FrequenciesSet useful for homogeneous and stationary models, codon implementation. More...

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

Inheritance diagram for bpp::FixedCodonFrequenciesSet:

Collaboration diagram for bpp::FixedCodonFrequenciesSet:

Public Member Functions
	FixedCodonFrequenciesSet (const GeneticCode *gCode, const std::vector< double > &initFreqs, const std::string &name="Fixed")

	FixedCodonFrequenciesSet (const GeneticCode *gCode, const std::string &name="Fixed")
	Construction with uniform frequencies on the letters of the alphabet. The stop codon frequencies are null. More...

	FixedCodonFrequenciesSet (const FixedCodonFrequenciesSet &fcfs)

FixedCodonFrequenciesSet &	operator= (const FixedCodonFrequenciesSet &fcfs)

FixedCodonFrequenciesSet *	clone () const

const GeneticCode *	getGeneticCode () const

const CodonAlphabet *	getAlphabet () const

void	setFrequencies (const std::vector< double > &frequencies)
	the given frequencies are normalized such thaat the sum of the frequencies on the non-stop codons equals 1. More...

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	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

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...

size_t	getNumberOfFrequencies () const

std::string	getName () 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
void	fireParameterChanged (const ParameterList &parameters)

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
const GeneticCode *	pgc_

Detailed Description

FrequenciesSet useful for homogeneous and stationary models, codon implementation.

This set contains no parameter.

Definition at line 177 of file CodonFrequenciesSet.h.

Constructor & Destructor Documentation

◆ FixedCodonFrequenciesSet() [1/3]

FixedCodonFrequenciesSet::FixedCodonFrequenciesSet	(	const GeneticCode *	gCode,
		const std::vector< double > &	initFreqs,
		const std::string &	name = `"Fixed"`
	)

Definition at line 331 of file CodonFrequenciesSet.cpp.

References setFrequencies().

Referenced by clone().

◆ FixedCodonFrequenciesSet() [2/3]

FixedCodonFrequenciesSet::FixedCodonFrequenciesSet	(	const GeneticCode *	gCode,
		const std::string &	name = `"Fixed"`
	)

Construction with uniform frequencies on the letters of the alphabet. The stop codon frequencies are null.

Definition at line 341 of file CodonFrequenciesSet.cpp.

References bpp::AbstractFrequenciesSet::getFreq_().

◆ FixedCodonFrequenciesSet() [3/3]

bpp::FixedCodonFrequenciesSet::FixedCodonFrequenciesSet ( const FixedCodonFrequenciesSet & fcfs )

inline

Definition at line 193 of file CodonFrequenciesSet.h.

Member Function Documentation

◆ clone()

FixedCodonFrequenciesSet* bpp::FixedCodonFrequenciesSet::clone ( ) const

inlinevirtual

Implements bpp::CodonFrequenciesSet.

Definition at line 210 of file CodonFrequenciesSet.h.

References FixedCodonFrequenciesSet().

◆ fireParameterChanged()

void bpp::FixedCodonFrequenciesSet::fireParameterChanged ( const ParameterList & parameters )

inlineprotected

Definition at line 229 of file CodonFrequenciesSet.h.

◆ getAlphabet()

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

inlinevirtual

Returns: The alphabet associated to this set.

Implements bpp::CodonFrequenciesSet.

Definition at line 216 of file CodonFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::getAlphabet().

Referenced by setFrequencies().

◆ 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.

◆ getFreq_() [1/2]

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

inlineprotectedinherited

Definition at line 203 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ 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().

◆ getGeneticCode()

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

inlinevirtual

Returns: The associated genetic code.

Implements bpp::CodonFrequenciesSet.

Definition at line 213 of file CodonFrequenciesSet.h.

References pgc_.

◆ 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().

◆ 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=()

FixedCodonFrequenciesSet& bpp::FixedCodonFrequenciesSet::operator= ( const FixedCodonFrequenciesSet & fcfs )

inline

Definition at line 198 of file CodonFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::operator=(), and pgc_.

◆ setFrequencies()

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

virtual

the given frequencies are normalized such thaat the sum of the frequencies on the non-stop codons equals 1.

Implements bpp::FrequenciesSet.

Definition at line 353 of file CodonFrequenciesSet.cpp.

References getAlphabet(), bpp::AbstractFrequenciesSet::getFreq_(), and pgc_.

Referenced by FixedCodonFrequenciesSet().

◆ 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.

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().

◆ pgc_

const GeneticCode* bpp::FixedCodonFrequenciesSet::pgc_

protected

Definition at line 182 of file CodonFrequenciesSet.h.

Referenced by getGeneticCode(), operator=(), and setFrequencies().

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

Detailed Description

Constructor & Destructor Documentation

◆ FixedCodonFrequenciesSet() [1/3]

◆ FixedCodonFrequenciesSet() [2/3]

◆ FixedCodonFrequenciesSet() [3/3]

Member Function Documentation

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies() [1/2]

◆ getAlphabetStatesFrequencies() [2/2]

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_()

◆ getFrequenciesSetForCodons()

◆ getGeneticCode()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ normalize()

◆ operator=()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

Member Data Documentation

◆ F0

◆ F1X4

◆ F3X4

◆ F61

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ pgc_