Abstract Class for substitution models on codons parametrized by frequencies. More...

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

Inheritance diagram for bpp::AbstractCodonFrequenciesSubstitutionModel:

Collaboration diagram for bpp::AbstractCodonFrequenciesSubstitutionModel:

Public Member Functions
	AbstractCodonFrequenciesSubstitutionModel (std::unique_ptr< CodonFrequencySetInterface > pfreq, const std::string &prefix)
	Build a AbstractCodonFrequenciesSubstitutionModel instance. More...

	AbstractCodonFrequenciesSubstitutionModel (const AbstractCodonFrequenciesSubstitutionModel &model)

AbstractCodonFrequenciesSubstitutionModel &	operator= (const AbstractCodonFrequenciesSubstitutionModel &model)

AbstractCodonFrequenciesSubstitutionModel *	clone () const override

virtual	~AbstractCodonFrequenciesSubstitutionModel ()

void	fireParameterChanged (const ParameterList &parameters) override

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

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

double	getCodonsMulRate (size_t, size_t) const override
	Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More...

const CodonFrequencySetInterface &	codonFrequencySet () const override

const FrequencySetInterface &	frequencySet () const

bool	hasCodonFrequencySet () const override

virtual size_t	getNumberOfIndependentParameters () const=0

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

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

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

virtual const ParameterList &	getIndependentParameters () const=0

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

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

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

virtual const ParameterList &	getParameters () const=0

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

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

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

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

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

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

virtual size_t	getNumberOfParameters () const=0

virtual std::string	getNamespace () const=0

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

bool	hasIndependentParameter (const std::string &name) const

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

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

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

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

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

std::string	getFrom (const std::string &name) const

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

const ParameterList &	getParameters () const override

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

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

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

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

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

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

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

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

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

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

ParameterList &	getParameters_ () override

Private Attributes
std::unique_ptr< CodonFrequencySetInterface >	pfreqset_

std::string	freqName_

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Abstract Class for substitution models on codons parametrized by frequencies.

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

Author: Laurent Guéguen

If we denote the equilibrium frequency, the generator term defined from inherited and inheriting classes, $Q_{ij})$ , is multiplied by $F_{j}$ .

Definition at line 29 of file AbstractCodonFrequenciesSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonFrequenciesSubstitutionModel() [1/2]

AbstractCodonFrequenciesSubstitutionModel::AbstractCodonFrequenciesSubstitutionModel	(	std::unique_ptr< CodonFrequencySetInterface >	pfreq,
		const std::string &	prefix
	)

Build a AbstractCodonFrequenciesSubstitutionModel instance.

Parameters

pfreq	pointer to the AbstractFrequencySet equilibrium frequencies. It is owned by the instance.
prefix	the Namespace

Definition at line 12 of file AbstractCodonFrequenciesSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), freqName_, and pfreqset_.

Referenced by clone().

◆ AbstractCodonFrequenciesSubstitutionModel() [2/2]

bpp::AbstractCodonFrequenciesSubstitutionModel::AbstractCodonFrequenciesSubstitutionModel ( const AbstractCodonFrequenciesSubstitutionModel & model )

inline

Definition at line 49 of file AbstractCodonFrequenciesSubstitutionModel.h.

◆ ~AbstractCodonFrequenciesSubstitutionModel()

AbstractCodonFrequenciesSubstitutionModel::~AbstractCodonFrequenciesSubstitutionModel ( )

virtual

Definition at line 26 of file AbstractCodonFrequenciesSubstitutionModel.cpp.

Member Function Documentation

◆ clone()

AbstractCodonFrequenciesSubstitutionModel* bpp::AbstractCodonFrequenciesSubstitutionModel::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Reimplemented in bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 63 of file AbstractCodonFrequenciesSubstitutionModel.h.

References AbstractCodonFrequenciesSubstitutionModel().

◆ codonFrequencySet()

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

inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 82 of file AbstractCodonFrequenciesSubstitutionModel.h.

References pfreqset_.

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

◆ fireParameterChanged()

void AbstractCodonFrequenciesSubstitutionModel::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 30 of file AbstractCodonFrequenciesSubstitutionModel.cpp.

References pfreqset_.

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

◆ frequencySet()

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

inline

Definition at line 87 of file AbstractCodonFrequenciesSubstitutionModel.h.

References pfreqset_.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::frequencySet().

◆ getCodonsMulRate()

double AbstractCodonFrequenciesSubstitutionModel::getCodonsMulRate	(	size_t	,
		size_t
	)		const

overridevirtual

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 45 of file AbstractCodonFrequenciesSubstitutionModel.cpp.

References pfreqset_.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::DFPDistanceFrequenciesSubstitutionModel::getCodonsMulRate(), and bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::getCodonsMulRate().

◆ hasCodonFrequencySet()

bool bpp::AbstractCodonFrequenciesSubstitutionModel::hasCodonFrequencySet ( ) const

inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 92 of file AbstractCodonFrequenciesSubstitutionModel.h.

References pfreqset_.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::hasCodonFrequencySet(), bpp::DFPDistanceFrequenciesSubstitutionModel::hasCodonFrequencySet(), and bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::hasCodonFrequencySet().

◆ operator=()

AbstractCodonFrequenciesSubstitutionModel& bpp::AbstractCodonFrequenciesSubstitutionModel::operator= ( const AbstractCodonFrequenciesSubstitutionModel & model )

inline

Definition at line 55 of file AbstractCodonFrequenciesSubstitutionModel.h.

References freqName_, bpp::AbstractParameterAliasable::operator=(), and pfreqset_.