the Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of stop codons set to zero. More...

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

Inheritance diagram for bpp::CodonFromUniqueFrequencySet:

Collaboration diagram for bpp::CodonFromUniqueFrequencySet:

Public Member Functions
	CodonFromUniqueFrequencySet (std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< FrequencySetInterface > pfreq, const std::string &name="Codon", const std::string &mgmtStopCodon="quadratic")
	Constructor from a CodonAlphabet* and a std::shared_ptr<FrequencySet> repeated three times. More...

	CodonFromUniqueFrequencySet (const CodonFromUniqueFrequencySet &iwfs)

virtual	~CodonFromUniqueFrequencySet ()

CodonFromUniqueFrequencySet &	operator= (const CodonFromUniqueFrequencySet &iwfs)

CodonFromUniqueFrequencySet *	clone () const override

std::shared_ptr< const CodonAlphabet >	getCodonAlphabet () const override

std::shared_ptr< const GeneticCode >	getGeneticCode () const override

void	updateFrequencies () override
	Update the frequencies given the parameters. More...

std::string	getMgmtStopCodon () const
	Retrieve the mgmt method for the stop codons. More...

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

virtual void	fireParameterChanged (const ParameterList &pl) override

virtual void	setFrequencies (const std::vector< double > &frequencies) override
	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. The frequencies of each letter is the average of the frequencies of that letter at all positions. More...

const FrequencySetInterface &	frequencySetForLetter (size_t i) const override
	Return the n-th FrequencySet&. More...

size_t	getLength () const override

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

std::string	getDescription () const

std::shared_ptr< const CoreWordAlphabet >	getWordAlphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

const Alphabet &	alphabet () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

const Vdouble &	getFrequencies () const override

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

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

size_t	getNumberOfFrequencies () const override

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

void	unaliasParameters (const std::string &p1, const std::string &p2)

const ParameterList &	getIndependentParameters () const

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

void	normalize ()

bool	hasIndependentParameter (const std::string &name) const

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

std::string	getFrom (const std::string &name) const

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

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

size_t	getSizeFromVector (const std::vector< std::unique_ptr< FrequencySetInterface >> &freqVector) override

ParameterList &	getParameters_ () override

std::vector< double > &	getFrequencies_ ()

double &	getFreq_ (size_t i)

const double &	getFreq_ (size_t i) const

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

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

Protected Attributes
std::unique_ptr< FrequencySetInterface >	pFreq_

std::string	NestedPrefix_

size_t	length_

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

unsigned short	mgmtStopCodon_

std::shared_ptr< const GeneticCode >	pgc_

std::shared_ptr< const Alphabet >	alphabet_

std::shared_ptr< const StateMapInterface >	stateMap_

std::vector< double >	freq_

std::string	name_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Detailed Description

the Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of stop codons set to zero.

Author: Laurent Guéguen

Definition at line 427 of file CodonFrequencySet.h.

Constructor & Destructor Documentation

◆ CodonFromUniqueFrequencySet() [1/2]

CodonFromUniqueFrequencySet::CodonFromUniqueFrequencySet	(	std::shared_ptr< const GeneticCode >	gCode,
		std::unique_ptr< FrequencySetInterface >	pfreq,
		const std::string &	name = `"Codon"`,
		const std::string &	mgmtStopCodon = `"quadratic"`
	)

Constructor from a CodonAlphabet* and a std::shared_ptr<FrequencySet> repeated three times.

Parameters

gCode	a pointer to a genetic code.
pfreq	a pointer to the nucleotidic FrequencySet
name	the optional name of the FrequencySet (default codon)
mgmtStopCodon	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 524 of file CodonFrequencySet.cpp.

References getCodonAlphabet(), mgmtStopCodon_, mStopNeigh_, pgc_, bpp::pow(), and updateFrequencies().

Referenced by clone().

