Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...

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

Inheritance diagram for bpp::SENCA:

Collaboration diagram for bpp::SENCA:

Public Member Functions
	SENCA (std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod, std::unique_ptr< FrequencySetInterface > pfit, std::shared_ptr< const AlphabetIndex2 > pdist=nullptr)

	SENCA (std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod1, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod2, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod3, std::unique_ptr< FrequencySetInterface > pfit, std::shared_ptr< const AlphabetIndex2 > pdist=nullptr)

virtual	~SENCA ()

SENCA *	clone () const override

void	fireParameterChanged (const ParameterList &parameterlist) override

std::string	getName () const override
	Get the name of the model. More...

double	getCodonsMulRate (size_t i, size_t j) const override
	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 &) override

void	setFreq (std::map< int, double > &frequencies) override
	set the fitness of the model from given frequencies, such that the equilibrium frequencies of the model matches at best the given ones. More...

const CodonFrequencySetInterface &	codonFrequencySet () const override

bool	hasCodonFrequencySet () const override

virtual double	Qij (size_t i, size_t j) const =0
	A method for computing all necessary matrices. More...

virtual const Matrix< double > &	generator () const =0

virtual const Matrix< double > &	exchangeabilityMatrix () const =0

virtual double	Sij (size_t i, size_t j) 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 Vdouble &	getEigenValues () const =0

virtual const Vdouble &	getIEigenValues () 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 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...

virtual bool	isScalable () const =0
	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...

virtual void	setScale (double scale)=0
	Multiplies the current generator by the given scale. More...

virtual void	normalize ()=0
	Normalize the generator. More...

virtual void	setDiagonal ()=0
	set the diagonal of the generator such that sum on each line equals 0. More...

virtual double	freq (size_t i) 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 Vdouble &	getFrequencies () const =0

virtual bool	computeFrequencies () const =0

virtual void	computeFrequencies (bool yn)=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 const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const =0

virtual const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const =0

virtual const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0

virtual void	setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0)=0
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

virtual const std::vector< int > &	getAlphabetStates () const =0

virtual const StateMapInterface &	stateMap () const =0

virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0

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...

virtual int	getAlphabetStateAsInt (size_t index) const =0

virtual std::string	getAlphabetStateAsChar (size_t index) const =0

virtual const Alphabet &	alphabet () const =0

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0

virtual const FrequencySetInterface &	frequencySet () const =0

virtual size_t	getNumberOfStates () const =0
	Get the number of states. More...

virtual double	getInitValue (size_t i, int state) const =0

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 size_t	getNumberOfIndependentParameters () const=0

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

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

virtual const ParameterList &	getIndependentParameters () const=0

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

virtual std::map< std::string, std::string >	getAliases () const=0

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

std::shared_ptr< const GeneticCode >	getGeneticCode () const override

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

void	unaliasParameters (const std::string &p1, const std::string &p2)

const ParameterList &	getIndependentParameters () const

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

virtual double	Qij (size_t i, size_t j) const
	A method for computing all necessary matrices. More...

const Matrix< double > &	generator () const

const Matrix< double > &	exchangeabilityMatrix () const

double	Sij (size_t i, size_t j) const

void	enableEigenDecomposition (bool yn)
	Set if eigenValues and Vectors must be computed. More...

bool	enableEigenDecomposition ()
	Tell if eigenValues and Vectors must be computed. More...

const Vdouble &	getEigenValues () const

const Vdouble &	getIEigenValues () const

bool	isDiagonalizable () const

bool	isNonSingular () const

const Matrix< double > &	getRowLeftEigenVectors () const

const Matrix< double > &	getColumnRightEigenVectors () const

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
	returns if model is scalable More...

double	getScale () const
	return scale More...

void	setScale (double scale)
	Multiplies the current generator by the given scale. More...

void	normalize ()
	normalize the generator More...

void	setDiagonal ()
	set the diagonal of the generator such that sum on each line equals 0. More...

virtual double	freq (size_t i) const override

virtual double	Pij_t (size_t i, size_t j, double t) const override

virtual double	dPij_dt (size_t i, size_t j, double t) const override

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const override

const Vdouble &	getFrequencies () const override

bool	computeFrequencies () const

void	computeFrequencies (bool yn)

const Matrix< double > &	getPij_t (double t) const

const Matrix< double > &	getdPij_dt (double t) const

const Matrix< double > &	getd2Pij_dt2 (double t) const

const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const override

const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const override

const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override

void	setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0) override
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

const std::vector< int > &	getAlphabetStates () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

std::vector< size_t >	getModelStates (int code) const override
	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 override
	Get the state in the model corresponding to a particular state in the alphabet. More...

int	getAlphabetStateAsInt (size_t index) const override

std::string	getAlphabetStateAsChar (size_t index) const override

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

const FrequencySetInterface &	frequencySet () const override

size_t	getNumberOfStates () const override
	Get the number of states. More...

double	getInitValue (size_t i, int state) const override

virtual double	getRate () const override
	The rate of the substitution process. More...

virtual void	setRate (double rate) override
	Set the rate of the model (must be positive). More...

void	addRateParameter () override
	add a "rate" parameter to the model, that handles the overall rate of the process. More...

const SubstitutionModelInterface &	nModel (size_t i) const
	returns the ith model, or throw an exception if i is not a valid number. More...

size_t	getNumberOfModels () const

void	setVerboseLevel (short level)

short	verboseLevel () 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 > &	getParameter (const std::string &name) const

const FrequencySetInterface &	fitness () const

Protected Member Functions
virtual Vdouble &	getFrequencies_ ()=0

virtual ParameterList &	getParameters_ ()=0

void	completeMatrices_ () override
	Method inherited from AbstractWordSubstitutionModel. More...

void	updateMatrices_ () override
	Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...

ParameterList &	getParameters_ () override

Vdouble &	getFrequencies_ () override

virtual void	fillBasicGenerator_ ()
	First fill of the generator, from the position model. More...

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (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_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

Protected Attributes
std::vector< std::shared_ptr< SubstitutionModelInterface > >	VSubMod_

std::vector< std::string >	VnestedPrefix_

std::vector< double >	Vrate_

bool	isScalable_
	If the model is scalable (ie generator can be normalized automatically). More...

RowMatrix< double >	generator_
	The generator matrix of the model. More...

bool	computeFreq_
	if the Frequencies must be computed from the generator More...

RowMatrix< double >	exchangeability_
	The exchangeability matrix of the model, defined as $S_{ij}=\frac{Q_{ij}}{\pi_j}$ . When the model is reversible, this matrix is symmetric. More...

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 matrix made of right eigen vectors (by column). More...

bool	isNonSingular_
	boolean value for non-singularity of rightEigenVectors_ More...

RowMatrix< double >	leftEigenVectors_
	The 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...

std::shared_ptr< const Alphabet >	alphabet_
	The alphabet relevant to this model. More...

std::shared_ptr< const StateMapInterface >	stateMap_
	The map of model states with alphabet states. More...

size_t	size_
	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...

Vdouble	freq_
	The vector $\pi_e$ of equilibrium frequencies. More...

RowMatrix< double >	pijt_
	These ones are for bookkeeping: More...

RowMatrix< double >	dpijt_

RowMatrix< double >	d2pijt_

short	verboseLevel_

Private Attributes
bool	hasParametrizedRates_
	boolean for the parametrization of the position relative rates. Default : false. More...

std::shared_ptr< const GeneticCode >	gCode_

bool	newAlphabet_
	boolean flag to check if a specific WordAlphabet has been built More...

Eigen::VectorXd	lik_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

std::shared_ptr< const AlphabetIndex2 >	pdistance_

std::shared_ptr< const GeneticCode >	pgencode_

double	alpha_

double	beta_

double	gamma_

std::unique_ptr< FrequencySetInterface >	pfitset_

std::string	fitName_

Detailed Description

Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models.

Author: Fanny Pouyet, Laurent Guéguen

See description in AbstractCodonDistanceSubstitutionModel class, AbstractCodonFitnessSubstitutionModel class.

Only substitutions with one letter changed are accepted.

The ratio between non-synonymous and synonymous substitutions rates is $\beta$ with positive parameter "beta".

The fitness of a codon is a value between 0 and 1 defining the relative advantage of a codon, compared to others. If a codon has a fitness $\phi_i$ and another one ( ) has a fitness $\phi_j$ , the substitution rate from codon to codon is multiplied by

$-\frac{ \log(\frac{\phi_i}{\phi_j})}{1-\frac{\phi_i}{\phi_j}}$

The set of fitnesses is implemented through a Codon FrequencySet object. The parameters are named "fit_NameOfTheParameterInTheFrequencySet".

Note: equilibrium frequencies are computed from the generator. To be done : implement analytic computation.

Reference:

Pouyet & al, Genome Biology and Evolution, 2016

Definition at line 47 of file SENCA.h.

Constructor & Destructor Documentation

◆ SENCA() [1/2]

SENCA::SENCA	(	std::shared_ptr< const GeneticCode >	gCode,
		std::unique_ptr< NucleotideSubstitutionModelInterface >	pmod,
		std::unique_ptr< FrequencySetInterface >	pfit,
		std::shared_ptr< const AlphabetIndex2 >	pdist = `nullptr`
	)

Definition at line 10 of file SENCA.cpp.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::AbstractCodonSubstitutionModel::updateMatrices_().

Referenced by clone().

◆ SENCA() [2/2]

SENCA::SENCA	(	std::shared_ptr< const GeneticCode >	gCode,
		std::unique_ptr< NucleotideSubstitutionModelInterface >	pmod1,
		std::unique_ptr< NucleotideSubstitutionModelInterface >	pmod2,
		std::unique_ptr< NucleotideSubstitutionModelInterface >	pmod3,
		std::unique_ptr< FrequencySetInterface >	pfit,
		std::shared_ptr< const AlphabetIndex2 >	pdist = `nullptr`
	)

Definition at line 24 of file SENCA.cpp.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::AbstractCodonSubstitutionModel::updateMatrices_().

◆ ~SENCA()

virtual bpp::SENCA::~SENCA ( )

inlinevirtual

Definition at line 68 of file SENCA.h.

Member Function Documentation

◆ addRateParameter() [1/2]

void AbstractTransitionModel::addRateParameter ( )

overridevirtualinherited

add a "rate" parameter to the model, that handles the overall rate of the process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 63 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::getNamespace(), bpp::Parameter::R_PLUS_STAR, and bpp::AbstractTransitionModel::rate_.

◆ addRateParameter() [2/2]

virtual void bpp::BranchModelInterface::addRateParameter ( )

pure virtualinherited

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::AbstractTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractBiblioTransitionModel.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::addRateParameter(), bpp::MultinomialFromTransitionModel::addRateParameter(), bpp::TransitionFromTransitionModel::addRateParameter(), and bpp::BppOSubstitutionModelFormat::updateParameters_().

◆ alphabet() [1/2]

virtual const Alphabet& bpp::BranchModelInterface::alphabet ( ) const

pure virtualinherited

Returns: A reference to the alphabet associated to this model.

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

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::alphabet(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), and setFreq().

◆ alphabet() [2/2]

const Alphabet& bpp::AbstractTransitionModel::alphabet ( ) const

inlineoverridevirtualinherited

Returns: A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 167 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ clone()

SENCA* bpp::SENCA::clone ( ) const

inlineoverridevirtual

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 70 of file SENCA.h.

References SENCA().

◆ codonFrequencySet()

const CodonFrequencySetInterface& bpp::SENCA::codonFrequencySet ( ) const

inlineoverridevirtual

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 101 of file SENCA.h.

References bpp::AbstractCodonFitnessSubstitutionModel::codonFrequencySet().

◆ completeMatrices_()

void AbstractCodonSubstitutionModel::completeMatrices_ ( )

overrideprotectedvirtualinherited

Method inherited from AbstractWordSubstitutionModel.

This method sets the rates to/from stop codons to zero and performs the multiplication by the specific codon-codon rate.

Implements bpp::AbstractWordSubstitutionModel.

Definition at line 130 of file AbstractCodonSubstitutionModel.cpp.

References bpp::AbstractCodonSubstitutionModel::gCode_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractTransitionModel::getAlphabetStateAsInt(), bpp::CoreCodonSubstitutionModelInterface::getCodonsMulRate(), and bpp::AbstractTransitionModel::getNumberOfStates().

◆ computeFrequencies() [1/4]

bool bpp::AbstractSubstitutionModel::computeFrequencies ( ) const

inlinevirtualinherited

Returns: Says if equilibrium frequencies should be computed

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 404 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

Referenced by bpp::CodonAdHocSubstitutionModel::CodonAdHocSubstitutionModel(), bpp::CodonDistanceFrequenciesSubstitutionModel::CodonDistanceFrequenciesSubstitutionModel(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel(), bpp::CodonDistanceSubstitutionModel::CodonDistanceSubstitutionModel(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::F81::F81(), bpp::gBGC::gBGC(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::KroneckerCodonDistanceFrequenciesSubstitutionModel(), bpp::KroneckerCodonDistanceSubstitutionModel::KroneckerCodonDistanceSubstitutionModel(), bpp::L95::L95(), bpp::POMO::POMO(), bpp::RN95::RN95(), bpp::RN95s::RN95s(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::WordSubstitutionModel::WordSubstitutionModel(), and bpp::YpR::YpR().

◆ computeFrequencies() [2/4]

virtual bool bpp::TransitionModelInterface::computeFrequencies ( ) const

pure virtualinherited

Returns: Says if equilibrium frequencies should be computed

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies(), bpp::InMixedSubstitutionModel::computeFrequencies(), bpp::RELAX::RELAX(), SENCA(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ computeFrequencies() [3/4]

void bpp::AbstractSubstitutionModel::computeFrequencies ( bool yn )

inlinevirtualinherited

Returns: Set if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 406 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

◆ computeFrequencies() [4/4]

virtual void bpp::TransitionModelInterface::computeFrequencies ( bool yn )

pure virtualinherited

Returns: Set if equilibrium frequencies should be computed

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractSubstitutionModel.

◆ d2Lik_dt2() [1/2]

virtual const Eigen::VectorXd& bpp::TransitionModelInterface::d2Lik_dt2	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ d2Lik_dt2() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::d2Lik_dt2	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 64 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::AbstractLkTransitionModel::lik_.

◆ d2Pij_dt2() [1/2]

virtual double bpp::TransitionModelInterface::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::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::d2Pij_dt2(), bpp::InMixedSubstitutionModel::d2Pij_dt2(), and bpp::OneChangeRegisterTransitionModel::d2Pij_dt2().

◆ d2Pij_dt2() [2/2]

virtual double bpp::AbstractTransitionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtualinherited

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::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 199 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getd2Pij_dt2().

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

◆ dLik_dt() [1/2]

virtual const Eigen::VectorXd& bpp::TransitionModelInterface::dLik_dt	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ dLik_dt() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::dLik_dt	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 47 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::AbstractLkTransitionModel::lik_.

◆ dPij_dt() [1/2]

virtual double bpp::TransitionModelInterface::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::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::dPij_dt(), and bpp::InMixedSubstitutionModel::dPij_dt().

◆ dPij_dt() [2/2]

virtual double bpp::AbstractTransitionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtualinherited

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::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 198 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getdPij_dt().

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

◆ enableEigenDecomposition() [1/4]

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )

inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 434 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractDFPSubstitutionModel::AbstractDFPSubstitutionModel(), bpp::AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel(), bpp::KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::WordSubstitutionModel::WordSubstitutionModel().

◆ enableEigenDecomposition() [2/4]

virtual bool bpp::SubstitutionModelInterface::enableEigenDecomposition ( )

pure virtualinherited

Tell if eigenValues and Vectors must be computed.

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

Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel().

◆ enableEigenDecomposition() [3/4]

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

inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 432 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

◆ enableEigenDecomposition() [4/4]

virtual void bpp::SubstitutionModelInterface::enableEigenDecomposition ( bool yn )

pure virtualinherited

Set if eigenValues and Vectors must be computed.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition(), and bpp::InMixedSubstitutionModel::enableEigenDecomposition().

◆ exchangeabilityMatrix() [1/2]

const Matrix<double>& bpp::AbstractSubstitutionModel::exchangeabilityMatrix ( ) 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::SubstitutionModelInterface.

Definition at line 410 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ exchangeabilityMatrix() [2/2]

virtual const Matrix<double>& bpp::SubstitutionModelInterface::exchangeabilityMatrix ( ) 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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::Coala::Coala(), bpp::AbstractTotallyWrappedSubstitutionModel::exchangeabilityMatrix(), and bpp::InMixedSubstitutionModel::exchangeabilityMatrix().

◆ fillBasicGenerator_()

void AbstractWordSubstitutionModel::fillBasicGenerator_ ( )

protectedvirtualinherited

First fill of the generator, from the position model.

Reimplemented in bpp::AbstractKroneckerWordSubstitutionModel.

Definition at line 303 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::generator_, bpp::AbstractTransitionModel::getNumberOfStates(), RowMatrix< double >::getRow(), bpp::AbstractWordSubstitutionModel::Vrate_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::AbstractWordSubstitutionModel::updateMatrices_().

◆ fireParameterChanged()

void SENCA::fireParameterChanged ( const ParameterList & parameterlist )

overridevirtual

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 40 of file SENCA.cpp.

References bpp::AbstractTransitionModel::fireParameterChanged(), bpp::AbstractCodonDistanceSubstitutionModel::fireParameterChanged(), and bpp::AbstractCodonFitnessSubstitutionModel::fireParameterChanged().

◆ fitness()

const FrequencySetInterface& bpp::AbstractCodonFitnessSubstitutionModel::fitness ( ) const

inlineinherited

Definition at line 88 of file AbstractCodonFitnessSubstitutionModel.h.

References bpp::AbstractCodonFitnessSubstitutionModel::pfitset_.

◆ freq() [1/2]

virtual double bpp::TransitionModelInterface::freq ( size_t i ) const

pure virtualinherited

Returns: Equilibrium frequency associated to character i.

See also: getFrequencies(), getStates()

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::freq(), bpp::InMixedSubstitutionModel::freq(), bpp::OneChangeRegisterTransitionModel::freq(), and bpp::OneChangeTransitionModel::freq().

◆ freq() [2/2]

virtual double bpp::AbstractTransitionModel::freq ( size_t i ) const

inlineoverridevirtualinherited

Returns: Equilibrium frequency associated to character i.

See also: getFrequencies(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 195 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

Referenced by bpp::CodonSameAARateSubstitutionModel::compute_().

◆ frequencySet() [1/2]

virtual const FrequencySetInterface& bpp::BranchModelInterface::frequencySet ( ) const

pure virtualinherited

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YN98, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::AbstractWrappedTransitionModel, bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, and bpp::AbstractBiblioMixedTransitionModel.

Referenced by bpp::RE08Codon::codonFrequencySet(), bpp::AbstractWrappedModel::frequencySet(), bpp::AbstractWrappedTransitionModel::frequencySet(), bpp::OneChangeRegisterTransitionModel::frequencySet(), bpp::OneChangeTransitionModel::frequencySet(), and bpp::BppOSubstitutionModelFormat::write().

◆ frequencySet() [2/2]

const FrequencySetInterface& bpp::AbstractTransitionModel::frequencySet ( ) const

inlineoverridevirtualinherited

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 207 of file AbstractSubstitutionModel.h.

◆ generator() [1/2]

const Matrix<double>& bpp::AbstractSubstitutionModel::generator ( ) 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 are measured in units of expected number of changes per site. Additionally, the rate_ attribute 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::SubstitutionModelInterface.

Definition at line 408 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

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

◆ generator() [2/2]

virtual const Matrix<double>& bpp::SubstitutionModelInterface::generator ( ) 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 are measured in units of expected number of changes per site. Additionally, the rate_ attribute 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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::AbstractTotallyWrappedSubstitutionModel::generator(), bpp::InMixedSubstitutionModel::generator(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::Pij_t(), bpp::OneChangeRegisterTransitionModel::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().

◆ getAlphabet() [1/2]

virtual std::shared_ptr<const Alphabet> bpp::BranchModelInterface::getAlphabet ( ) const

pure virtualinherited

Returns: A pointer toward the alphabet associated to this model.

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

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::YpR::checkModel(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), bpp::AbstractWrappedModel::getAlphabet(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), setFreq(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

◆ getAlphabet() [2/2]

std::shared_ptr<const Alphabet> bpp::AbstractTransitionModel::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns: A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 169 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices_(), and bpp::RE08::getInitValue().

◆ getAlphabetStateAsChar() [1/2]

virtual std::string bpp::BranchModelInterface::getAlphabetStateAsChar ( size_t index ) const

pure virtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

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

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().

◆ getAlphabetStateAsChar() [2/2]

std::string bpp::AbstractTransitionModel::getAlphabetStateAsChar ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 179 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getAlphabetStateAsInt() [1/2]

virtual int bpp::BranchModelInterface::getAlphabetStateAsInt ( size_t index ) const

pure virtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

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

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

◆ getAlphabetStateAsInt() [2/2]

int bpp::AbstractTransitionModel::getAlphabetStateAsInt ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 181 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), and bpp::AbstractTransitionModel::getInitValue().

◆ getAlphabetStates() [1/2]

virtual const std::vector<int>& bpp::BranchModelInterface::getAlphabetStates ( ) const

pure virtualinherited

Returns: The alphabet states of each state of the model, as a vector of int codes.

See also: Alphabet

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

Referenced by bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractWrappedModel::getAlphabetStates().

◆ getAlphabetStates() [2/2]

const std::vector<int>& bpp::AbstractTransitionModel::getAlphabetStates ( ) const

inlineoverridevirtualinherited

Returns: The alphabet states of each state of the model, as a vector of int codes.

See also: Alphabet

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 177 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::DFP07::DFP07(), bpp::YNGP_M3::YNGP_M3(), and bpp::YNGP_M8::YNGP_M8().

◆ getCodonsMulRate()

double SENCA::getCodonsMulRate	(	size_t	,
		size_t
	)		const

overridevirtual

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 48 of file SENCA.cpp.

References bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate().

◆ getColumnRightEigenVectors() [1/2]

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::SubstitutionModelInterface.

Definition at line 428 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

◆ getColumnRightEigenVectors() [2/2]

virtual const Matrix<double>& bpp::SubstitutionModelInterface::getColumnRightEigenVectors ( ) const

pure virtualinherited

Returns: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getColumnRightEigenVectors(), and bpp::InMixedSubstitutionModel::getColumnRightEigenVectors().

◆ getd2Pij_dt2() [1/2]

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::AbstractTransitionModel.

Reimplemented in bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 557 of file AbstractSubstitutionModel.cpp.

Referenced by bpp::JCprot::getd2Pij_dt2().

◆ getd2Pij_dt2() [2/2]

virtual const Matrix<double>& bpp::TransitionModelInterface::getd2Pij_dt2 ( double t ) const

pure 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()

Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getd2Pij_dt2(), bpp::InMixedSubstitutionModel::getd2Pij_dt2(), and bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2().

◆ getdPij_dt() [1/2]

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::AbstractTransitionModel.

Reimplemented in bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 486 of file AbstractSubstitutionModel.cpp.

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

◆ getdPij_dt() [2/2]

virtual const Matrix<double>& bpp::TransitionModelInterface::getdPij_dt ( double t ) const

pure 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()

Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::AbstractLkTransitionModel::dLik_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getdPij_dt(), and bpp::OneChangeRegisterTransitionModel::getdPij_dt().

◆ getEigenValues() [1/2]

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::SubstitutionModelInterface.

Definition at line 418 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

◆ getEigenValues() [2/2]

virtual const Vdouble& bpp::SubstitutionModelInterface::getEigenValues ( ) const

pure virtualinherited

Returns: A vector with all real parts of the eigen values of the generator of this model;

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getEigenValues(), and bpp::InMixedSubstitutionModel::getEigenValues().

◆ getFrequencies() [1/2]

virtual const Vdouble& bpp::TransitionModelInterface::getFrequencies ( ) const

pure virtualinherited

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::EquilibriumFrequenciesFromModel::compute(), bpp::AbstractTotallyWrappedTransitionModel::getFrequencies(), bpp::InMixedSubstitutionModel::getFrequencies(), bpp::OneChangeRegisterTransitionModel::getFrequencies(), and bpp::OneChangeTransitionModel::getFrequencies().

◆ getFrequencies() [2/2]

const Vdouble& bpp::AbstractTransitionModel::getFrequencies ( ) const

inlineoverridevirtualinherited

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 187 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

Referenced by setFreq().

◆ getFrequencies_() [1/2]

Vdouble& bpp::AbstractTransitionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::setFreq(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq(), and bpp::DFPDistanceFrequenciesSubstitutionModel::setFreq().

◆ getFrequencies_() [2/2]

virtual Vdouble& bpp::TransitionModelInterface::getFrequencies_ ( )

protectedpure virtualinherited

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractFromSubstitutionModelTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_(), and bpp::InMixedSubstitutionModel::getFrequencies_().

◆ getGeneticCode()

std::shared_ptr<const GeneticCode> bpp::AbstractCodonSubstitutionModel::getGeneticCode ( ) const

inlineoverridevirtualinherited

Implements bpp::CodonSubstitutionModelInterface.

Definition at line 125 of file AbstractCodonSubstitutionModel.h.

References bpp::AbstractCodonSubstitutionModel::gCode_.

◆ getIEigenValues() [1/2]

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::SubstitutionModelInterface.

Definition at line 420 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

◆ getIEigenValues() [2/2]

virtual const Vdouble& bpp::SubstitutionModelInterface::getIEigenValues ( ) const

pure virtualinherited

Returns: A vector with all imaginary parts of the eigen values of the generator of this model;

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getIEigenValues(), and bpp::InMixedSubstitutionModel::getIEigenValues().

◆ getInitValue() [1/2]

virtual double bpp::BranchModelInterface::getInitValue	(	size_t	i,
		int	state
	)		const

pure virtualinherited

This method is used to initialize likelihoods in recursions. 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

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See also: getStates();

Implemented in bpp::TransitionFromTransitionModel, bpp::RE08, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getInitValue(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::MultinomialFromTransitionModel::getInitValue(), bpp::OneChangeRegisterTransitionModel::getInitValue(), bpp::OneChangeTransitionModel::getInitValue(), and bpp::TransitionFromTransitionModel::getInitValue().

◆ getInitValue() [2/2]

double AbstractTransitionModel::getInitValue	(	size_t	i,
		int	state
	)		const

overridevirtualinherited

This method is used to initialize likelihoods in recursions. 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

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See also: getStates();

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RE08.

Definition at line 70 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::alphabet_, bpp::AbstractTransitionModel::getAlphabetStateAsInt(), and bpp::AbstractTransitionModel::size_.

◆ getModelStates() [1/4]

virtual std::vector<size_t> bpp::BranchModelInterface::getModelStates ( const std::string & code ) const

pure virtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

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

◆ getModelStates() [2/4]

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

inlineoverridevirtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 185 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getModelStates() [3/4]

virtual std::vector<size_t> bpp::BranchModelInterface::getModelStates ( int code ) const

pure virtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

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

Referenced by bpp::SubstitutionModelSet::getModelStates(), and bpp::AbstractWrappedModel::getModelStates().

◆ getModelStates() [4/4]

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

inlineoverridevirtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 183 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getName()

std::string bpp::SENCA::getName ( ) const

inlineoverridevirtual

Get the name of the model.

Returns: The name of this model.

Implements bpp::BranchModelInterface.

Definition at line 78 of file SENCA.h.

◆ getNumberOfModels()

size_t bpp::AbstractWordSubstitutionModel::getNumberOfModels ( ) const

inlineinherited

Definition at line 196 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

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

◆ getNumberOfStates() [1/2]

virtual size_t bpp::BranchModelInterface::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::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::MarkovModulatedSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ getNumberOfStates() [2/2]

size_t bpp::AbstractTransitionModel::getNumberOfStates ( ) const

inlineoverridevirtualinherited

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.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.

Definition at line 175 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedTransitionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractMixedTransitionModel::getdPij_dt(), bpp::RE08Nucleotide::getNumberOfStates(), bpp::RE08Protein::getNumberOfStates(), bpp::RE08Codon::getNumberOfStates(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractMixedTransitionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::MixtureOfATransitionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ getPij_t() [1/2]

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::AbstractTransitionModel.

Reimplemented in bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 395 of file AbstractSubstitutionModel.cpp.

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

◆ getPij_t() [2/2]

virtual const Matrix<double>& bpp::TransitionModelInterface::getPij_t ( double t ) const

pure virtualinherited

Returns: All probabilities of change from state i to state j during time t.

See also: Pij_t()

Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::AbstractTotallyWrappedTransitionModel::getPij_t(), bpp::InMixedSubstitutionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::getPij_t(), and bpp::AbstractLkTransitionModel::Lik_t().

◆ getRate() [1/2]

virtual double bpp::BranchModelInterface::getRate ( ) const

pure virtualinherited

Get the rate.

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::InMixedSubstitutionModel::getRate(), bpp::MultinomialFromTransitionModel::getRate(), bpp::OneChangeRegisterTransitionModel::getRate(), bpp::OneChangeTransitionModel::getRate(), bpp::RegisterRatesSubstitutionModel::getRate(), and bpp::TransitionFromTransitionModel::getRate().

◆ getRate() [2/2]

double AbstractTransitionModel::getRate ( ) const

overridevirtualinherited

The rate of the substitution process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 45 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::rate_.

◆ getRowLeftEigenVectors() [1/2]

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::SubstitutionModelInterface.

Definition at line 426 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

◆ getRowLeftEigenVectors() [2/2]

virtual const Matrix<double>& bpp::SubstitutionModelInterface::getRowLeftEigenVectors ( ) const

pure virtualinherited

Returns: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getRowLeftEigenVectors(), and bpp::InMixedSubstitutionModel::getRowLeftEigenVectors().

◆ getScale() [1/2]

double AbstractSubstitutionModel::getScale ( ) const

virtualinherited

return scale

Implements bpp::SubstitutionModelInterface.

Definition at line 632 of file AbstractSubstitutionModel.cpp.

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

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

◆ getScale() [2/2]

virtual double bpp::SubstitutionModelInterface::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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getScale(), and bpp::InMixedSubstitutionModel::getScale().

◆ getStateMap() [1/2]

virtual std::shared_ptr<const StateMapInterface> bpp::BranchModelInterface::getStateMap ( ) const

pure virtualinherited

Returns: A shared_ptr to the mapping of model states with alphabet states.

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

Referenced by bpp::SubstitutionModelSet::getStateMap(), bpp::SubstitutionProcessCollectionMember::getStateMap(), and bpp::AbstractWrappedModel::getStateMap().

◆ getStateMap() [2/2]

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::getStateMap ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr to the mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 173 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), and bpp::EquiprobableSubstitutionModel::EquiprobableSubstitutionModel().

◆ hasCodonFrequencySet()

bool bpp::SENCA::hasCodonFrequencySet ( ) const

inlineoverridevirtual

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 106 of file SENCA.h.

References bpp::AbstractCodonFitnessSubstitutionModel::hasCodonFrequencySet().

◆ isDiagonalizable() [1/2]

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const

inlinevirtualinherited

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModelInterface.

Definition at line 422 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

◆ isDiagonalizable() [2/2]

virtual bool bpp::SubstitutionModelInterface::isDiagonalizable ( ) const

pure virtualinherited

Returns: True if the model is diagonalizable in R.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isDiagonalizable(), and bpp::InMixedSubstitutionModel::isDiagonalizable().

◆ isNonSingular() [1/2]

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const

inlinevirtualinherited

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModelInterface.

Definition at line 424 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

◆ isNonSingular() [2/2]

virtual bool bpp::SubstitutionModelInterface::isNonSingular ( ) const

pure virtualinherited

Returns: True is the model is non-singular.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isNonSingular(), and bpp::InMixedSubstitutionModel::isNonSingular().

◆ isScalable() [1/2]

virtual bool bpp::AbstractSubstitutionModel::isScalable ( ) const

inlinevirtualinherited

returns if model is scalable

Implements bpp::SubstitutionModelInterface.

Definition at line 469 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

Referenced by bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isScalable() [2/2]

virtual bool bpp::SubstitutionModelInterface::isScalable ( ) const

pure virtualinherited

returns if model is scalable

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isScalable(), and bpp::InMixedSubstitutionModel::isScalable().

◆ Lik_t() [1/2]

virtual const Eigen::VectorXd& bpp::TransitionModelInterface::Lik_t	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters

values	An vector of states on the site.
t	the branch length

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ Lik_t() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::Lik_t	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters

values	An vector of states on the site.
t	the branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::AbstractLkTransitionModel::lik_.

◆ nModel()

const SubstitutionModelInterface& bpp::AbstractWordSubstitutionModel::nModel ( size_t i ) const

inlineinherited

returns the ith model, or throw an exception if i is not a valid number.

Definition at line 188 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

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

◆ normalize() [1/2]

void AbstractSubstitutionModel::normalize ( )

virtualinherited

normalize the generator

Implements bpp::SubstitutionModelInterface.

Definition at line 673 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::isScalable_, and bpp::AbstractSubstitutionModel::setScale().

Referenced by bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), and bpp::gBGC::updateMatrices_().

◆ normalize() [2/2]

virtual void bpp::SubstitutionModelInterface::normalize ( )

pure virtualinherited

Normalize the generator.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::normalize(), and bpp::InMixedSubstitutionModel::normalize().

◆ Pij_t() [1/2]

virtual double bpp::TransitionModelInterface::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The probability of change from state i to state j during time t.

See also: getPij_t(), getStates()

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::Pij_t(), bpp::InMixedSubstitutionModel::Pij_t(), and bpp::OneChangeRegisterTransitionModel::Pij_t().

◆ Pij_t() [2/2]

virtual double bpp::AbstractTransitionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtualinherited

Returns: The probability of change from state i to state j during time t.

See also: getPij_t(), getStates()

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 197 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getPij_t().

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

◆ Qij() [1/2]

virtual double bpp::AbstractSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

A method for computing all necessary matrices.

Returns: The rate in the generator of change from state i to state j.

See also: getStates();

Implements bpp::SubstitutionModelInterface.

Definition at line 430 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

◆ Qij() [2/2]

virtual double bpp::SubstitutionModelInterface::Qij	(	size_t	i,
		size_t	j
	)		const

pure virtualinherited

A method for computing all necessary matrices.

Returns: The rate in the generator of change from state i to state j.

See also: getStates();

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

◆ setDiagonal() [1/2]

void AbstractSubstitutionModel::setDiagonal ( )

virtualinherited

set the diagonal of the generator such that sum on each line equals 0.

Implements bpp::SubstitutionModelInterface.

Definition at line 654 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::generator_, RowMatrix< double >::getRow(), and bpp::AbstractTransitionModel::size_.

Referenced by bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), bpp::AbstractDFPSubstitutionModel::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().

◆ setDiagonal() [2/2]

virtual void bpp::SubstitutionModelInterface::setDiagonal ( )

pure virtualinherited

set the diagonal of the generator such that sum on each line equals 0.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setDiagonal(), and bpp::InMixedSubstitutionModel::setDiagonal().

◆ setFreq()

void SENCA::setFreq ( std::map< int, double > & frequencies )

overridevirtual

set the fitness of the model from given frequencies, such that the equilibrium frequencies of the model matches at best the given ones.

Matching is done in two steps : first, frequencies from nucleotide substitution model are matched at best, then the resulting discrepancy (in terms of ratios between the given one and the one computed by the pahse frequencies) is given for matching to the fitness.

Parameters

frequencies the frequencies to match on.

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 62 of file SENCA.cpp.

References bpp::BranchModelInterface::alphabet(), bpp::BranchModelInterface::getAlphabet(), bpp::AbstractTransitionModel::getFrequencies(), bpp::Alphabet::getStateIndex(), bpp::AbstractTransitionModel::setFreq(), bpp::AbstractCodonFitnessSubstitutionModel::setFreq(), and bpp::AbstractCodonSubstitutionModel::updateMatrices_().

◆ setFreqFromData() [1/2]

void AbstractTransitionModel::setFreqFromData	(	const SequenceDataInterface &	data,
		double	pseudoCount = `0`
	)

overridevirtualinherited

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

Parameters

data	The sequences to use.
pseudoCount	A 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::TransitionModelInterface.

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

Definition at line 88 of file AbstractSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getFrequencies(), and bpp::AbstractTransitionModel::setFreq().

◆ setFreqFromData() [2/2]

virtual void bpp::TransitionModelInterface::setFreqFromData	(	const SequenceDataInterface &	data,
		double	pseudoCount = `0`
	)

pure virtualinherited

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

Parameters

data	The sequences to use.
pseudoCount	A 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::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::K80, bpp::JCnuc, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractBiblioTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, and bpp::AbstractMixedTransitionModel.

Referenced by bpp::TransitionFromTransitionModel::setFreqFromData(), bpp::OneChangeRegisterTransitionModel::setFreqFromData(), bpp::OneChangeTransitionModel::setFreqFromData(), bpp::MultinomialFromTransitionModel::setFreqFromData(), and bpp::InMixedSubstitutionModel::setFreqFromData().

◆ setNamespace()

void SENCA::setNamespace ( const std::string & st )

overridevirtual

Reimplemented from bpp::AbstractCodonFitnessSubstitutionModel.

Definition at line 54 of file SENCA.cpp.

References bpp::AbstractParameterAliasable::setNamespace(), bpp::AbstractCodonFitnessSubstitutionModel::setNamespace(), and bpp::AbstractCodonSubstitutionModel::setNamespace().

◆ setRate() [1/2]

void AbstractTransitionModel::setRate ( double rate )

overridevirtualinherited

Set the rate of the model (must be positive).

Parameters

rate	must be positive.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, and bpp::AbstractMixedTransitionModel.

Definition at line 52 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::hasParameter(), bpp::AbstractTransitionModel::rate_, bpp::AbstractParameterAliasable::setParameterValue(), and bpp::TextTools::toString().

Referenced by bpp::AbstractMixedTransitionModel::setRate().

◆ setRate() [2/2]

virtual void bpp::BranchModelInterface::setRate ( double rate )

pure virtualinherited

Set the rate of the model (must be positive).

Parameters

rate	must be positive.

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractMixedTransitionModel.

Referenced by bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::AbstractTotallyWrappedTransitionModel::setRate(), bpp::InMixedSubstitutionModel::setRate(), bpp::MultinomialFromTransitionModel::setRate(), bpp::OneChangeRegisterTransitionModel::setRate(), bpp::OneChangeTransitionModel::setRate(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::TransitionFromTransitionModel::setRate().

◆ setScalable() [1/2]

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::SubstitutionModelInterface.

Definition at line 461 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

◆ setScalable() [2/2]

virtual void bpp::SubstitutionModelInterface::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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

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

◆ setScale() [1/2]

void AbstractSubstitutionModel::setScale ( double scale )

virtualinherited

Multiplies the current generator by the given scale.

Parameters

scale the scale by which the generator is multiplied.

Implements bpp::SubstitutionModelInterface.

Definition at line 641 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isScalable_, and bpp::MatrixTools::scale().

Referenced by bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::L95::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ setScale() [2/2]

virtual void bpp::SubstitutionModelInterface::setScale ( double scale )

pure virtualinherited

Multiplies the current generator by the given scale.

Parameters

scale the scale by which the generator is multiplied.

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

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScale(), and bpp::InMixedSubstitutionModel::setScale().

◆ setVerboseLevel()

void bpp::AbstractTransitionModel::setVerboseLevel ( short level )

inlineinherited

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

◆ Sij() [1/2]

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::SubstitutionModelInterface.

Definition at line 416 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ Sij() [2/2]

virtual double bpp::SubstitutionModelInterface::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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::Sij(), and bpp::InMixedSubstitutionModel::Sij().

◆ stateMap() [1/2]

virtual const StateMapInterface& bpp::BranchModelInterface::stateMap ( ) const

pure virtualinherited

Returns: The mapping of model states with alphabet states.

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

Referenced by bpp::SubstitutionModelSet::stateMap(), bpp::SubstitutionProcessCollectionMember::stateMap(), and bpp::AbstractWrappedModel::stateMap().

◆ stateMap() [2/2]

const StateMapInterface& bpp::AbstractTransitionModel::stateMap ( ) const

inlineoverridevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 171 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ updateMatrices_()

void AbstractCodonSubstitutionModel::updateMatrices_ ( )

overrideprotectedvirtualinherited

Diagonalize the 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 107 of file AbstractCodonSubstitutionModel.cpp.

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

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

◆ verboseLevel()

short bpp::AbstractTransitionModel::verboseLevel ( ) const

inlineinherited

Definition at line 241 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

Member Data Documentation

◆ alpha_

double bpp::AbstractCodonDistanceSubstitutionModel::alpha_

privateinherited

Definition at line 54 of file AbstractCodonDistanceSubstitutionModel.h.

Referenced by bpp::AbstractCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonDistanceSubstitutionModel::operator=().

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTransitionModel::alphabet_

protectedinherited

The alphabet relevant to this model.

Definition at line 121 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractTransitionModel::alphabet(), bpp::POMO::getAllelicAlphabet(), bpp::AbstractTransitionModel::getAlphabet(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::AbstractNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::AbstractReversibleNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::RE08Nucleotide::getNucleicAlphabet(), bpp::AbstractProteinSubstitutionModel::getProteicAlphabet(), bpp::AbstractReversibleProteinSubstitutionModel::getProteicAlphabet(), bpp::RE08Protein::getProteicAlphabet(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ beta_

double bpp::AbstractCodonDistanceSubstitutionModel::beta_

privateinherited

Definition at line 54 of file AbstractCodonDistanceSubstitutionModel.h.

Referenced by bpp::AbstractCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonDistanceSubstitutionModel::operator=().

◆ computeFreq_

bool bpp::AbstractSubstitutionModel::computeFreq_

protectedinherited

if the Frequencies must be computed from the generator

Definition at line 303 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::computeFrequencies(), and bpp::AbstractSubstitutionModel::operator=().

◆ d2pijt_

RowMatrix<double> bpp::AbstractTransitionModel::d2pijt_

mutableprotectedinherited

Definition at line 150 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), and bpp::AbstractMixedTransitionModel::getd2Pij_dt2().

◆ dpijt_

RowMatrix<double> bpp::AbstractTransitionModel::dpijt_

mutableprotectedinherited

Definition at line 149 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractMixedTransitionModel::getdPij_dt().

◆ eigenDecompose_

bool bpp::AbstractSubstitutionModel::eigenDecompose_

protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 315 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractSubstitutionModel::operator=().

◆ eigenValues_

Vdouble bpp::AbstractSubstitutionModel::eigenValues_

protectedinherited

The vector of eigen values.

Definition at line 320 of file AbstractSubstitutionModel.h.

◆ exchangeability_

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_

protectedinherited

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

Definition at line 310 of file AbstractSubstitutionModel.h.

◆ fitName_

std::string bpp::AbstractCodonFitnessSubstitutionModel::fitName_

privateinherited

Definition at line 42 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractCodonFitnessSubstitutionModel::operator=(), and bpp::AbstractCodonFitnessSubstitutionModel::setNamespace().

◆ freq_

Vdouble bpp::AbstractTransitionModel::freq_

protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 143 of file AbstractSubstitutionModel.h.

◆ gamma_

double bpp::AbstractCodonDistanceSubstitutionModel::gamma_

privateinherited

Definition at line 56 of file AbstractCodonDistanceSubstitutionModel.h.

Referenced by bpp::AbstractCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonDistanceSubstitutionModel::operator=().

◆ gCode_

std::shared_ptr<const GeneticCode> bpp::AbstractCodonSubstitutionModel::gCode_

privateinherited

Definition at line 48 of file AbstractCodonSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), bpp::AbstractCodonSubstitutionModel::getGeneticCode(), and bpp::AbstractCodonSubstitutionModel::operator=().

◆ generator_

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_

protectedinherited

The generator matrix of the model.

Definition at line 298 of file AbstractSubstitutionModel.h.

◆ hasParametrizedRates_

bool bpp::AbstractCodonSubstitutionModel::hasParametrizedRates_

privateinherited

boolean for the parametrization of the position relative rates. Default : false.

Definition at line 47 of file AbstractCodonSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::operator=(), and bpp::AbstractCodonSubstitutionModel::updateMatrices_().

◆ iEigenValues_

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_

protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 325 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getIEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isDiagonalizable_

bool bpp::AbstractSubstitutionModel::isDiagonalizable_

protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 330 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isDiagonalizable(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isNonSingular_

bool bpp::AbstractSubstitutionModel::isNonSingular_

protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 340 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isNonSingular(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isScalable_

bool bpp::AbstractSubstitutionModel::isScalable_

protectedinherited

If the model is scalable (ie generator can be normalized automatically).

Definition at line 293 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::isScalable(), bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractSubstitutionModel::setScalable(), and bpp::AbstractSubstitutionModel::setScale().

◆ leftEigenVectors_

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_

protectedinherited

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

Definition at line 346 of file AbstractSubstitutionModel.h.

◆ lik_

Eigen::VectorXd bpp::AbstractLkTransitionModel::lik_

mutableprivateinherited

Definition at line 23 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractLkTransitionModel::dLik_dt(), and bpp::AbstractLkTransitionModel::Lik_t().

◆ newAlphabet_

bool bpp::AbstractWordSubstitutionModel::newAlphabet_

privateinherited

boolean flag to check if a specific WordAlphabet has been built

Definition at line 109 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ pdistance_

std::shared_ptr<const AlphabetIndex2> bpp::AbstractCodonDistanceSubstitutionModel::pdistance_

privateinherited

Definition at line 50 of file AbstractCodonDistanceSubstitutionModel.h.

Referenced by bpp::AbstractCodonDistanceSubstitutionModel::AbstractCodonDistanceSubstitutionModel(), bpp::AbstractCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonDistanceSubstitutionModel::operator=().

◆ pfitset_

std::unique_ptr<FrequencySetInterface> bpp::AbstractCodonFitnessSubstitutionModel::pfitset_

privateinherited

Definition at line 38 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractCodonFitnessSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonFitnessSubstitutionModel::fitness(), bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonFitnessSubstitutionModel::operator=(), bpp::AbstractCodonFitnessSubstitutionModel::setFreq(), and bpp::AbstractCodonFitnessSubstitutionModel::setNamespace().

◆ pgencode_

std::shared_ptr<const GeneticCode> bpp::AbstractCodonDistanceSubstitutionModel::pgencode_

privateinherited

Definition at line 52 of file AbstractCodonDistanceSubstitutionModel.h.

Referenced by bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonDistanceSubstitutionModel::operator=().

◆ pijt_

RowMatrix<double> bpp::AbstractTransitionModel::pijt_

mutableprotectedinherited

These ones are for bookkeeping:

Definition at line 148 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), and bpp::AbstractMixedTransitionModel::getPij_t().

◆ rate_

double bpp::AbstractTransitionModel::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 138 of file AbstractSubstitutionModel.h.

◆ rightEigenVectors_

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_

protectedinherited

The matrix made of right eigen vectors (by column).

Definition at line 335 of file AbstractSubstitutionModel.h.

◆ size_

size_t bpp::AbstractTransitionModel::size_

protectedinherited

The number of states.

Definition at line 131 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractTransitionModel::AbstractTransitionModel(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::EquiprobableSubstitutionModel::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::EquiprobableSubstitutionModel::dPij_dt(), bpp::RE08::dPij_dt(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::EquiprobableSubstitutionModel::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::EquiprobableSubstitutionModel::getPij_t(), bpp::JCnuc::getPij_t(), bpp::JCprot::getPij_t(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::EquiprobableSubstitutionModel::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::RE08::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::stateMap_

protectedinherited

The map of model states with alphabet states.

Definition at line 126 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractTransitionModel::getAlphabetStateAsChar(), bpp::AbstractTransitionModel::getAlphabetStateAsInt(), bpp::AbstractTransitionModel::getAlphabetStates(), bpp::AbstractTransitionModel::getModelStates(), bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractTransitionModel::getStateMap(), and bpp::AbstractTransitionModel::stateMap().

◆ tmpMat_

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_

mutableprotectedinherited

For computational issues.

Definition at line 357 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ verboseLevel_

short bpp::AbstractTransitionModel::verboseLevel_

protectedinherited

Definition at line 152 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractTransitionModel::setVerboseLevel(), bpp::AbstractSubstitutionModel::updateMatrices_(), and bpp::AbstractTransitionModel::verboseLevel().

◆ VnestedPrefix_

std::vector<std::string> bpp::AbstractWordSubstitutionModel::VnestedPrefix_

protectedinherited

Definition at line 117 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::setNamespace(), and bpp::TripletSubstitutionModel::TripletSubstitutionModel().

◆ vPowGen_

std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_

protectedinherited

vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).

Definition at line 352 of file AbstractSubstitutionModel.h.

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

◆ Vrate_

std::vector<double> bpp::AbstractWordSubstitutionModel::Vrate_

protectedinherited

Definition at line 119 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::TripletSubstitutionModel::TripletSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::updateMatrices_(), and bpp::WordSubstitutionModel::updateMatrices_().

◆ VSubMod_

std::vector<std::shared_ptr<SubstitutionModelInterface> > bpp::AbstractWordSubstitutionModel::VSubMod_

protectedinherited

Vector of shared_ptr, to allow multiple positions to share the same model.

Definition at line 115 of file AbstractWordSubstitutionModel.h.

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

Bpp/Phyl/Model/Codon/SENCA.h
Bpp/Phyl/Model/Codon/SENCA.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SENCA() [1/2]

◆ SENCA() [2/2]

◆ ~SENCA()

Member Function Documentation

◆ addRateParameter() [1/2]

◆ addRateParameter() [2/2]

◆ alphabet() [1/2]

◆ alphabet() [2/2]

◆ clone()

◆ codonFrequencySet()

◆ completeMatrices_()

◆ computeFrequencies() [1/4]

◆ computeFrequencies() [2/4]

◆ computeFrequencies() [3/4]

◆ computeFrequencies() [4/4]

◆ d2Lik_dt2() [1/2]

◆ d2Lik_dt2() [2/2]

◆ d2Pij_dt2() [1/2]

◆ d2Pij_dt2() [2/2]

◆ dLik_dt() [1/2]

◆ dLik_dt() [2/2]

◆ dPij_dt() [1/2]

◆ dPij_dt() [2/2]

◆ enableEigenDecomposition() [1/4]

◆ enableEigenDecomposition() [2/4]

◆ enableEigenDecomposition() [3/4]

◆ enableEigenDecomposition() [4/4]

◆ exchangeabilityMatrix() [1/2]

◆ exchangeabilityMatrix() [2/2]

◆ fillBasicGenerator_()

◆ fireParameterChanged()

◆ fitness()

◆ freq() [1/2]

◆ freq() [2/2]

◆ frequencySet() [1/2]

◆ frequencySet() [2/2]

◆ generator() [1/2]

◆ generator() [2/2]

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getAlphabetStateAsChar() [1/2]

◆ getAlphabetStateAsChar() [2/2]

◆ getAlphabetStateAsInt() [1/2]

◆ getAlphabetStateAsInt() [2/2]

◆ getAlphabetStates() [1/2]

◆ getAlphabetStates() [2/2]

◆ getCodonsMulRate()

◆ getColumnRightEigenVectors() [1/2]

◆ getColumnRightEigenVectors() [2/2]

◆ getd2Pij_dt2() [1/2]

◆ getd2Pij_dt2() [2/2]

◆ getdPij_dt() [1/2]

◆ getdPij_dt() [2/2]

◆ getEigenValues() [1/2]

◆ getEigenValues() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_() [1/2]

◆ getFrequencies_() [2/2]

◆ getGeneticCode()

◆ getIEigenValues() [1/2]

◆ getIEigenValues() [2/2]

◆ getInitValue() [1/2]

◆ getInitValue() [2/2]

◆ getModelStates() [1/4]

◆ getModelStates() [2/4]

◆ getModelStates() [3/4]

◆ getModelStates() [4/4]

◆ getName()

◆ getNumberOfModels()

◆ getNumberOfStates() [1/2]

◆ getNumberOfStates() [2/2]

◆ getPij_t() [1/2]

◆ getPij_t() [2/2]