The Le et al (2008) CAT substitution model for proteins. More...

#include <Bpp/Phyl/Model/Protein/LGL08_CAT.h>

Inheritance diagram for bpp::LGL08_CAT:

Collaboration diagram for bpp::LGL08_CAT:

Classes
class	EmbeddedModel

Public Member Functions
	LGL08_CAT (std::shared_ptr< const ProteicAlphabet > alpha, unsigned int nbCat=10)
	Build a CAT model, with original equilibrium frequencies, probabilities and rates. More...

LGL08_CAT *	clone () const override

	LGL08_CAT (const LGL08_CAT &mod2)

LGL08_CAT &	operator= (const LGL08_CAT &mod2)

uint	getNumberOfCategories () const

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

const TransitionModelInterface &	nModel (size_t i) const override
	Returns the submodel from the mixture. More...

std::shared_ptr< const TransitionModelInterface >	getNModel (size_t i) const override

double	getNProbability (size_t i) const override
	Returns the probability of a specific model from the mixture. More...

const std::vector< double > &	getProbabilities () const override
	Returns the vector of the probabilities of the submodels of the mixture. More...

void	setNProbability (size_t i, double prob) override
	Sets the probabilities of the submodels of the mixture. More...

size_t	getNumberOfModels () const override
	Returns the number of submodels. More...

void	setVRates (const Vdouble &vd) override
	sets the rates of the submodels. More...

void	normalizeVRates () override
	normalizes the rates of the submodels. More...

const std::vector< double > &	getVRates () const override
	Returns the vector of all the rates of the mixture. More...

double	getNRate (size_t i) const override
	Returns the rate of a specific model from the mixture. More...

const TransitionModelInterface &	model (const std::string &name) const override
	Access the submodel with the given name. More...

const BranchModelInterface &	model () const override

Vuint	getSubmodelNumbers (const std::string &desc) const override
	Returns the vector of numbers of the submodels in the mixture that match a description. More...

const TransitionModelInterface &	transitionModel () const override

const MixedTransitionModelInterface &	mixedModel () const

const FrequencySetInterface &	frequencySet () const override

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

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

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

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

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

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

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 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 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

size_t	getNumberOfIndependentParameters () const

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

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

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

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

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

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

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

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

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

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

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

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

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

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

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

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

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

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

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

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

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

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

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

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

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

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

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

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

std::string	getParNameFromPmodel (const std::string &name) const
	get the name of a parameter from its name in a submodel More...

std::string	getPmodelParName (const std::string &name) const
	get the name of a parameter in the submodel from its apparent name More...

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


double	freq (size_t i) const override
	Methods to supersede TransitionModel methods. More...

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

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

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

const Vdouble &	getFrequencies () const override

bool	computeFrequencies () const override

void	computeFrequencies (bool yn) override

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

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

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

double	getInitValue (size_t i, int state) const override

double	getRate () const override
	Get the rate. More...

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


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

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

void	addRateParameter () override
	Methods to supersede TransitionModel methods. More...

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

virtual void	fireParameterChanged (const ParameterList &parameters) override
	Methods to supersede AbstractTransitionModel methods. 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 i) const override

std::string	getAlphabetStateAsChar (size_t i) const override

const Alphabet &	alphabet () const override

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

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

Protected Member Functions
TransitionModelInterface &	transitionModel_ () override

MixedTransitionModelInterface &	mixedModel_ ()

TransitionModelInterface &	nModel_ (size_t i) override

virtual Vdouble &	getFrequencies_ ()=0

Vdouble &	getFrequencies_ () override

virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

virtual void	updateMatrices_ ()

BranchModelInterface &	model_ ()

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::unique_ptr< MixedTransitionModelInterface >	mixedModelPtr_

std::map< std::string, std::string >	mapParNamesFromPmodel_
	Tools to make the link between the Parameters of the object and those of pmixmodel_. More...

ParameterList	lParPmodel_

Private Attributes
ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Eigen::VectorXd	lik_

Detailed Description

The Le et al (2008) CAT substitution model for proteins.

Author: Mathieu Groussin

This model is a mixture of N profiles empirically built with an EM algorithm (see ref). The submodels are called C1, C2, ..., CN. For each model, exchangeabilities are equal (F81 model).

This model includes 2N-2 parameters :

relrate1, ..., relrate(N-1) are the relative rates of model C1, ..., C(N-1);
relproba1, ..., relproba(N-1) are the relative proportions of model C1, ..., C(N-1);

Important: See the relation between these parameters and the rates and probabilities of the models in the description of MixtureOfSubstitutionModels class.

Reference:

Le S.Q., Gascuel O. & Lartillot N. (2008) Bioinformatics 24:2317Ã¢ÂÂ2323.

Definition at line 38 of file LGL08_CAT.h.

Constructor & Destructor Documentation

◆ LGL08_CAT() [1/2]

LGL08_CAT::LGL08_CAT	(	std::shared_ptr< const ProteicAlphabet >	alpha,
		unsigned int	nbCat = `10`
	)

Build a CAT model, with original equilibrium frequencies, probabilities and rates.

Parameters

alpha	A proteic alphabet.
nbCat	number of profiles

Definition at line 16 of file LGL08_CAT.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_, bpp::ParameterList::size(), bpp::TextTools::toString(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

Referenced by clone().

◆ LGL08_CAT() [2/2]

bpp::LGL08_CAT::LGL08_CAT ( const LGL08_CAT & mod2 )

inline

Definition at line 76 of file LGL08_CAT.h.

Member Function Documentation

◆ addRateParameter() [1/2]

void AbstractBiblioTransitionModel::addRateParameter ( )

overridevirtualinherited

Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Definition at line 76 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::addParameters(), bpp::BranchModelInterface::addRateParameter(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractWrappedTransitionModel::model(), bpp::AbstractWrappedTransitionModel::model_(), bpp::Parameter::R_PLUS_STAR, and bpp::ParameterList::reset().

◆ 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 bpp::SENCA::setFreq().

◆ alphabet() [2/2]

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

inlineoverridevirtualinherited

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 53 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::alphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::alphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ clone()

LGL08_CAT* bpp::LGL08_CAT::clone ( ) const

inlineoverridevirtual

Implements bpp::MixedTransitionModelInterface.

Definition at line 74 of file LGL08_CAT.h.

References LGL08_CAT().

◆ computeFrequencies() [1/4]

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(), 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() [2/4]

bool bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies ( ) const

inlineoverridevirtualinherited

Returns: Says if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 162 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::DFP07::DFP07(), and bpp::YN98::YN98().

◆ computeFrequencies() [3/4]

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

inlineoverridevirtualinherited

Returns: Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModelInterface.

Definition at line 171 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::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.

Definition at line 124 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::d2Pij_dt2(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::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.

Definition at line 123 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::dPij_dt(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ fireParameterChanged()

virtual void bpp::AbstractBiblioTransitionModel::fireParameterChanged ( const ParameterList & parameters )

inlineoverridevirtualinherited

Methods to supersede AbstractTransitionModel methods.

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 86 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::AbstractWrappedTransitionModel::model_(), bpp::BranchModelInterface::setRate(), bpp::ParameterList::size(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::freq ( size_t i ) const

inlineoverridevirtualinherited

Methods to supersede TransitionModel methods.

Implements bpp::TransitionModelInterface.

Definition at line 120 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::freq(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractBiblioMixedTransitionModel::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.

Definition at line 138 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

Referenced by bpp::RELAX::RELAX(), 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().

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

◆ getAlphabet() [2/2]

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

inlineoverridevirtualinherited

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 55 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ getAlphabetStateAsChar() [1/2]

std::string bpp::AbstractWrappedModel::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 46 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsChar().

◆ getAlphabetStateAsChar() [2/2]

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().

◆ getAlphabetStateAsInt() [1/2]

int bpp::AbstractWrappedModel::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 44 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsInt().

◆ getAlphabetStateAsInt() [2/2]

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().

◆ 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::AbstractWrappedModel::getAlphabetStates ( ) const

inlineoverridevirtualinherited

@ brief Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 38 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStates().

◆ getd2Pij_dt2() [1/2]

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().

◆ getd2Pij_dt2() [2/2]

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

inlineoverridevirtualinherited

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::TransitionModelInterface.

Definition at line 132 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getdPij_dt() [1/2]

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().

◆ getdPij_dt() [2/2]

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

inlineoverridevirtualinherited

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::TransitionModelInterface.

Definition at line 130 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ 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::AbstractTotallyWrappedTransitionModel::getFrequencies ( ) const

inlineoverridevirtualinherited

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 126 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getFrequencies(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getFrequencies_() [1/2]

Vdouble& bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 181 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getFrequencies_(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ 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_().

◆ 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 bpp::AbstractTotallyWrappedTransitionModel::getInitValue	(	size_t	i,
		int	state
	)		const

inlineoverridevirtualinherited

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.

Definition at line 134 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getInitValue(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ 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::AbstractWrappedModel::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 50 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

◆ 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::AbstractWrappedModel::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 48 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getModelStates().

◆ getName()

std::string bpp::LGL08_CAT::getName ( ) const

inlineoverridevirtual

Get the name of the model.

Returns: The name of this model.

Implements bpp::BranchModelInterface.

Definition at line 96 of file LGL08_CAT.h.

◆ getNModel()

std::shared_ptr<const TransitionModelInterface> bpp::AbstractBiblioMixedTransitionModel::getNModel ( size_t i ) const

inlineoverridevirtualinherited

Implements bpp::MixedTransitionModelInterface.

Definition at line 43 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNModel(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ getNProbability()

double bpp::AbstractBiblioMixedTransitionModel::getNProbability ( size_t i ) const

inlineoverridevirtualinherited

Returns the probability of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 51 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNProbability(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ getNRate()

double bpp::AbstractBiblioMixedTransitionModel::getNRate ( size_t i ) const

inlineoverridevirtualinherited

Returns the rate of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 112 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNRate(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ getNumberOfCategories()

uint bpp::LGL08_CAT::getNumberOfCategories ( ) const

inline

Definition at line 91 of file LGL08_CAT.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

◆ getNumberOfModels()

size_t bpp::AbstractBiblioMixedTransitionModel::getNumberOfModels ( ) const

inlineoverridevirtualinherited

Returns the number of submodels.

Implements bpp::MixedTransitionModelInterface.

Definition at line 78 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNumberOfModels(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ 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::AbstractWrappedModel::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.

Definition at line 57 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getNumberOfStates(), and bpp::WrappedModelInterface::model().

◆ getParNameFromPmodel()

std::string AbstractBiblioTransitionModel::getParNameFromPmodel ( const std::string & name ) const

inherited

get the name of a parameter from its name in a submodel

Parameters

name	the name of the parameter in the submodel

Definition at line 37 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_.

◆ getPij_t() [1/2]

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().

◆ getPij_t() [2/2]

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

inlineoverridevirtualinherited

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

See also: Pij_t()

Implements bpp::TransitionModelInterface.

Definition at line 128 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getPmodelParName()

std::string AbstractBiblioTransitionModel::getPmodelParName ( const std::string & name ) const

inherited

get the name of a parameter in the submodel from its apparent name

Parameters

name	the name of the parameter

Definition at line 47 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_.

◆ getProbabilities()

const std::vector<double>& bpp::AbstractBiblioMixedTransitionModel::getProbabilities ( ) const

inlineoverridevirtualinherited

Returns the vector of the probabilities of the submodels of the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 61 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getProbabilities(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ 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 bpp::AbstractTotallyWrappedTransitionModel::getRate ( ) const

inlineoverridevirtualinherited

Get the rate.

Implements bpp::BranchModelInterface.

Definition at line 139 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getRate(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), and bpp::FromMixtureSubstitutionModel::addRateParameter().

◆ 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::AbstractWrappedModel::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 42 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getStateMap(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getStateMap().

◆ getSubmodelNumbers()

Vuint AbstractBiblioMixedTransitionModel::getSubmodelNumbers ( const std::string & desc ) const

overridevirtualinherited

Returns the vector of numbers of the submodels in the mixture that match a description.

Implements bpp::MixedTransitionModelInterface.

Definition at line 32 of file AbstractBiblioMixedTransitionModel.cpp.

References bpp::ParameterAliasable::getParameterNameWithoutNamespace(), bpp::MixedTransitionModelInterface::getSubmodelNumbers(), bpp::StringTokenizer::hasMoreToken(), bpp::AbstractBiblioMixedTransitionModel::mixedModel(), and bpp::StringTokenizer::nextToken().

◆ getVRates()

const std::vector<double>& bpp::AbstractBiblioMixedTransitionModel::getVRates ( ) const

inlineoverridevirtualinherited

Returns the vector of all the rates of the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 104 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getVRates(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ 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_.

◆ mixedModel()

const MixedTransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::mixedModel ( ) const

inlineinherited

Definition at line 136 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

◆ mixedModel_()

MixedTransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::mixedModel_ ( )

inlineprotectedinherited

Definition at line 149 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

Referenced by bpp::AbstractBiblioMixedTransitionModel::nModel_(), bpp::AbstractBiblioMixedTransitionModel::normalizeVRates(), bpp::AbstractBiblioMixedTransitionModel::setNProbability(), and bpp::AbstractBiblioMixedTransitionModel::setVRates().

◆ model() [1/2]

const BranchModelInterface& bpp::AbstractWrappedTransitionModel::model ( ) const

inlineoverridevirtualinherited

Implements bpp::WrappedModelInterface.

Definition at line 98 of file AbstractWrappedModel.h.

References bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::FromMixtureSubstitutionModel::getName(), bpp::RegisterRatesSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), and bpp::BppOSubstitutionModelFormat::write().

◆ model() [2/2]

const TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::model ( const std::string & name ) const

inlineoverridevirtualinherited

Access the submodel with the given name.

Exceptions

NullPointerException if no model with the given name is found.

Implements bpp::MixedTransitionModelInterface.

Definition at line 123 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel(), and bpp::MixedTransitionModelInterface::model().

◆ model_()

BranchModelInterface& bpp::AbstractWrappedTransitionModel::model_ ( )

inlineprotectedinherited

Definition at line 85 of file AbstractWrappedModel.h.

References bpp::AbstractWrappedTransitionModel::transitionModel_().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::FromMixtureSubstitutionModel::fireParameterChanged(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::FromMixtureSubstitutionModel::setNamespace(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ nModel()

const TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::nModel ( size_t i ) const

inlineoverridevirtualinherited

Returns the submodel from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 38 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel(), and bpp::MixedTransitionModelInterface::nModel().

Referenced by bpp::DFP07::proteinModel().

◆ nModel_()

TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::nModel_ ( size_t i )

inlineoverrideprotectedvirtualinherited

Implements bpp::MixedTransitionModelInterface.

Definition at line 151 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), and bpp::MixedTransitionModelInterface::nModel_().

◆ normalizeVRates()

void bpp::AbstractBiblioMixedTransitionModel::normalizeVRates ( )

inlineoverridevirtualinherited

normalizes the rates of the submodels.

Implements bpp::MixedTransitionModelInterface.

Definition at line 96 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), and bpp::MixedTransitionModelInterface::normalizeVRates().

◆ operator=()

LGL08_CAT& bpp::LGL08_CAT::operator= ( const LGL08_CAT & mod2 )

inline

Definition at line 85 of file LGL08_CAT.h.

References bpp::AbstractBiblioMixedTransitionModel::operator=().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::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.

Definition at line 122 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::Pij_t(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ setFreq() [1/2]

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

overridevirtualinherited

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::YN98, bpp::MG94, and bpp::KCM.

Definition at line 111 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractParameterAliasable::matchParametersValues(), bpp::AbstractWrappedTransitionModel::model(), and bpp::AbstractTotallyWrappedTransitionModel::setFreq().

Referenced by bpp::KCM::setFreq(), bpp::MG94::setFreq(), bpp::YN98::setFreq(), and bpp::AbstractBiblioTransitionModel::setFreqFromData().

◆ setFreq() [2/2]

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() [1/2]

void AbstractBiblioTransitionModel::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.

Definition at line 125 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getFrequencies(), and bpp::AbstractBiblioTransitionModel::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.