamma & \cdots & \kappa.\alpha.(1-\theta) \\ \gamma & \kappa.(1-\beta).\theta & \kappa.\beta.\theta & \cdots \\ \end{pmatrix} \]

The equilibrium frequencies are

\[ \pi = \left(\frac{1-\theta}{2}, \frac{\theta}{2}, \frac{\theta}{2}, \frac{1-\theta}{2}\right) \]

and then $\sum_i Q_{i,i}\pi_i = -1$.

The generator of this model is diagonalized numerically. See AbstractSubstitutionModel for details of how the probabilities are computed.

The parameters are named "alpha", "beta", "gamma", "kappa" and "theta". The values of "alpha", "beta", "gamma" are between 0 and 1, The values of "gamma" are between 0 and 1 excluded, the values of "kappa" which are positive. Their values may be retrieved with the command:

for instance.

Reference:

  • Lobry J R (1995), Journal_ Of Molecular Evolution_ 40 326-330.

Definition at line 93 of file L95.h.

Constructor & Destructor Documentation

virtual bpp::L95::~L95 ( )
inlinevirtual

Definition at line 109 of file L95.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited
virtual void bpp::SubstitutionModel::addRateParameter ( )
pure virtualinherited
L95* bpp::L95::clone ( ) const
inlinevirtual

Implements bpp::AbstractSubstitutionModel.

Definition at line 116 of file L95.h.

References L95().

virtual double bpp::SubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
Returns
The second order derivative of the probability of change from state i to state j with respect to time t, at time t.
See Also
getd2Pij_dt2(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(), and bpp::RE08::d2Pij_dt2().

virtual double bpp::AbstractSubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
Returns
The second order derivative of the probability of change from state i to state j with respect to time t, at time t.
See Also
getd2Pij_dt2(), getStates()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 280 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_dt2().

virtual double bpp::SubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
Returns
The first order derivative of the probability of change from state i to state j with respect to time t, at time t.
See Also
getdPij_dt(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::dPij_dt(), and bpp::RE08::dPij_dt().

virtual double bpp::AbstractSubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
Returns
The first order derivative of the probability of change from state i to state j with respect to time t, at time t.
See Also
getdPij_dt(), getStates()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 279 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool  yn)
inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 288 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( )
pure virtualinherited

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

virtual void bpp::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList parameters)
inlinevirtualinherited
virtual double bpp::AbstractSubstitutionModel::freq ( size_t  i) const
inlinevirtualinherited
Returns
Equilibrium frequency associated to character i.
See Also
getFrequencies(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 274 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

virtual int bpp::SubstitutionModel::getAlphabetChar ( size_t  i) const
pure virtualinherited

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters
iThe index of the state.
Returns
The corresponding state in the alphabet.
See Also
MarkovModulatedSubstitutionModel
getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

int bpp::AbstractSubstitutionModel::getAlphabetChar ( size_t  i) const
inlinevirtualinherited

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters
iThe index of the state.
Returns
The corresponding state in the alphabet.
See Also
MarkovModulatedSubstitutionModel
getStates()

Implements bpp::SubstitutionModel.

Definition at line 246 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetChars ( ) const
pure virtualinherited
const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetChars ( ) const
inlinevirtualinherited
Returns
The supported states of the model, as a vector of int codes.
See Also
Alphabet

Implements bpp::SubstitutionModel.

Definition at line 244 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getColumnRightEigenVectors ( ) const
inlinevirtualinherited
Returns
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 272 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const
pure virtualinherited
const Matrix< double > & AbstractSubstitutionModel::getd2Pij_dt2 ( double  t) const
virtualinherited
Returns
All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See Also
d2Pij_dt2()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 275 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), bpp::MatrixTools::copy(), bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::MatrixTools::getId(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::MatrixTools::mult(), bpp::MatrixTools::mult(), bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::MatrixTools::scale(), bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::NumTools::sqr(), bpp::NumTools::sqr(), bpp::NumTools::sqr(), bpp::NumTools::sqr(), bpp::NumTools::sqr(), bpp::NumTools::sqr(), bpp::NumTools::sqr(), bpp::AbstractSubstitutionModel::tmpMat_, bpp::AbstractSubstitutionModel::tmpMat_, bpp::AbstractSubstitutionModel::vPowGen_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::AbstractSubstitutionModel::d2Pij_dt2().

const Matrix< double > & AbstractSubstitutionModel::getdPij_dt ( double  t) const
virtualinherited
Returns
Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See Also
dPij_dt()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 206 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), bpp::MatrixTools::copy(), bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::MatrixTools::getId(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::MatrixTools::mult(), bpp::MatrixTools::mult(), bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::MatrixTools::scale(), bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, bpp::AbstractSubstitutionModel::tmpMat_, bpp::AbstractSubstitutionModel::vPowGen_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::AbstractSubstitutionModel::dPij_dt().

const Vdouble& bpp::AbstractSubstitutionModel::getEigenValues ( ) const
inlinevirtualinherited
Returns
A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 262 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const
pure virtualinherited
const Matrix<double>& bpp::AbstractSubstitutionModel::getExchangeabilityMatrix ( ) const
inlinevirtualinherited
Returns
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

Implements bpp::SubstitutionModel.

Definition at line 254 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const
pure virtualinherited
Returns
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Vdouble& bpp::AbstractSubstitutionModel::getFrequencies ( ) const
inlinevirtualinherited
Returns
A vector of all equilibrium frequencies.
See Also
freq()

Implements bpp::SubstitutionModel.

Definition at line 250 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const
inlinevirtualinherited
const Matrix<double>& bpp::AbstractSubstitutionModel::getGenerator ( ) const
inlinevirtualinherited
Returns
The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $ \forall i; \sum_j Q_{i,j} = 0 $, meaning that $ $ \forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$, and (ii) $ \sum_i Q_{i,i} \times \pi_i = -1$. This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time $t$ are measured in units of expected number of changes per site. Additionnaly, the rate_ attibute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See Also
Qij()

Implements bpp::SubstitutionModel.

Definition at line 252 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const
pure virtualinherited
Returns
The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $ \forall i; \sum_j Q_{i,j} = 0 $, meaning that $ $ \forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$, and (ii) $ \sum_i Q_{i,i} \times \pi_i = -1$. This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time $t$ are measured in units of expected number of changes per site. Additionnaly, the rate_ attibute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See Also
Qij()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Vdouble& bpp::AbstractSubstitutionModel::getIEigenValues ( ) const
inlinevirtualinherited
Returns
A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 264 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const
pure virtualinherited
Returns
A vector with all imaginary parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().

double AbstractSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const throw (IndexOutOfBoundsException, BadIntException)
virtualinherited

This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters
ithe index of the state in the model.
stateAn observed state in the sequence/site.
Returns
1 or 0 depending if the two states are compatible.
Exceptions
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif states are not allowed in the associated alphabet.
See Also
getStates();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08.

Definition at line 350 of file AbstractSubstitutionModel.cpp.

virtual double bpp::SubstitutionModel::getInitValue ( size_t  i,
int  state 
) const throw (IndexOutOfBoundsException, BadIntException)
pure virtualinherited

This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters
ithe index of the state in the model.
stateAn observed state in the sequence/site.
Returns
1 or 0 depending if the two states are compatible.
Exceptions
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif states are not allowed in the associated alphabet.
See Also
getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int  i) const
pure virtualinherited

Get the state in the model corresponding to a particular char in the alphabet.

Parameters
iThe alphabet char to check.
Returns
A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( int  i) const
inlinevirtualinherited

Get the state in the model corresponding to a particular char in the alphabet.

Parameters
iThe alphabet char to check.
Returns
A vector of indices of model states.

Implements bpp::SubstitutionModel.

Definition at line 248 of file AbstractSubstitutionModel.h.

References bpp::VectorTools::whichAll().

std::string bpp::L95::getName ( ) const
inlinevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 119 of file L95.h.

virtual size_t bpp::NucleotideSubstitutionModel::getNumberOfStates ( ) const
inlinevirtualinherited

Get the number of states.

For most models, this equals the size of the alphabet.

Returns
The number of different states in the model.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::gBGC.

Definition at line 68 of file NucleotideSubstitutionModel.h.

const Matrix< double > & AbstractSubstitutionModel::getPij_t ( double  t) const
virtualinherited
Returns
All probabilities of change from state i to state j during time t.
See Also
Pij_t()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 135 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), bpp::AbstractSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::MatrixTools::getId(), bpp::MatrixTools::getId(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, bpp::AbstractSubstitutionModel::vPowGen_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::AbstractSubstitutionModel::Pij_t().

double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 416 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

virtual double bpp::SubstitutionModel::getRate ( ) const
pure virtualinherited
const Matrix<double>& bpp::AbstractSubstitutionModel::getRowLeftEigenVectors ( ) const
inlinevirtualinherited
Returns
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 270 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const
pure virtualinherited
double AbstractSubstitutionModel::getScale ( ) const
virtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns
Minus the scalar product of diagonal elements and the frequencies vector.

Implements bpp::SubstitutionModel.

Definition at line 401 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::diag(), and bpp::AbstractSubstitutionModel::freq_.

Referenced by bpp::AbstractReversibleSubstitutionModel::updateMatrices().

virtual double bpp::SubstitutionModel::getScale ( ) const
pure virtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns
Minus the scalar product of diagonal elements and the frequencies vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const
inlinevirtualinherited
Returns
True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 266 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const
pure virtualinherited
bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const
inlinevirtualinherited
Returns
True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const
pure virtualinherited
virtual double bpp::AbstractSubstitutionModel::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
Returns
The probability of change from state i to state j during time t.
See Also
getPij_t(), getStates()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 278 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_t().

virtual double bpp::AbstractSubstitutionModel::Qij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited
Returns
The rate in the generator of change from state i to state j.
See Also
getStates();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 276 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void L95::setFreq ( std::map< int, double > &  freqs)
virtual

This method is redefined to actualize the corresponding parameters theta too.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 111 of file L95.cpp.

References bpp::AbstractParameterAliasable::setParameterValue(), and updateMatrices().

void AbstractSubstitutionModel::setFreqFromData ( const SequenceContainer data,
double  pseudoCount = 0 
)
virtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters
dataThe sequences to use.
pseudoCountA quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as

\[ \pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)} \]

Implements bpp::SubstitutionModel.

Definition at line 367 of file AbstractSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getCounts(), bpp::AbstractSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::size_, and bpp::AbstractSubstitutionModel::size_.

virtual void bpp::SubstitutionModel::setFreqFromData ( const SequenceContainer data,
double  pseudoCount = 0 
)
pure virtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters
dataThe sequences to use.
pseudoCountA quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as

\[ \pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)} \]

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), and bpp::MarkovModulatedSubstitutionModel::setFreqFromData().

void AbstractSubstitutionModel::setRate ( double  rate)
virtualinherited
virtual void bpp::SubstitutionModel::setRate ( double  rate)
pure virtualinherited
void AbstractSubstitutionModel::setScale ( double  scale)
virtualinherited

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implements bpp::SubstitutionModel.

Definition at line 410 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::scale().

virtual void bpp::SubstitutionModel::setScale ( double  scale)
pure virtualinherited

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().

double bpp::AbstractSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited
Returns
The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implements bpp::SubstitutionModel.

Definition at line 256 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual double bpp::SubstitutionModel::Sij ( size_t  i,
size_t  j 
) const
pure virtualinherited
Returns
The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::Sij().

void L95::updateMatrices ( )
virtual

Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The generator_ matrix and freq_ vector must be initialized.

Eigen values and vectors are computed from the generator and assigned to the eigenValues_ for the real part, iEigenValues_ for the imaginary part, rightEigenVectors_ and leftEigenVectors_ variables. isDiagonalizable_ checks if the generator_ is diagonalizable in R.

The optional rate parameter is not taken into account in this method to prevent unnecessary computation.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 74 of file L95.cpp.

References alpha_, alpha_, alpha_, alpha_, alpha_, beta_, beta_, beta_, beta_, beta_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::freq_, gamma_, gamma_, gamma_, gamma_, gamma_, gamma_, gamma_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::getParameterValue(), kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, kappa_, bpp::MatrixTools::scale(), theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, theta_, and bpp::AbstractSubstitutionModel::updateMatrices().

Referenced by L95(), and setFreq().

Member Data Documentation

double bpp::L95::alpha_
private

Definition at line 98 of file L95.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

double bpp::L95::beta_
private

Definition at line 98 of file L95.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::eigenValues_
protectedinherited

The vector of eigen values.

Definition at line 139 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_
protectedinherited

The exchangeability matrix $S$ of the model, defined as $ S_{ij}=\frac{Q_{ij}}{\pi_j}$. When the model is reversible, this matrix is symetric.

Definition at line 122 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::AbstractSubstitutionModel::getExchangeabilityMatrix(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::Coala::readFromFile(), bpp::Coala::readFromFile(), bpp::Coala::readFromFile(), bpp::Coala::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::Sij(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::WordSubstitutionModel::completeMatrices(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::Coala::computeEquilibriumFrequencies(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::DSO78::DSO78(), bpp::DSO78::DSO78(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::AbstractSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RN95s::getPij_t(), bpp::RE08::getPij_t(), bpp::RE08::getPij_t(), bpp::RE08::getPij_t(), bpp::RE08::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::RN95::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JCprot::JCprot(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::JTT92::JTT92(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::LG08::LG08(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RN95s::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::SSR::updateMatrices(), bpp::MixtureOfASubstitutionModel::updateMatrices(), bpp::MixtureOfASubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::RN95::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::WAG01::WAG01(), bpp::WAG01::WAG01(), and bpp::WAG01::WAG01().

double bpp::L95::gamma_
private
RowMatrix<double> bpp::AbstractSubstitutionModel::generator_
protectedinherited

The generator matrix $Q$ of the model.

Definition at line 107 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), bpp::Coala::Coala(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractSubstitutionModel::getGenerator(), bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::Qij(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_
protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 144 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getIEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_
protectedinherited

The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.

Definition at line 168 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRowLeftEigenVectors(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

double bpp::AbstractSubstitutionModel::rate_
protectedinherited

The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized.

Definition at line 97 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::RN95s::d2Pij_dt2(), bpp::RN95s::d2Pij_dt2(), bpp::RN95s::d2Pij_dt2(), bpp::RN95s::d2Pij_dt2(), bpp::RN95s::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::RN95s::dPij_dt(), bpp::RN95s::dPij_dt(), bpp::RN95s::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::TN93::dPij_dt(), bpp::RN95::dPij_dt(), bpp::RN95::dPij_dt(), bpp::RN95::dPij_dt(), bpp::RN95::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::T92::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::RN95s::getPij_t(), bpp::JCnuc::getPij_t(), bpp::TN93::getPij_t(), bpp::RN95::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::JCprot::getPij_t(), bpp::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::JCnuc::Pij_t(), bpp::JCnuc::Pij_t(), bpp::TN93::Pij_t(), bpp::RN95::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::JCprot::Pij_t(), bpp::JCprot::Pij_t(), bpp::HKY85::Pij_t(), bpp::F84::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), and bpp::BinarySubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_
protectedinherited

The $U^-1$ matrix made of right eigen vectors (by column).

Definition at line 155 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getColumnRightEigenVectors(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

size_t bpp::AbstractSubstitutionModel::size_
protectedinherited

The size of the generator, i.e. the number of states.

Definition at line 89 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::JCnuc::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::RE08::getNumberOfStates(), bpp::JCnuc::getPij_t(), bpp::JCnuc::getPij_t(), bpp::RE08::getPij_t(), bpp::JCprot::getPij_t(), bpp::JCprot::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::LG08::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractSubstitutionModel::setFreqFromData(), bpp::AbstractSubstitutionModel::setFreqFromData(), bpp::T92::T92(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RE08::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().


The documentation for this class was generated from the following files: