Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models. More...

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

Inheritance diagram for bpp::AbstractCodonDistanceSubstitutionModel:

Collaboration diagram for bpp::AbstractCodonDistanceSubstitutionModel:

Public Member Functions
	AbstractCodonDistanceSubstitutionModel (std::shared_ptr< const AlphabetIndex2 > pdist, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix, bool paramSynRate=false)
	Build a new AbstractCodonDistanceSubstitutionModel object. More...

	AbstractCodonDistanceSubstitutionModel (const AbstractCodonDistanceSubstitutionModel &model)

AbstractCodonDistanceSubstitutionModel &	operator= (const AbstractCodonDistanceSubstitutionModel &model)

AbstractCodonDistanceSubstitutionModel *	clone () const override

virtual	~AbstractCodonDistanceSubstitutionModel ()

void	fireParameterChanged (const ParameterList &parameters) override

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

const CodonFrequencySetInterface &	codonFrequencySet () const override

bool	hasCodonFrequencySet () const override

void	setFreq (std::map< int, double > &frequencies) 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 void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

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

void	setNamespace (const std::string &prefix)

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::shared_ptr< const AlphabetIndex2 >	pdistance_

std::shared_ptr< const GeneticCode >	pgencode_

double	alpha_

double	beta_

double	gamma_

std::shared_ptr< const StateMapInterface >	stateMap_

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models.

Author: Laurent Guéguen

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

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

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

References:

Goldman N. and Yang Z. (1994), Molecular Biology And Evolution 11(5) 725–736.
Kosakovsky Pond, S. and Muse, S.V. (2005), Molecular Biology And Evolution, 22(12), 2375–2385.
Mayrose, I. and Doron-Faigenboim, A. and Bacharach, E. and Pupko T. (2007), Bioinformatics, 23, i319–i327.

Definition at line 45 of file AbstractCodonDistanceSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonDistanceSubstitutionModel() [1/2]

AbstractCodonDistanceSubstitutionModel::AbstractCodonDistanceSubstitutionModel	(	std::shared_ptr< const AlphabetIndex2 >	pdist,
		std::shared_ptr< const GeneticCode >	pgencode,
		const std::string &	prefix,
		bool	paramSynRate = `false`
	)

Build a new AbstractCodonDistanceSubstitutionModel object.

Parameters

pdist	optional pointer to a distance between amino-acids
pgencode	the genetic code
prefix	the Namespace
paramSynRate	is true iff synonymous rate is parametrised (default=false).

Definition at line 14 of file AbstractCodonDistanceSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), pdistance_, bpp::Parameter::R_PLUS_STAR, and bpp::NumConstants::SMALL().

Referenced by clone().

◆ AbstractCodonDistanceSubstitutionModel() [2/2]

bpp::AbstractCodonDistanceSubstitutionModel::AbstractCodonDistanceSubstitutionModel ( const AbstractCodonDistanceSubstitutionModel & model )

inline

Definition at line 76 of file AbstractCodonDistanceSubstitutionModel.h.

◆ ~AbstractCodonDistanceSubstitutionModel()

virtual bpp::AbstractCodonDistanceSubstitutionModel::~AbstractCodonDistanceSubstitutionModel ( )

inlinevirtual

Definition at line 105 of file AbstractCodonDistanceSubstitutionModel.h.

Member Function Documentation

◆ clone()

AbstractCodonDistanceSubstitutionModel* bpp::AbstractCodonDistanceSubstitutionModel::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Reimplemented in bpp::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceSubstitutionModel.

Definition at line 100 of file AbstractCodonDistanceSubstitutionModel.h.

References AbstractCodonDistanceSubstitutionModel().

◆ codonFrequencySet()

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

inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

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

Definition at line 112 of file AbstractCodonDistanceSubstitutionModel.h.

◆ fireParameterChanged()

void AbstractCodonDistanceSubstitutionModel::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceSubstitutionModel.

Definition at line 36 of file AbstractCodonDistanceSubstitutionModel.cpp.

References alpha_, beta_, gamma_, bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::hasParameter(), and pdistance_.

Referenced by bpp::CodonDistanceSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::DFPDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceSubstitutionModel::fireParameterChanged(), and bpp::SENCA::fireParameterChanged().

◆ getCodonsMulRate()

double AbstractCodonDistanceSubstitutionModel::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::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, and bpp::CodonDistanceSubstitutionModel.

Definition at line 46 of file AbstractCodonDistanceSubstitutionModel.cpp.

References alpha_, beta_, bpp::exp(), gamma_, pdistance_, pgencode_, and stateMap_.

Referenced by bpp::CodonDistanceSubstitutionModel::getCodonsMulRate(), bpp::CodonDistanceFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::DFPDistanceFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::KroneckerCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::SENCA::getCodonsMulRate().

◆ hasCodonFrequencySet()

bool bpp::AbstractCodonDistanceSubstitutionModel::hasCodonFrequencySet ( ) const

inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

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

Definition at line 117 of file AbstractCodonDistanceSubstitutionModel.h.

◆ operator=()

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

inline

Definition at line 86 of file AbstractCodonDistanceSubstitutionModel.h.

References alpha_, beta_, gamma_, bpp::AbstractParameterAliasable::operator=(), pdistance_, pgencode_, and stateMap_.