bpp-phyl  2.4.0
bpp::CodonDistanceFrequenciesSubstitutionModel Class Referenceabstract

Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models. More...

#include <Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h>

+ Inheritance diagram for bpp::CodonDistanceFrequenciesSubstitutionModel:
+ Collaboration diagram for bpp::CodonDistanceFrequenciesSubstitutionModel:

Public Member Functions

 CodonDistanceFrequenciesSubstitutionModel (const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0, bool paramSynRate=false)
 Build a new CodonDistanceFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones. More...
 
 CodonDistanceFrequenciesSubstitutionModel (const GeneticCode *gCode, NucleotideSubstitutionModel *pmod1, NucleotideSubstitutionModel *pmod2, NucleotideSubstitutionModel *pmod3, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0, bool paramSynRate=false)
 Build a new CodonDistanceFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones. More...
 
virtual ~CodonDistanceFrequenciesSubstitutionModel ()
 
CodonDistanceFrequenciesSubstitutionModelclone () const
 
void fireParameterChanged (const ParameterList &parameterlist)
 
std::string getName () const
 Get the name of the model. More...
 
double getCodonsMulRate (size_t i, size_t j) const
 Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More...
 
void setNamespace (const std::string &)
 
void setFreq (std::map< int, double > &frequencies)
 Estimation of the parameters of the models so that the equilibrium frequencies match the given ones. More...
 
const FrequenciesSetgetFrequenciesSet () const
 
void updateMatrices ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
const GeneticCodegetGeneticCode () const
 
virtual size_t getNumberOfIndependentParameters () const =0
 
size_t getNumberOfIndependentParameters () const
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
virtual const ParameterListgetIndependentParameters () const =0
 
const ParameterListgetIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const =0
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const =0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const =0
 
bool hasParameter (const std::string &name) const
 
virtual const ParameterListgetParameters () const =0
 
const ParameterListgetParameters () const
 
virtual const ParametergetParameter (const std::string &name) const =0
 
const ParametergetParameter (const std::string &name) const
 
virtual double getParameterValue (const std::string &name) const =0
 
double getParameterValue (const std::string &name) const
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
void setAllParametersValues (const ParameterList &parameters)
 
virtual void setParameterValue (const std::string &name, double value)=0
 
void setParameterValue (const std::string &name, double value)
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
void setParametersValues (const ParameterList &parameters)
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
bool matchParametersValues (const ParameterList &parameters)
 
virtual size_t getNumberOfParameters () const =0
 
size_t getNumberOfParameters () const
 
virtual std::string getNamespace () const =0
 
std::string getNamespace () const
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 
virtual double Qij (size_t i, size_t j) const =0
 
virtual double Qij (size_t i, size_t j) const
 
virtual const Matrix< double > & getGenerator () const =0
 
const Matrix< double > & getGenerator () const
 
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
 
const Matrix< double > & getExchangeabilityMatrix () const
 
virtual double Sij (size_t i, size_t j) const =0
 
double Sij (size_t i, size_t j) const
 
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...
 
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 const VdoublegetEigenValues () const =0
 
const VdoublegetEigenValues () const
 
virtual const VdoublegetIEigenValues () const =0
 
const VdoublegetIEigenValues () const
 
virtual bool isDiagonalizable () const =0
 
bool isDiagonalizable () const
 
virtual bool isNonSingular () const =0
 
bool isNonSingular () const
 
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
 
const Matrix< double > & getRowLeftEigenVectors () const
 
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
 
const Matrix< double > & getColumnRightEigenVectors () const
 
virtual void setScalable (bool scalable)=0
 sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...
 
void setScalable (bool scalable)
 sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...
 
virtual bool isScalable () const =0
 returns if model is scalable More...
 
virtual bool isScalable () const
 returns if model is scalable More...
 
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...
 
double getScale () const
 return scale More...
 
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale. More...
 
void setScale (double scale)
 Multiplies the current generator by the given scale. More...
 
virtual void normalize ()=0
 Normalize the generator. More...
 
void normalize ()
 normalize the generator More...
 
virtual void setDiagonal ()=0
 set the diagonal of the generator such that sum on each line equals 0. More...
 
void setDiagonal ()
 set the diagonal of the generator such that sum on each line equals 0. More...
 
virtual const std::vector< int > & getAlphabetStates () const =0
 
const std::vector< int > & getAlphabetStates () const
 
virtual const StateMapgetStateMap () const =0
 
const StateMapgetStateMap () const
 
virtual std::vector< size_t > getModelStates (int code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual std::vector< size_t > getModelStates (const std::string &code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
std::vector< size_t > getModelStates (int code) const
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
std::vector< size_t > getModelStates (const std::string &code) const
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual int getAlphabetStateAsInt (size_t index) const =0
 
int getAlphabetStateAsInt (size_t index) const
 
virtual std::string getAlphabetStateAsChar (size_t index) const =0
 
std::string getAlphabetStateAsChar (size_t index) const
 
virtual double freq (size_t i) const =0
 
virtual double freq (size_t i) const
 
virtual double Pij_t (size_t i, size_t j, double t) const =0
 
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 =0
 
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 =0
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const
 
virtual const VdoublegetFrequencies () const =0
 
const VdoublegetFrequencies () const
 
virtual bool computeFrequencies () const =0
 
virtual void computeFrequencies (bool yn)=0
 
bool computeFrequencies () const
 
void computeFrequencies (bool yn)
 
virtual const Matrix< double > & getPij_t (double t) const =0
 
virtual const Matrix< double > & getPij_t (double t) const
 
virtual const Matrix< double > & getdPij_dt (double t) const =0
 
virtual const Matrix< double > & getdPij_dt (double t) const
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const
 
virtual const AlphabetgetAlphabet () const =0
 
const AlphabetgetAlphabet () const
 
virtual size_t getNumberOfStates () const =0
 Get the number of states. More...
 
virtual size_t getNumberOfStates () const
 Get the number of states. More...
 
virtual double getInitValue (size_t i, int state) const =0
 
double getInitValue (size_t i, int state) const
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual double getRate () const
 The rate of the substitution process. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
void addRateParameter ()
 add a "rate" parameter to the model, that handles the overall rate of the process. More...
 
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
const SubstitutionModelgetNModel (size_t i) const
 returns the ith model, or Null if i is not a valid number. More...
 
size_t getNumberOfModels () const
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 

Protected Member Functions

void completeMatrices ()
 Method inherited from AbstractWordSubstitutionModel. More...
 
virtual VdoublegetFrequencies_ ()=0
 
VdoublegetFrequencies_ ()
 
virtual void fillBasicGenerator ()
 First fill of the generator, from the position model. More...
 
const std::shared_ptr< Parameter > & getSharedParameter (size_t i) const
 
std::shared_ptr< Parameter > & getSharedParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
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

std::vector< SubstitutionModel * > VSubMod_
 
std::vector< std::string > VnestedPrefix_
 
std::vector< double > Vrate_
 
const Alphabetalphabet_
 The alphabet relevant to this model. More...
 
std::shared_ptr< const StateMapstateMap_
 The map of model states with alphabet states. More...
 
size_t size_
 The size of the generator, i.e. the number of states. More...
 
bool isScalable_
 If the model is scalable (ie generator can be normalized automatically). 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...
 
RowMatrix< double > generator_
 The generator matrix $Q$ of the model. More...
 
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies. More...
 
bool computeFreq_
 if the Frequencies must be computed from the generator 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...
 

Detailed Description

Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models.

Author
Laurent Gu├ęguen

This class should be used with models which equilibrium distribution is fixed, ans does not depend on the parameters. Otherwise there may be problems of identifiability of the parameters.

See description in AbstractCodonDistanceSubstitutionModel and AbstractCodonFrequenciesSubstitutionModel class.

Only substitutions with one letter changed are accepted.

The additional parameters to CodonFrequenciesSubstitutionModel are the rates of nonsynonymous over synonymous substitutions.

If a distance $d$ between amino-acids is defined, the non-synonymous rate is multiplied with, if the coded amino-acids are $x$ and $y$, $\beta*\exp(-\alpha.d(x,y))$ with non-negative parameter "alpha" and positive parameter "beta".

If such a distance is not defined, the non-synonymous substitution rate is multiplied with $\beta$ with positive parameter "beta" (ie $d=0$).

If such a distance is not defined, the ratio between non-synonymous and synonymous substitutions rates is $\beta$ with positive parameter "beta".

If paramSynRate is true, the synonymous substitution rate is multiplied with $\gamma$ (with optional positive parameter "gamma"), else it is multiplied with 1.

Definition at line 87 of file CodonDistanceFrequenciesSubstitutionModel.h.

Constructor & Destructor Documentation

CodonDistanceFrequenciesSubstitutionModel::CodonDistanceFrequenciesSubstitutionModel ( const GeneticCode gCode,
NucleotideSubstitutionModel pmod,
FrequenciesSet pfreq,
const AlphabetIndex2 pdist = 0,
bool  paramSynRate = false 
)

Build a new CodonDistanceFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones.

Parameters
gCodepointer to a GeneticCode
pmodpointer to the NucleotideSubstitutionModel to use in the three positions. It is owned by the instance.
pfreqpointer to the FrequenciesSet* equilibrium frequencies
pdistoptional pointer to the AlphabetIndex2 amino-acids distance object.
paramSynRateis true iff synonymous rate is parametrised (default=false).

Definition at line 47 of file CodonDistanceFrequenciesSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::computeFrequencies(), and bpp::AbstractCodonSubstitutionModel::updateMatrices().

Referenced by clone().

CodonDistanceFrequenciesSubstitutionModel::CodonDistanceFrequenciesSubstitutionModel ( const GeneticCode gCode,
NucleotideSubstitutionModel pmod1,
NucleotideSubstitutionModel pmod2,
NucleotideSubstitutionModel pmod3,
FrequenciesSet pfreq,
const AlphabetIndex2 pdist = 0,
bool  paramSynRate = false 
)

Build a new CodonDistanceFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones.

Parameters
gCodepointer to a GeneticCode
pmod1,pmod2,pmod3are pointers to the NucleotideSubstitutionModel to use in the three positions. All the models must be different objects to avoid redundant parameters. They are owned by the instance.
pfreqpointer to the FrequenciesSet* equilibrium frequencies
pdistoptional pointer to the AlphabetIndex2 amino-acids distance object.
paramSynRateis true iff synonymous rate is parametrised (default=false).

Definition at line 63 of file CodonDistanceFrequenciesSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::computeFrequencies(), and bpp::AbstractCodonSubstitutionModel::updateMatrices().

virtual bpp::CodonDistanceFrequenciesSubstitutionModel::~CodonDistanceFrequenciesSubstitutionModel ( )
inlinevirtual

Definition at line 139 of file CodonDistanceFrequenciesSubstitutionModel.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited
void AbstractCodonSubstitutionModel::completeMatrices ( )
protectedvirtualinherited
virtual void bpp::TransitionModel::computeFrequencies ( bool  yn)
pure virtualinherited
void bpp::AbstractSubstitutionModel::computeFrequencies ( bool  yn)
inlinevirtualinherited
Returns
Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModel.

Definition at line 269 of file AbstractSubstitutionModel.h.

virtual double bpp::TransitionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
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::TransitionModel.

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

Definition at line 299 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getInitValue(), bpp::AbstractSubstitutionModel::setFreq(), and bpp::AbstractSubstitutionModel::setFreqFromData().

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

virtual double bpp::TransitionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
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::TransitionModel.

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

Definition at line 298 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

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

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 307 of file AbstractSubstitutionModel.h.

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( )
pure virtualinherited
virtual double bpp::AbstractSubstitutionModel::freq ( size_t  i) const
inlinevirtualinherited
Returns
Equilibrium frequency associated to character i.
See also
getFrequencies(), getStates()

Implements bpp::TransitionModel.

Definition at line 293 of file AbstractSubstitutionModel.h.

virtual const Alphabet* bpp::TransitionModel::getAlphabet ( ) const
pure virtualinherited
Returns
Get the alphabet associated to this model.

Implemented in bpp::RE08Protein, bpp::AbstractSubstitutionModel, bpp::RE08Nucleotide, bpp::MarkovModulatedSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::AbstractReversibleProteinSubstitutionModel, bpp::AbstractNucleotideSubstitutionModel, bpp::AbstractProteinSubstitutionModel, bpp::AbstractWrappedModel, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::YpR::check_model(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::SubstitutionMappingTools::computeCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::computeCountsPerSitePerType(), bpp::SubstitutionMappingTools::computeCountsPerTypePerBranch(), bpp::SubstitutionModelSetTools::createHomogeneousModelSet(), bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractWrappedModel::getAlphabet(), bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getInitValue(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::PhylogeneticsApplicationTools::getSubstitutionRegister(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::SENCA::setFreq(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::DecompositionReward::setSubstitutionModel(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::TwoTreeLikelihood::TwoTreeLikelihood(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), bpp::AAExteriorSubstitutionRegister::updateMatrix_(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

virtual std::string bpp::TransitionModel::getAlphabetStateAsChar ( size_t  index) const
pure virtualinherited
std::string bpp::AbstractSubstitutionModel::getAlphabetStateAsChar ( size_t  index) const
inlinevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 257 of file AbstractSubstitutionModel.h.

int bpp::AbstractSubstitutionModel::getAlphabetStateAsInt ( size_t  index) const
inlinevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 259 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices(), and bpp::AbstractSubstitutionModel::getInitValue().

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetStates ( ) const
inlinevirtualinherited
Returns
The alphabet states of each state of the model, as a vector of int codes.
See also
Alphabet

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 255 of file AbstractSubstitutionModel.h.

double CodonDistanceFrequenciesSubstitutionModel::getCodonsMulRate ( size_t  ,
size_t   
) const
virtual

Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides.

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 96 of file CodonDistanceFrequenciesSubstitutionModel.cpp.

References bpp::AbstractCodonFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonSubstitutionModel::getCodonsMulRate().

Referenced by clone().

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 291 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

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 281 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 273 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::AbstractTotallyWrappedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::InMixedSubstitutionModel.

Referenced by bpp::Coala::Coala(), bpp::InMixedSubstitutionModel::getExchangeabilityMatrix(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

Implements bpp::TransitionModel.

Definition at line 265 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

Referenced by bpp::SENCA::setFreq().

const FrequenciesSet* bpp::CodonDistanceFrequenciesSubstitutionModel::getFrequenciesSet ( ) const
inlinevirtual
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 271 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator().

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::AbstractTotallyWrappedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::InMixedSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getGenerator(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::Pij_t(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::OneChangeRegisterTransitionModel::updateMatrices(), bpp::RegisterRatesSubstitutionModel::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const GeneticCode* bpp::AbstractCodonSubstitutionModel::getGeneticCode ( ) const
inlinevirtualinherited
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 283 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const
pure virtualinherited
virtual double bpp::TransitionModel::getInitValue ( size_t  i,
int  state 
) const
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, bpp::OneChangeRegisterTransitionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::OneChangeTransitionModel::getInitValue(), bpp::AbstractTotallyWrappedModel::getInitValue(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), and bpp::TwoTreeLikelihood::initTreeLikelihoods().

double AbstractSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const
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::TransitionModel.

Reimplemented in bpp::RE08.

Definition at line 541 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::alphabet_, bpp::Alphabet::getAlias(), bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(), bpp::Alphabet::intToChar(), and bpp::AbstractSubstitutionModel::size_.

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

virtual std::vector<size_t> bpp::TransitionModel::getModelStates ( int  code) const
pure virtualinherited
virtual std::vector<size_t> bpp::TransitionModel::getModelStates ( const std::string &  code) const
pure virtualinherited

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RegisterRatesSubstitutionModel, and bpp::AbstractWrappedModel.

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

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 261 of file AbstractSubstitutionModel.h.

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( const std::string &  code) const
inlinevirtualinherited

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 263 of file AbstractSubstitutionModel.h.

std::string CodonDistanceFrequenciesSubstitutionModel::getName ( ) const
virtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::TransitionModel.

Definition at line 81 of file CodonDistanceFrequenciesSubstitutionModel.cpp.

Referenced by clone().

const SubstitutionModel* bpp::AbstractWordSubstitutionModel::getNModel ( size_t  i) const
inlineinherited

returns the ith model, or Null if i is not a valid number.

Definition at line 234 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::BppOSubstitutionModelFormat::write().

size_t bpp::AbstractWordSubstitutionModel::getNumberOfModels ( ) const
inlineinherited
virtual size_t bpp::TransitionModel::getNumberOfStates ( ) const
pure virtualinherited

Get the number of states.

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

See also
getAlphabetChars for the list of supported states.
Returns
The number of different states in the model.

Implemented in bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::AbstractWordSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::AbstractWrappedModel, bpp::AnonymousSubstitutionModel, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::TwoTreeLikelihood::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::RegisterRatesSubstitutionModel::getNumberOfStates(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionMethods::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::TwoTreeLikelihood::TwoTreeLikelihood(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

The rate of the substitution process.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 643 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

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

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 289 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const
pure virtualinherited
double AbstractSubstitutionModel::getScale ( ) const
virtualinherited
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, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::InMixedSubstitutionModel.

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

const StateMap& bpp::AbstractSubstitutionModel::getStateMap ( ) const
inlinevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 253 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

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

Implements bpp::SubstitutionModel.

Definition at line 285 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const
inlinevirtualinherited
Returns
True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 287 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const
pure virtualinherited
virtual bool bpp::SubstitutionModel::isScalable ( ) 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::TransitionModel.

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

Definition at line 297 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_t().

Referenced by bpp::JCprot::Pij_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 295 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

virtual void bpp::SubstitutionModel::setDiagonal ( )
pure virtualinherited
void CodonDistanceFrequenciesSubstitutionModel::setFreq ( std::map< int, double > &  freqs)
virtual

Estimation of the parameters of the models so that the equilibrium frequencies match the given ones.

Parameters
freqsmap of the frequencies

When there is one submodel for all the positions, the submodel parameters are fit on the means of the frequencies on each position. Otherwise, each model is fit on the frequencies on its corresponding position in the word.

Reimplemented from bpp::AbstractWordSubstitutionModel.

Definition at line 111 of file CodonDistanceFrequenciesSubstitutionModel.cpp.

References bpp::FrequenciesSet::getFrequencies(), bpp::AbstractSubstitutionModel::getFrequencies_(), bpp::AbstractCodonFrequenciesSubstitutionModel::getFrequenciesSet(), and bpp::AbstractCodonFrequenciesSubstitutionModel::setFreq().

Referenced by clone().

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::TransitionModel.

Reimplemented in bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::JTT92, bpp::DSO78, bpp::LG08, and bpp::Coala.

Definition at line 559 of file AbstractSubstitutionModel.cpp.

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

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

void CodonDistanceFrequenciesSubstitutionModel::setNamespace ( const std::string &  st)
virtual
void AbstractSubstitutionModel::setRate ( double  rate)
virtualinherited
void bpp::AbstractSubstitutionModel::setScalable ( bool  scalable)
inlinevirtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implements bpp::SubstitutionModel.

Definition at line 376 of file AbstractSubstitutionModel.h.

virtual void bpp::SubstitutionModel::setScalable ( bool  scalable)
pure virtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::InMixedSubstitutionModel.

Referenced by bpp::InMixedSubstitutionModel::setScalable(), and bpp::MarkovModulatedSubstitutionModel::setScalable().

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

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::InMixedSubstitutionModel.

Referenced by bpp::InMixedSubstitutionModel::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 275 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractSubstitutionModel::getPij_t().

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, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::InMixedSubstitutionModel.

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

void AbstractCodonSubstitutionModel::updateMatrices ( )
virtualinherited

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.

!! Here there is no normalization of the generator.

Now check inversion and diagonalization

Reimplemented from bpp::AbstractWordSubstitutionModel.

Definition at line 151 of file AbstractCodonSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractCodonSubstitutionModel::hasParametrizedRates_, bpp::TextTools::toString(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::Vrate_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::CodonAdHocSubstitutionModel::CodonAdHocSubstitutionModel(), CodonDistanceFrequenciesSubstitutionModel(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel(), bpp::CodonDistanceSubstitutionModel::CodonDistanceSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::operator=(), bpp::SENCA::SENCA(), and bpp::SENCA::setFreq().

Member Data Documentation

bool bpp::AbstractSubstitutionModel::computeFreq_
protectedinherited
bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited
Vdouble bpp::AbstractSubstitutionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 121 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::Coala::computeEquilibriumFrequencies(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::AbstractSubstitutionModel::getFrequencies_(), bpp::RN95s::getPij_t(), bpp::RN95::getPij_t(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::L95::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), bpp::MixtureOfASubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::F84::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

bool bpp::AbstractSubstitutionModel::isScalable_
protectedinherited
RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_
mutableprotectedinherited
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 111 of file AbstractSubstitutionModel.h.

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

std::shared_ptr<const StateMap> bpp::AbstractSubstitutionModel::stateMap_
protectedinherited

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