A generic FrequenciesSet for Full Codon alphabets. More...

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

Inheritance diagram for bpp::FullCodonFrequenciesSet:

Collaboration diagram for bpp::FullCodonFrequenciesSet:

Public Member Functions
	FullCodonFrequenciesSet (const GeneticCode *gCode, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")
	Construction with uniform frequencies on the letters of the alphabet. The stop codon frequencies are null. More...

	FullCodonFrequenciesSet (const GeneticCode *gCode, const std::vector< double > &initFreqs, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")

	FullCodonFrequenciesSet (const FullCodonFrequenciesSet &fcfs)

FullCodonFrequenciesSet &	operator= (const FullCodonFrequenciesSet &fcfs)

FullCodonFrequenciesSet *	clone () const

const GeneticCode *	getGeneticCode () const

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

const CodonAlphabet *	getAlphabet () const

void	setNamespace (const std::string &nameSpace)

unsigned short	getMethod () const

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)

void	updateFreq_ ()

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_

Private Attributes
Simplex	sFreq_
	Simplex to handle the probabilities and the parameters. More...

Detailed Description

A generic FrequenciesSet for Full Codon alphabets.

It is very similar to FullFrequencySet, but only the non-stop codon frequencies are parameterized.

Definition at line 108 of file CodonFrequenciesSet.h.

Constructor & Destructor Documentation

◆ FullCodonFrequenciesSet() [1/3]

FullCodonFrequenciesSet::FullCodonFrequenciesSet	(	const GeneticCode *	gCode,
		bool	allowNullFreqs = `false`,
		unsigned short	method = `1`,
		const std::string &	name = `"Full"`
	)

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

Definition at line 53 of file CodonFrequenciesSet.cpp.

References sFreq_, and updateFreq_().

Referenced by clone().

◆ FullCodonFrequenciesSet() [2/3]

FullCodonFrequenciesSet::FullCodonFrequenciesSet	(	const GeneticCode *	gCode,
		const std::vector< double > &	initFreqs,
		bool	allowNullFreqs = `false`,
		unsigned short	method = `1`,
		const std::string &	name = `"Full"`
	)

Definition at line 74 of file CodonFrequenciesSet.cpp.

References getAlphabet(), pgc_, sFreq_, and updateFreq_().

◆ FullCodonFrequenciesSet() [3/3]

FullCodonFrequenciesSet::FullCodonFrequenciesSet ( const FullCodonFrequenciesSet & fcfs )

Definition at line 106 of file CodonFrequenciesSet.cpp.

Member Function Documentation

◆ clone()

FullCodonFrequenciesSet* bpp::FullCodonFrequenciesSet::clone ( ) const

inlinevirtual

Implements bpp::CodonFrequenciesSet.

Definition at line 139 of file CodonFrequenciesSet.h.

References FullCodonFrequenciesSet().

◆ fireParameterChanged()

void FullCodonFrequenciesSet::fireParameterChanged ( const ParameterList & parameters )

protected

Definition at line 151 of file CodonFrequenciesSet.cpp.

References sFreq_, and updateFreq_().

◆ getAlphabet()

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

inlinevirtual

Returns: The alphabet associated to this set.

Implements bpp::CodonFrequenciesSet.

Definition at line 152 of file CodonFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::getAlphabet().

Referenced by FullCodonFrequenciesSet(), setFrequencies(), and updateFreq_().

◆ 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_.

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(), updateFreq_(), bpp::FullFrequenciesSet::updateFreq_(), bpp::MvaFrequenciesSet::updateFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::FullPerAACodonFrequenciesSet::updateFrequencies(), bpp::CodonFromIndependentFrequenciesSet::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().

◆ getGeneticCode()

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

inlinevirtual

Returns: The associated genetic code.

Implements bpp::CodonFrequenciesSet.

Definition at line 142 of file CodonFrequenciesSet.h.

References pgc_.

◆ getMethod()

unsigned short bpp::FullCodonFrequenciesSet::getMethod ( ) const

inline

Definition at line 160 of file CodonFrequenciesSet.h.

References sFreq_.

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().

◆ 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=()

FullCodonFrequenciesSet & FullCodonFrequenciesSet::operator= ( const FullCodonFrequenciesSet & fcfs )

Definition at line 112 of file CodonFrequenciesSet.cpp.

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

◆ setFrequencies()

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

virtual

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

Implements bpp::FrequenciesSet.

Definition at line 127 of file CodonFrequenciesSet.cpp.

References getAlphabet(), pgc_, sFreq_, and updateFreq_().

◆ 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 FullCodonFrequenciesSet::setNamespace ( const std::string & nameSpace )

Definition at line 121 of file CodonFrequenciesSet.cpp.

References sFreq_.

◆ updateFreq_()

void FullCodonFrequenciesSet::updateFreq_ ( )

protected

Definition at line 157 of file CodonFrequenciesSet.cpp.

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

Referenced by fireParameterChanged(), FullCodonFrequenciesSet(), and setFrequencies().

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::FullCodonFrequenciesSet::pgc_

protected

Definition at line 113 of file CodonFrequenciesSet.h.

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

◆ sFreq_

Simplex bpp::FullCodonFrequenciesSet::sFreq_

private

Simplex to handle the probabilities and the parameters.

Definition at line 121 of file CodonFrequenciesSet.h.

Referenced by fireParameterChanged(), FullCodonFrequenciesSet(), getMethod(), operator=(), setFrequencies(), setNamespace(), and updateFreq_().

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

◆ FullCodonFrequenciesSet() [1/3]

◆ FullCodonFrequenciesSet() [2/3]

◆ FullCodonFrequenciesSet() [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()

◆ getMethod()

◆ 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]

◆ setNamespace()

◆ updateFreq_()

Member Data Documentation

◆ F0

◆ F1X4

◆ F3X4

◆ F61

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ pgc_

◆ sFreq_