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

#include <Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h>

Inheritance diagram for bpp::CodonFrequenciesSet:

Collaboration diagram for bpp::CodonFrequenciesSet:

Public Member Functions
CodonFrequenciesSet *	clone () const =0

const CodonAlphabet *	getAlphabet () const =0

virtual const GeneticCode *	getGeneticCode () const =0

virtual const StateMap &	getStateMap () const =0

virtual const std::vector< double >	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

Static Public Member Functions
static FrequenciesSet *	getFrequenciesSetForCodons (short option, const GeneticCode *gCode, const std::string &mgmtStopFreq="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 IntervalConstraint	FREQUENCE_CONSTRAINT_SMALL

static IntervalConstraint	FREQUENCE_CONSTRAINT_MILLI

Detailed Description

Parametrize a set of state frequencies for codons.

Definition at line 56 of file CodonFrequenciesSet.h.

Member Function Documentation

◆ clone()

CodonFrequenciesSet* bpp::CodonFrequenciesSet::clone ( ) const

pure virtual

Implements bpp::FrequenciesSet.

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::FixedCodonFrequenciesSet, and bpp::FullCodonFrequenciesSet.

◆ getAlphabet()

const CodonAlphabet* bpp::CodonFrequenciesSet::getAlphabet ( ) const

pure virtual

Returns: The alphabet associated to this set.

Implements bpp::FrequenciesSet.

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::FixedCodonFrequenciesSet, and bpp::FullCodonFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel().

◆ getAlphabetStatesFrequencies()

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

pure virtualinherited

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

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel::setFreq().

◆ getFrequencies()

virtual const std::vector<double> bpp::FrequenciesSet::getFrequencies ( ) const

pure virtualinherited

Returns: The frequencies values of the set.

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::WAG01::WAG01(), and bpp::BppOFrequenciesSetFormat::write().

◆ getFrequenciesSetForCodons()

FrequenciesSet * CodonFrequenciesSet::getFrequenciesSetForCodons	(	short	option,
		const GeneticCode *	gCode,
		const std::string &	mgmtStopFreq = `"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 FrequenciesSet instance.
mgmtStopFreq	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 623 of file CodonFrequenciesSet.cpp.

References F0, F1X4, F3X4, and F61.

Referenced by bpp::BppOFrequenciesSetFormat::read().

◆ getGeneticCode()

virtual const GeneticCode* bpp::CodonFrequenciesSet::getGeneticCode ( ) const

pure virtual

Returns: The associated genetic code.

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::FixedCodonFrequenciesSet, and bpp::FullCodonFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel().

◆ getName()

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

pure virtualinherited

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::AbstractCodonFrequenciesSubstitutionModel::AbstractCodonFrequenciesSubstitutionModel(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::WordFromUniqueFrequenciesSet::getDescription(), bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(), bpp::BppOFrequenciesSetFormat::read(), and bpp::BppOFrequenciesSetFormat::write().

◆ getNumberOfFrequencies()

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

pure virtualinherited

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

Implemented in bpp::AbstractFrequenciesSet.

◆ getStateMap()

virtual const StateMap& bpp::FrequenciesSet::getStateMap ( ) const

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequenciesSet.

◆ setFrequencies()

virtual void bpp::FrequenciesSet::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::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::FullFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::MvaFrequenciesSet, and bpp::GCFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::BppOFrequenciesSetFormat::initialize_(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::LG08::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::WordFromUniqueFrequenciesSet::setFrequencies(), bpp::MarkovModulatedFrequenciesSet::setFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

◆ setFrequenciesFromAlphabetStatesFrequencies()

virtual void bpp::FrequenciesSet::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::AbstractFrequenciesSet.

Referenced by bpp::BppOFrequenciesSetFormat::initialize_(), bpp::AbstractCodonFitnessSubstitutionModel::setFreq(), bpp::AbstractCodonFrequenciesSubstitutionModel::setFreq(), and bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::setFreq().

Member Data Documentation

◆ F0

const short CodonFrequenciesSet::F0 = 0

static

Definition at line 95 of file CodonFrequenciesSet.h.

Referenced by getFrequenciesSetForCodons(), and bpp::BppOFrequenciesSetFormat::read().

◆ F1X4

const short CodonFrequenciesSet::F1X4 = 1

static

Definition at line 96 of file CodonFrequenciesSet.h.

Referenced by getFrequenciesSetForCodons(), and bpp::BppOFrequenciesSetFormat::read().

◆ F3X4

const short CodonFrequenciesSet::F3X4 = 2

static

Definition at line 97 of file CodonFrequenciesSet.h.

Referenced by getFrequenciesSetForCodons(), and bpp::BppOFrequenciesSetFormat::read().

◆ F61

const short CodonFrequenciesSet::F61 = 3

static

Definition at line 98 of file CodonFrequenciesSet.h.

Referenced by getFrequenciesSetForCodons(), and bpp::BppOFrequenciesSetFormat::read().

◆ FREQUENCE_CONSTRAINT_MILLI

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_MILLI

staticinherited

Definition at line 118 of file FrequenciesSet.h.

◆ FREQUENCE_CONSTRAINT_SMALL

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_SMALL

staticinherited

Definition at line 117 of file FrequenciesSet.h.

Referenced by bpp::F84::F84(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), 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/FrequenciesSet/CodonFrequenciesSet.h
Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Detailed Description

Member Function Documentation

◆ clone()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies()

◆ getFrequencies()

◆ getFrequenciesSetForCodons()

◆ getGeneticCode()

◆ getName()

◆ getNumberOfFrequencies()

◆ getStateMap()

◆ setFrequencies()

◆ setFrequenciesFromAlphabetStatesFrequencies()

Member Data Documentation

◆ F0

◆ F1X4

◆ F3X4

◆ F61

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL