Parametrize a set of state frequencies for codons. More...

#include <Bpp/Phyl/Model/FrequencySet/CodonFrequencySet.h>

Inheritance diagram for bpp::CodonFrequencySetInterface:

Collaboration diagram for bpp::CodonFrequencySetInterface:

Public Member Functions
CodonFrequencySetInterface *	clone () const override=0

virtual std::shared_ptr< const CodonAlphabet >	getCodonAlphabet () const =0

virtual std::shared_ptr< const GeneticCode >	getGeneticCode () const =0

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

virtual const Alphabet &	alphabet () const =0

virtual const StateMapInterface &	stateMap () const =0

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

virtual const Vdouble &	getFrequencies () const =0

virtual const std::map< int, double >	getAlphabetStatesFrequencies () const =0

virtual void	setFrequencies (const std::vector< double > &frequencies)=0
	Set the parameters in order to match a given set of frequencies. More...

virtual void	setFrequenciesFromAlphabetStatesFrequencies (const std::map< int, double > &frequencies)=0
	Set the Frequencies from the one of the map which keys match with a letter of the Alphabet. The frequencies are normalized so that the matching values sum 1. More...

virtual std::string	getName () const =0

virtual size_t	getNumberOfFrequencies () const =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

Static Public Member Functions
static std::unique_ptr< CodonFrequencySetInterface >	getFrequencySetForCodons (short option, std::shared_ptr< const GeneticCode > gCode, const std::string &mgmtStopCodon="quadratic", unsigned short method=1)
	A helper function that provide frequencies set for codon models according to PAML option. More...

Static Public Attributes
static const short	F0 = 0

static const short	F1X4 = 1

static const short	F3X4 = 2

static const short	F61 = 3

static std::shared_ptr< IntervalConstraint >	FREQUENCE_CONSTRAINT_SMALL

static std::shared_ptr< IntervalConstraint >	FREQUENCE_CONSTRAINT_MILLI

static std::shared_ptr< IntervalConstraint >	FREQUENCE_CONSTRAINT_CENTI

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

Detailed Description

Parametrize a set of state frequencies for codons.

Definition at line 21 of file CodonFrequencySet.h.

Member Function Documentation

◆ alphabet()

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

pure virtualinherited

Returns: The alphabet associated to this set.

Implemented in bpp::AbstractFrequencySet.

◆ clone()

CodonFrequencySetInterface * bpp::CodonFrequencySetInterface::clone ( ) const

overridepure virtual

Implements bpp::FrequencySetInterface.

Implemented in bpp::FullCodonFrequencySet, bpp::FixedCodonFrequencySet, bpp::UserCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::CodonFromIndependentFrequencySet, and bpp::CodonFromUniqueFrequencySet.

◆ getAlphabet()

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

pure virtualinherited

Returns: The alphabet associated to this set.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::UserCodonFrequencySet::getCodonAlphabet(), bpp::FixedNucleotideFrequencySet::getNucleicAlphabet(), bpp::UserNucleotideFrequencySet::getNucleicAlphabet(), bpp::FullProteinFrequencySet::getProteicAlphabet(), bpp::FixedProteinFrequencySet::getProteicAlphabet(), and bpp::UserProteinFrequencySet::getProteicAlphabet().

◆ getAlphabetStatesFrequencies()

virtual const std::map< int, double > bpp::FrequencySetInterface::getAlphabetStatesFrequencies ( ) const

pure virtualinherited

Returns: The frequencies of each alphabet states according to this model.

Implemented in bpp::AbstractFrequencySet.

◆ getCodonAlphabet()

virtual std::shared_ptr< const CodonAlphabet > bpp::CodonFrequencySetInterface::getCodonAlphabet ( ) const

pure virtual

Implemented in bpp::FullCodonFrequencySet, bpp::FixedCodonFrequencySet, bpp::UserCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::CodonFromIndependentFrequencySet, and bpp::CodonFromUniqueFrequencySet.

◆ getFrequencies()

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

pure virtualinherited

Returns: The frequencies values of the set.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::NonHomogeneousSubstitutionProcess::getRootFrequencies(), bpp::SubstitutionProcessCollectionMember::getRootFrequencies(), bpp::CodonDistanceFrequenciesSubstitutionModel::setFreq(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq(), bpp::DFPDistanceFrequenciesSubstitutionModel::setFreq(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

◆ getFrequencySetForCodons()

unique_ptr< CodonFrequencySetInterface > CodonFrequencySetInterface::getFrequencySetForCodons	(	short	option,
		std::shared_ptr< const GeneticCode >	gCode,
		const std::string &	mgmtStopCodon = `"quadratic"`,
		unsigned short	method = `1`
	)

static

A helper function that provide frequencies set for codon models according to PAML option.

Parameters

option	A code describing the option, one of F61, F1X4 or F3X4.
gCode	The genetic code to use. The underlying codon alphabet object will be passed to the FrequencySet instance.
mgmtStopCodon	the optional way the frequencies assigned to the stop codons are redistributed to the other codons, with F1X4 and F3X4 options. The available values are: uniform : each stop frequency is distributed evenly linear : each stop frequency is distributed to the neighbour codons (ie 1 substitution away), in proportion to each target codon frequency. quadratic (default): each stop frequency is distributed to the neighbour codons (ie 1 substitution away), in proportion to the square of each target codon frequency.
method	The parametrization used for F61. Default method is 1 (ie global ratio).

See also: Simplex

Definition at line 641 of file CodonFrequencySet.cpp.

References F0, F1X4, F3X4, and F61.

Referenced by bpp::BppOFrequencySetFormat::readFrequencySet().

◆ getGeneticCode()

virtual std::shared_ptr< const GeneticCode > bpp::CodonFrequencySetInterface::getGeneticCode ( ) const

pure virtual

Returns: The associated genetic code.

Implemented in bpp::FullCodonFrequencySet, bpp::FixedCodonFrequencySet, bpp::UserCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::CodonFromIndependentFrequencySet, and bpp::CodonFromUniqueFrequencySet.

◆ getName()

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

pure virtualinherited

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::BppOFrequencySetFormat::writeFrequencySet().

◆ getNumberOfFrequencies()

virtual size_t bpp::FrequencySetInterface::getNumberOfFrequencies ( ) const

pure virtualinherited

Returns: The number of frequencies in the set. This is equivalent to getStateMap().getNumberOfModelStates().

Implemented in bpp::AbstractFrequencySet.

◆ getStateMap()

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

pure virtualinherited

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

Implemented in bpp::AbstractFrequencySet.

◆ setFrequencies()

virtual void bpp::FrequencySetInterface::setFrequencies ( const std::vector< double > & frequencies )

pure virtualinherited

Set the parameters in order to match a given set of frequencies.

Parameters

frequencies The set of frequencies to match.

Exceptions

DimensionException	If the number of frequencies does not match the size of the alphabet.
Exception	If the frequencies do not sum to 1.

Implemented in bpp::FullCodonFrequencySet, bpp::FixedCodonFrequencySet, bpp::UserCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::FullFrequencySet, bpp::FromModelFrequencySet, bpp::MarkovModulatedFrequencySet, bpp::FixedFrequencySet, bpp::UserFrequencySet, bpp::MvaFrequencySet, bpp::GCFrequencySet, bpp::FullNucleotideFrequencySet, bpp::WordFromIndependentFrequencySet, and bpp::WordFromUniqueFrequencySet.

Referenced by bpp::BppOFrequencySetFormat::initialize_(), and bpp::AbstractFrequencySet::setFrequenciesFromAlphabetStatesFrequencies().

◆ setFrequenciesFromAlphabetStatesFrequencies()

virtual void bpp::FrequencySetInterface::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > & frequencies )

pure virtualinherited

Set the Frequencies from the one of the map which keys match with a letter of the Alphabet. The frequencies are normalized so that the matching values sum 1.

Parameters

frequencies The set of frequencies to match.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::BppOFrequencySetFormat::initialize_().

◆ stateMap()

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

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequencySet.

Member Data Documentation

◆ F0

const short CodonFrequencySetInterface::F0 = 0

static

Definition at line 62 of file CodonFrequencySet.h.

Referenced by getFrequencySetForCodons(), and bpp::BppOFrequencySetFormat::readFrequencySet().

◆ F1X4

const short CodonFrequencySetInterface::F1X4 = 1

static

Definition at line 63 of file CodonFrequencySet.h.

Referenced by getFrequencySetForCodons(), and bpp::BppOFrequencySetFormat::readFrequencySet().

◆ F3X4

const short CodonFrequencySetInterface::F3X4 = 2

static

Definition at line 64 of file CodonFrequencySet.h.

Referenced by getFrequencySetForCodons(), and bpp::BppOFrequencySetFormat::readFrequencySet().

◆ F61

const short CodonFrequencySetInterface::F61 = 3

static

Definition at line 65 of file CodonFrequencySet.h.

Referenced by getFrequencySetForCodons(), and bpp::BppOFrequencySetFormat::readFrequencySet().

◆ FREQUENCE_CONSTRAINT_CENTI

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_CENTI

staticinherited

Definition at line 92 of file FrequencySet.h.

Referenced by bpp::FullNucleotideFrequencySet::FullNucleotideFrequencySet().

◆ FREQUENCE_CONSTRAINT_MILLI

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_MILLI

staticinherited

Definition at line 91 of file FrequencySet.h.

◆ FREQUENCE_CONSTRAINT_SMALL

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_SMALL

staticinherited

Definition at line 90 of file FrequencySet.h.

Referenced by bpp::F81::F81(), bpp::F84::F84(), bpp::GTR::GTR(), bpp::HKY85::HKY85(), bpp::T92::T92(), and bpp::TN93::TN93().

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

Bpp/Phyl/Model/FrequencySet/CodonFrequencySet.h
Bpp/Phyl/Model/FrequencySet/CodonFrequencySet.cpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Detailed Description

Member Function Documentation

◆ alphabet()

◆ clone()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies()

◆ getCodonAlphabet()

◆ getFrequencies()

◆ getFrequencySetForCodons()

◆ getGeneticCode()

◆ getName()

◆ getNumberOfFrequencies()

◆ getStateMap()

◆ setFrequencies()

◆ setFrequenciesFromAlphabetStatesFrequencies()

◆ stateMap()

Member Data Documentation

◆ F0

◆ F1X4

◆ F3X4

◆ F61

◆ FREQUENCE_CONSTRAINT_CENTI

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL