the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero. More...

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

Inheritance diagram for bpp::CodonFromIndependentFrequenciesSet:

Collaboration diagram for bpp::CodonFromIndependentFrequenciesSet:

Public Member Functions
	CodonFromIndependentFrequenciesSet (const GeneticCode gCode, const std::vector< FrequenciesSet > &freqvector, const std::string &name="Codon", const std::string &mgmtStopFreq="quadratic")
	Constructor from a CodonAlphabet* and a vector of different FrequenciesSet*. Throws an Exception if their lengths do not match. More...

	CodonFromIndependentFrequenciesSet (const CodonFromIndependentFrequenciesSet &iwfs)

virtual	~CodonFromIndependentFrequenciesSet ()

CodonFromIndependentFrequenciesSet &	operator= (const CodonFromIndependentFrequenciesSet &iwfs)

CodonFromIndependentFrequenciesSet *	clone () const

const CodonAlphabet *	getAlphabet () const

const GeneticCode *	getGeneticCode () const

void	updateFrequencies ()

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

void	fireParameterChanged (const ParameterList &pl)

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

const FrequenciesSet &	getFrequenciesSetForLetter (size_t i) const

virtual size_t	getLength () const

void	setNamespace (const std::string &prefix)

std::string	getDescription () const

const StateMap &	getStateMap () const

const std::vector< double >	getFrequencies () const

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

void	setFrequenciesFromAlphabetStatesFrequencies (const std::map< int, double > &frequencies)
	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...

std::string	getName () const

size_t	getNumberOfFrequencies () const

void	normalize ()

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

Protected Member Functions
size_t	getSizeFromVector (const std::vector< FrequenciesSet *> &freqVector)

std::vector< double > &	getFrequencies_ ()

double &	getFreq_ (size_t i)

const double &	getFreq_ (size_t i) const

void	setFrequencies_ (const std::vector< double > &frequencies)

Protected Attributes
std::vector< FrequenciesSet * >	vFreq_

std::vector< std::string >	vNestedPrefix_

Private Attributes
std::map< int, Vint >	mStopNeigh_

unsigned short	mgmtStopFreq_

const GeneticCode *	pgc_

Detailed Description

the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero.

Author: Laurent Guéguen

Definition at line 338 of file CodonFrequenciesSet.h.

Constructor & Destructor Documentation

◆ CodonFromIndependentFrequenciesSet() [1/2]

CodonFromIndependentFrequenciesSet::CodonFromIndependentFrequenciesSet	(	const GeneticCode *	gCode,
		const std::vector< FrequenciesSet *> &	freqvector,
		const std::string &	name = `"Codon"`,
		const std::string &	mgmtStopFreq = `"quadratic"`
	)

Constructor from a CodonAlphabet* and a vector of different FrequenciesSet*. Throws an Exception if their lengths do not match.

Parameters

gCode	a pointer to the genetic code to use.
freqvector	a vector of pointers to the phase specific FrequenciesSets
name	the optional name of the FrequenciesSet (default codon)
mgmtStopFreq	the optional way the frequencies assigned to the stop codons are redistributed to the other codons. 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.

Definition at line 377 of file CodonFrequenciesSet.cpp.

References getAlphabet(), mgmtStopFreq_, mStopNeigh_, pgc_, and updateFrequencies().

Referenced by clone().

◆ CodonFromIndependentFrequenciesSet() [2/2]

CodonFromIndependentFrequenciesSet::CodonFromIndependentFrequenciesSet ( const CodonFromIndependentFrequenciesSet & iwfs )

Definition at line 419 of file CodonFrequenciesSet.cpp.

References updateFrequencies().

◆ ~CodonFromIndependentFrequenciesSet()

virtual bpp::CodonFromIndependentFrequenciesSet::~CodonFromIndependentFrequenciesSet ( )

inlinevirtual

Definition at line 374 of file CodonFrequenciesSet.h.

Member Function Documentation

◆ clone()

CodonFromIndependentFrequenciesSet* bpp::CodonFromIndependentFrequenciesSet::clone ( ) const

inlinevirtual

Implements bpp::CodonFrequenciesSet.

Definition at line 378 of file CodonFrequenciesSet.h.

References CodonFromIndependentFrequenciesSet().

◆ fireParameterChanged()

void WordFromIndependentFrequenciesSet::fireParameterChanged ( const ParameterList & pl )

inherited

Definition at line 143 of file WordFrequenciesSet.cpp.

References bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), and bpp::WordFromIndependentFrequenciesSet::vFreq_.

◆ getAlphabet()

const CodonAlphabet * CodonFromIndependentFrequenciesSet::getAlphabet ( ) const

virtual

Returns: The alphabet associated to this set.

Implements bpp::CodonFrequenciesSet.

Definition at line 414 of file CodonFrequenciesSet.cpp.

References bpp::AbstractWordFrequenciesSet::getAlphabet().

Referenced by CodonFromIndependentFrequenciesSet(), and updateFrequencies().

◆ getAlphabetStatesFrequencies() [1/2]

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().

◆ getAlphabetStatesFrequencies() [2/2]

const std::map< int, double > AbstractFrequenciesSet::getAlphabetStatesFrequencies ( ) const

virtualinherited

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

Implements bpp::FrequenciesSet.

Definition at line 79 of file FrequenciesSet.cpp.

◆ getDescription()

std::string WordFromIndependentFrequenciesSet::getDescription ( ) const

inherited

Definition at line 239 of file WordFrequenciesSet.cpp.

References bpp::AbstractFrequenciesSet::getName(), and bpp::WordFromIndependentFrequenciesSet::vFreq_.

◆ getFreq_() [1/2]

double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t i )

inlineprotectedinherited

Definition at line 203 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::GCFrequenciesSet::fireParameterChanged(), bpp::FullNucleotideFrequenciesSet::fireParameterChanged(), bpp::FixedCodonFrequenciesSet::FixedCodonFrequenciesSet(), bpp::FixedFrequenciesSet::FixedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::GCFrequenciesSet::GCFrequenciesSet(), bpp::GCFrequenciesSet::setFrequencies(), bpp::FixedCodonFrequenciesSet::setFrequencies(), bpp::FullCodonFrequenciesSet::updateFreq_(), bpp::FullFrequenciesSet::updateFreq_(), bpp::MvaFrequenciesSet::updateFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::FullPerAACodonFrequenciesSet::updateFrequencies(), updateFrequencies(), and bpp::CodonFromUniqueFrequenciesSet::updateFrequencies().

◆ getFreq_() [2/2]

const double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t i ) const

inlineprotectedinherited

Definition at line 204 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getFrequencies() [1/2]

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().

◆ getFrequencies() [2/2]

const std::vector<double> bpp::AbstractFrequenciesSet::getFrequencies ( ) const

inlinevirtualinherited

Returns: The frequencies values of the set.

Implements bpp::FrequenciesSet.

Definition at line 174 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::MvaFrequenciesSet::updateFrequencies().

◆ getFrequencies_()

std::vector<double>& bpp::AbstractFrequenciesSet::getFrequencies_ ( )

inlineprotectedinherited

Definition at line 202 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getFrequenciesSetForCodons()

FrequenciesSet * CodonFrequenciesSet::getFrequenciesSetForCodons	(	short	option,
		const GeneticCode *	gCode,
		const std::string &	mgmtStopFreq = `"quadratic"`,
		unsigned short	method = `1`
	)

staticinherited

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 bpp::CodonFrequenciesSet::F0, bpp::CodonFrequenciesSet::F1X4, bpp::CodonFrequenciesSet::F3X4, and bpp::CodonFrequenciesSet::F61.

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

◆ getFrequenciesSetForLetter()

const FrequenciesSet& bpp::WordFromIndependentFrequenciesSet::getFrequenciesSetForLetter ( size_t i ) const

inlinevirtualinherited

@ brief Return the n-th FrequenciesSet&

Implements bpp::WordFrequenciesSet.

Definition at line 177 of file WordFrequenciesSet.h.

References bpp::WordFromIndependentFrequenciesSet::vFreq_.

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

◆ getGeneticCode()

const GeneticCode* bpp::CodonFromIndependentFrequenciesSet::getGeneticCode ( ) const

inlinevirtual

Returns: The associated genetic code.

Implements bpp::CodonFrequenciesSet.

Definition at line 382 of file CodonFrequenciesSet.h.

References pgc_.

◆ getLength()

size_t WordFromIndependentFrequenciesSet::getLength ( ) const

virtualinherited

@ brief Return the length of the words

Reimplemented from bpp::AbstractWordFrequenciesSet.

Definition at line 225 of file WordFrequenciesSet.cpp.

References bpp::WordFromIndependentFrequenciesSet::vFreq_.

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

◆ getName() [1/2]

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().

◆ getName() [2/2]

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

inlinevirtualinherited

Implements bpp::FrequenciesSet.

Definition at line 191 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::name_.

Referenced by bpp::WordFromIndependentFrequenciesSet::getDescription(), and bpp::WordFromUniqueFrequenciesSet::getDescription().

◆ getNumberOfFrequencies() [1/2]

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.

◆ getNumberOfFrequencies() [2/2]

size_t bpp::AbstractFrequenciesSet::getNumberOfFrequencies ( ) const

inlinevirtualinherited

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

Implements bpp::FrequenciesSet.

Definition at line 189 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::FixedFrequenciesSet::setFrequencies().

◆ getSizeFromVector()

size_t AbstractWordFrequenciesSet::getSizeFromVector ( const std::vector< FrequenciesSet *> & freqVector )

protectedvirtualinherited

Implements bpp::WordFrequenciesSet.

Definition at line 48 of file WordFrequenciesSet.cpp.

Referenced by bpp::WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet().

◆ getStateMap() [1/2]

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

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequenciesSet.

◆ getStateMap() [2/2]

const StateMap& bpp::AbstractFrequenciesSet::getStateMap ( ) const

inlinevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::FrequenciesSet.

Definition at line 172 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::stateMap_.

Referenced by bpp::FullPerAACodonFrequenciesSet::updateFrequencies().

◆ normalize()

void bpp::AbstractFrequenciesSet::normalize ( )

inlineinherited

Definition at line 193 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::FullPerAACodonFrequenciesSet::updateFrequencies().

◆ operator=()

CodonFromIndependentFrequenciesSet & CodonFromIndependentFrequenciesSet::operator= ( const CodonFromIndependentFrequenciesSet & iwfs )

Definition at line 428 of file CodonFrequenciesSet.cpp.

References mgmtStopFreq_, mStopNeigh_, bpp::WordFromIndependentFrequenciesSet::operator=(), and pgc_.

◆ setFrequencies() [1/2]

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().

◆ setFrequencies() [2/2]

void WordFromIndependentFrequenciesSet::setFrequencies ( const std::vector< double > & frequencies )

virtualinherited

@ brief Independent letter frequencies from given word frequencies. The frequencies of a letter at a position is the sum of the frequencies of the words that have this letter at this position.

Implements bpp::FrequenciesSet.

Definition at line 183 of file WordFrequenciesSet.cpp.

References bpp::AbstractWordFrequenciesSet::getAlphabet(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), and bpp::WordFromIndependentFrequenciesSet::vFreq_.

◆ setFrequencies_()

void bpp::AbstractFrequenciesSet::setFrequencies_ ( const std::vector< double > & frequencies )

inlineprotectedinherited

Definition at line 205 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::setFrequencies(), bpp::FixedFrequenciesSet::setFrequencies(), and bpp::MvaFrequenciesSet::updateFrequencies().

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

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().

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

void AbstractFrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > & frequencies )

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.

In this implementation, all model states with the same alphabet state are given the same frequency.

Parameters

frequencies The set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

◆ setNamespace()

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

inherited

Definition at line 230 of file WordFrequenciesSet.cpp.

References bpp::WordFromIndependentFrequenciesSet::vFreq_, and bpp::WordFromIndependentFrequenciesSet::vNestedPrefix_.

◆ updateFrequencies()

void CodonFromIndependentFrequenciesSet::updateFrequencies ( )

virtual

@ brief Update the frequencies given the parameters.

Reimplemented from bpp::WordFromIndependentFrequenciesSet.

Definition at line 437 of file CodonFrequenciesSet.cpp.

References getAlphabet(), bpp::AbstractFrequenciesSet::getFreq_(), mgmtStopFreq_, mStopNeigh_, pgc_, and bpp::WordFromIndependentFrequenciesSet::updateFrequencies().

Referenced by CodonFromIndependentFrequenciesSet().

Member Data Documentation

◆ F0

const short CodonFrequenciesSet::F0 = 0

staticinherited

Definition at line 95 of file CodonFrequenciesSet.h.

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

◆ F1X4

const short CodonFrequenciesSet::F1X4 = 1

staticinherited

Definition at line 96 of file CodonFrequenciesSet.h.

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

◆ F3X4

const short CodonFrequenciesSet::F3X4 = 2

staticinherited

Definition at line 97 of file CodonFrequenciesSet.h.

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

◆ F61

const short CodonFrequenciesSet::F61 = 3

staticinherited

Definition at line 98 of file CodonFrequenciesSet.h.

Referenced by bpp::CodonFrequenciesSet::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().

◆ mgmtStopFreq_

unsigned short bpp::CodonFromIndependentFrequenciesSet::mgmtStopFreq_

private

Definition at line 346 of file CodonFrequenciesSet.h.

Referenced by CodonFromIndependentFrequenciesSet(), operator=(), and updateFrequencies().

◆ mStopNeigh_

std::map<int, Vint> bpp::CodonFromIndependentFrequenciesSet::mStopNeigh_

private

Definition at line 344 of file CodonFrequenciesSet.h.

Referenced by CodonFromIndependentFrequenciesSet(), operator=(), and updateFrequencies().

◆ pgc_

const GeneticCode* bpp::CodonFromIndependentFrequenciesSet::pgc_

private

Definition at line 348 of file CodonFrequenciesSet.h.

Referenced by CodonFromIndependentFrequenciesSet(), getGeneticCode(), operator=(), and updateFrequencies().

◆ vFreq_

std::vector<FrequenciesSet*> bpp::WordFromIndependentFrequenciesSet::vFreq_

protectedinherited

Definition at line 143 of file WordFrequenciesSet.h.

◆ vNestedPrefix_

std::vector<std::string> bpp::WordFromIndependentFrequenciesSet::vNestedPrefix_

protectedinherited

Definition at line 144 of file WordFrequenciesSet.h.

Referenced by bpp::WordFromIndependentFrequenciesSet::operator=(), bpp::WordFromIndependentFrequenciesSet::setNamespace(), and bpp::WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet().

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

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CodonFromIndependentFrequenciesSet() [1/2]

◆ CodonFromIndependentFrequenciesSet() [2/2]

◆ ~CodonFromIndependentFrequenciesSet()

Member Function Documentation

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies() [1/2]

◆ getAlphabetStatesFrequencies() [2/2]

◆ getDescription()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_()

◆ getFrequenciesSetForCodons()

◆ getFrequenciesSetForLetter()

◆ getGeneticCode()

◆ getLength()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getSizeFromVector()

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ normalize()

◆ operator=()

◆ setFrequencies() [1/2]

◆ setFrequencies() [2/2]

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

◆ setNamespace()

◆ updateFrequencies()

Member Data Documentation

◆ F0

◆ F1X4

◆ F3X4

◆ F61

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ mgmtStopFreq_

◆ mStopNeigh_

◆ pgc_

◆ vFreq_

◆ vNestedPrefix_