Specialized interface for protein substitution model. More...

#include <Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h>

Inheritance diagram for bpp::ProteinSubstitutionModelInterface:

Collaboration diagram for bpp::ProteinSubstitutionModelInterface:

Public Member Functions
virtual	~ProteinSubstitutionModelInterface ()

virtual ProteinSubstitutionModelInterface *	clone () const override=0

virtual std::shared_ptr< const ProteicAlphabet >	getProteicAlphabet () const =0

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 void	setFreq (std::map< int, double > &frequencies)=0
	Set equilibrium frequencies. More...

virtual std::string	getName () const =0
	Get the name of the model. 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 void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

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

Protected Member Functions
virtual Vdouble &	getFrequencies_ ()=0

virtual ParameterList &	getParameters_ ()=0

Detailed Description

Specialized interface for protein substitution model.

Definition at line 20 of file ProteinSubstitutionModel.h.

Constructor & Destructor Documentation

◆ ~ProteinSubstitutionModelInterface()

virtual bpp::ProteinSubstitutionModelInterface::~ProteinSubstitutionModelInterface ( )

inlinevirtual

Definition at line 24 of file ProteinSubstitutionModel.h.

Member Function Documentation

◆ addRateParameter()

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()

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 bpp::SENCA::setFreq().

◆ clone()

virtual ProteinSubstitutionModelInterface* bpp::ProteinSubstitutionModelInterface::clone ( ) const

overridepure virtual

Implements bpp::SubstitutionModelInterface.

Implemented in bpp::AbstractReversibleProteinSubstitutionModel, bpp::AbstractProteinSubstitutionModel, bpp::ProteinReversibleSubstitutionModelInterface, bpp::RE08Protein, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, and bpp::LG10_EX_EHO::EmbeddedModel.

◆ computeFrequencies() [1/2]

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(), bpp::SENCA::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() [2/2]

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()

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

pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ d2Pij_dt2()

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().

◆ dLik_dt()

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

pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ dPij_dt()

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().

◆ enableEigenDecomposition() [1/2]

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() [2/2]

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()

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().

◆ freq()

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().

◆ frequencySet()

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().

◆ generator()

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()

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(), bpp::SENCA::setFreq(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

◆ getAlphabetStateAsChar()

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().

◆ getAlphabetStateAsInt()

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().

◆ getAlphabetStates()

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().

◆ getColumnRightEigenVectors()

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()

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()

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()

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()

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_()

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_().

◆ getIEigenValues()

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()

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().

◆ getModelStates() [1/2]

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() [2/2]

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().

◆ getName()

virtual std::string bpp::BranchModelInterface::getName ( ) const

pure virtualinherited

Get the name of the model.

Returns: The name of this model.

Referenced by bpp::YpR::checkModel(), bpp::TransitionMatrixFromModel::compute(), bpp::AbstractWrappedModel::getName(), bpp::FromMixtureSubstitutionModel::getName(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::BppOSubstitutionModelFormat::initialize_(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::MixtureOfATransitionModel::model(), bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesWithAliases(), bpp::ModelPath::toString(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

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().

◆ getPij_t()

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().

◆ getProteicAlphabet()

virtual std::shared_ptr<const ProteicAlphabet> bpp::ProteinSubstitutionModelInterface::getProteicAlphabet ( ) const

pure virtual

Implemented in bpp::RE08Protein, bpp::AbstractReversibleProteinSubstitutionModel, and bpp::AbstractProteinSubstitutionModel.

◆ getRate()

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().

◆ getRowLeftEigenVectors()

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()

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()

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().

◆ isDiagonalizable()

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()

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()

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()

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.

◆ normalize()

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()

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().

◆ Qij()

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()

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()

virtual void bpp::TransitionModelInterface::setFreq ( std::map< int, double > & frequencies )

pure virtualinherited

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::setFreq(), bpp::InMixedSubstitutionModel::setFreq(), bpp::RE08Codon::setFreq(), bpp::MultinomialFromTransitionModel::setFreq(), bpp::TransitionFromTransitionModel::setFreq(), bpp::OneChangeRegisterTransitionModel::setFreq(), bpp::OneChangeTransitionModel::setFreq(), and bpp::AbstractTotallyWrappedTransitionModel::setFreqFromData().

◆ setFreqFromData()

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