◆ CodonFromUniqueFrequencySet() [2/2]

CodonFromUniqueFrequencySet::CodonFromUniqueFrequencySet ( const CodonFromUniqueFrequencySet & iwfs )

Definition at line 568 of file CodonFrequencySet.cpp.

References updateFrequencies().

◆ ~CodonFromUniqueFrequencySet()

virtual bpp::CodonFromUniqueFrequencySet::~CodonFromUniqueFrequencySet ( )

inlinevirtual

Definition at line 466 of file CodonFrequencySet.h.

Member Function Documentation

◆ alphabet() [1/2]

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

pure virtualinherited

Returns: The alphabet associated to this set.

Implemented in bpp::AbstractFrequencySet.

◆ alphabet() [2/2]

const Alphabet& bpp::AbstractFrequencySet::alphabet ( ) const

inlineoverridevirtualinherited

Returns: The alphabet associated to this set.

Implements bpp::FrequencySetInterface.

Definition at line 142 of file FrequencySet.h.

References bpp::AbstractFrequencySet::alphabet_.

◆ clone()

CodonFromUniqueFrequencySet* bpp::CodonFromUniqueFrequencySet::clone ( ) const

inlineoverridevirtual

Implements bpp::CodonFrequencySetInterface.

Definition at line 470 of file CodonFrequencySet.h.

References CodonFromUniqueFrequencySet().

◆ fireParameterChanged()

void WordFromUniqueFrequencySet::fireParameterChanged ( const ParameterList & pl )

overridevirtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 319 of file WordFrequencySet.cpp.

References bpp::WordFromUniqueFrequencySet::pFreq_, and bpp::WordFromUniqueFrequencySet::updateFrequencies().

◆ frequencySetForLetter()

const FrequencySetInterface& bpp::WordFromUniqueFrequencySet::frequencySetForLetter ( size_t i ) const

inlineoverridevirtualinherited

Return the n-th FrequencySet&.

Implements bpp::WordFrequencySetInterface.

Definition at line 210 of file WordFrequencySet.h.

References bpp::WordFromUniqueFrequencySet::pFreq_.

◆ getAlphabet() [1/2]

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().

◆ getAlphabet() [2/2]

std::shared_ptr<const Alphabet> bpp::AbstractFrequencySet::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns: The alphabet associated to this set.

Implements bpp::FrequencySetInterface.

Definition at line 140 of file FrequencySet.h.

References bpp::AbstractFrequencySet::alphabet_.

Referenced by bpp::FullCodonFrequencySet::getCodonAlphabet(), bpp::FixedCodonFrequencySet::getCodonAlphabet(), bpp::FullPerAACodonFrequencySet::getCodonAlphabet(), bpp::CodonFromIndependentFrequencySet::getCodonAlphabet(), bpp::GCFrequencySet::getNucleicAlphabet(), bpp::FullNucleotideFrequencySet::getNucleicAlphabet(), bpp::MvaFrequencySet::getProteicAlphabet(), bpp::AbstractWordFrequencySet::getWordAlphabet(), bpp::UserFrequencySet::readFromFile_(), bpp::FullCodonFrequencySet::setFrequencies(), and bpp::FullFrequencySet::updateFreq_().

◆ getAlphabetStatesFrequencies() [1/2]

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.

◆ getAlphabetStatesFrequencies() [2/2]

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

overridevirtualinherited

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

Implements bpp::FrequencySetInterface.

Definition at line 57 of file FrequencySet.cpp.

◆ getCodonAlphabet()

shared_ptr< const CodonAlphabet > CodonFromUniqueFrequencySet::getCodonAlphabet ( ) const

overridevirtual

Implements bpp::CodonFrequencySetInterface.

Definition at line 562 of file CodonFrequencySet.cpp.

References bpp::AbstractWordFrequencySet::getWordAlphabet().

Referenced by CodonFromUniqueFrequencySet(), and updateFrequencies().

◆ getDescription()

string WordFromUniqueFrequencySet::getDescription ( ) const

inherited

Definition at line 403 of file WordFrequencySet.cpp.

References bpp::AbstractFrequencySet::getName(), bpp::WordFromUniqueFrequencySet::length_, bpp::WordFromUniqueFrequencySet::pFreq_, and bpp::TextTools::toString().

◆ getFreq_() [1/2]

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

inlineprotectedinherited

Definition at line 179 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::GCFrequencySet::fireParameterChanged(), bpp::FullNucleotideFrequencySet::fireParameterChanged(), bpp::FixedCodonFrequencySet::FixedCodonFrequencySet(), bpp::FullNucleotideFrequencySet::FullNucleotideFrequencySet(), bpp::GCFrequencySet::GCFrequencySet(), bpp::UserFrequencySet::readFromFile_(), bpp::FixedCodonFrequencySet::setFrequencies(), bpp::UserCodonFrequencySet::setFrequencies(), bpp::GCFrequencySet::setFrequencies(), bpp::FullCodonFrequencySet::updateFreq_(), bpp::FullFrequencySet::updateFreq_(), bpp::MvaFrequencySet::updateFrequencies(), bpp::WordFromIndependentFrequencySet::updateFrequencies(), bpp::WordFromUniqueFrequencySet::updateFrequencies(), bpp::CodonFromIndependentFrequencySet::updateFrequencies(), updateFrequencies(), and bpp::FullPerAACodonFrequencySet::updateFrequencies_().

◆ getFreq_() [2/2]

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

inlineprotectedinherited

Definition at line 180 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

◆ getFrequencies() [1/2]

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::CodonDistanceFrequenciesSubstitutionModel::setFreq(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq(), bpp::DFPDistanceFrequenciesSubstitutionModel::setFreq(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

◆ getFrequencies() [2/2]

const Vdouble& bpp::AbstractFrequencySet::getFrequencies ( ) const

inlineoverridevirtualinherited

Returns: The frequencies values of the set.

Implements bpp::FrequencySetInterface.

Definition at line 148 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

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

◆ getFrequencies_()

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

inlineprotectedinherited

Definition at line 178 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::UserFrequencySet::readFromFile_().

◆ getFrequencySetForCodons()

unique_ptr< CodonFrequencySetInterface > CodonFrequencySetInterface::getFrequencySetForCodons	(	short	option,
		std::shared_ptr< const GeneticCode >	gCode,
		const std::string &	mgmtStopCodon = `"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 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 bpp::CodonFrequencySetInterface::F0, bpp::CodonFrequencySetInterface::F1X4, bpp::CodonFrequencySetInterface::F3X4, and bpp::CodonFrequencySetInterface::F61.

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

◆ getGeneticCode()

std::shared_ptr<const GeneticCode> bpp::CodonFromUniqueFrequencySet::getGeneticCode ( ) const

inlineoverridevirtual

Returns: The associated genetic code.

Implements bpp::CodonFrequencySetInterface.

Definition at line 474 of file CodonFrequencySet.h.

References pgc_.

◆ getLength()

size_t bpp::WordFromUniqueFrequencySet::getLength ( ) const

inlineoverridevirtualinherited

@ brief Return the length of the words

Reimplemented from bpp::AbstractWordFrequencySet.

Definition at line 215 of file WordFrequencySet.h.

References bpp::WordFromUniqueFrequencySet::length_.

◆ getMgmtStopCodon()

std::string bpp::CodonFromUniqueFrequencySet::getMgmtStopCodon ( ) const

inline

Retrieve the mgmt method for the stop codons.

Definition at line 484 of file CodonFrequencySet.h.

References mgmtStopCodon_.

◆ getName() [1/2]

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

pure virtualinherited

Implemented in bpp::AbstractFrequencySet.

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

◆ getName() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::FrequencySetInterface.

Definition at line 165 of file FrequencySet.h.

References bpp::AbstractFrequencySet::name_.

Referenced by bpp::WordFromIndependentFrequencySet::getDescription(), and bpp::WordFromUniqueFrequencySet::getDescription().

◆ getNumberOfFrequencies() [1/2]

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.

◆ getNumberOfFrequencies() [2/2]

size_t bpp::AbstractFrequencySet::getNumberOfFrequencies ( ) const

inlineoverridevirtualinherited

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

Implements bpp::FrequencySetInterface.

Definition at line 163 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::FromModelFrequencySet::setFrequencies(), bpp::FixedFrequencySet::setFrequencies(), and bpp::UserFrequencySet::setFrequencies().

◆ getSizeFromVector()

size_t AbstractWordFrequencySet::getSizeFromVector ( const std::vector< std::unique_ptr< FrequencySetInterface >> & freqVector )

overrideprotectedvirtualinherited

Implements bpp::WordFrequencySetInterface.

Definition at line 12 of file WordFrequencySet.cpp.

Referenced by bpp::WordFromIndependentFrequencySet::WordFromIndependentFrequencySet().

◆ getStateMap() [1/2]

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.

◆ getStateMap() [2/2]

std::shared_ptr<const StateMapInterface> bpp::AbstractFrequencySet::getStateMap ( ) const

inlineoverridevirtualinherited

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

Implements bpp::FrequencySetInterface.

Definition at line 146 of file FrequencySet.h.

References bpp::AbstractFrequencySet::stateMap_.

◆ getWordAlphabet()

std::shared_ptr<const CoreWordAlphabet> bpp::AbstractWordFrequencySet::getWordAlphabet ( ) const

inlineoverridevirtualinherited

Implements bpp::WordFrequencySetInterface.

Definition at line 72 of file WordFrequencySet.h.

References bpp::AbstractFrequencySet::getAlphabet().

Referenced by getCodonAlphabet(), bpp::AbstractWordFrequencySet::getLength(), bpp::WordFromIndependentFrequencySet::setFrequencies(), bpp::WordFromUniqueFrequencySet::setFrequencies(), bpp::WordFromIndependentFrequencySet::updateFrequencies(), and bpp::WordFromUniqueFrequencySet::updateFrequencies().

◆ normalize()

void bpp::AbstractFrequencySet::normalize ( )

inlineinherited

Definition at line 167 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::FullPerAACodonFrequencySet::updateFrequencies_().

◆ operator=()

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

Definition at line 577 of file CodonFrequencySet.cpp.

References mgmtStopCodon_, mStopNeigh_, bpp::WordFromUniqueFrequencySet::operator=(), and pgc_.

◆ setFrequencies() [1/2]

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

overridevirtualinherited

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. The frequencies of each letter is the average of the frequencies of that letter at all positions.

Implements bpp::FrequencySetInterface.

Definition at line 347 of file WordFrequencySet.cpp.

References bpp::AbstractWordFrequencySet::getWordAlphabet(), bpp::WordFromUniqueFrequencySet::length_, bpp::AbstractParameterAliasable::matchParametersValues(), bpp::WordFromUniqueFrequencySet::pFreq_, bpp::TextTools::toString(), and bpp::WordFromUniqueFrequencySet::updateFrequencies().

◆ setFrequencies() [2/2]

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

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

◆ setFrequencies_()

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

inlineprotectedinherited

Definition at line 181 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::FromModelFrequencySet::fireParameterChanged(), bpp::MarkovModulatedFrequencySet::fireParameterChanged(), bpp::FixedFrequencySet::FixedFrequencySet(), bpp::FromModelFrequencySet::FromModelFrequencySet(), bpp::MarkovModulatedFrequencySet::MarkovModulatedFrequencySet(), bpp::FixedFrequencySet::setFrequencies(), bpp::UserFrequencySet::setFrequencies(), bpp::FullNucleotideFrequencySet::setFrequencies(), and bpp::MvaFrequencySet::updateFrequencies().

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

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

overridevirtualinherited

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::FrequencySetInterface.

Definition at line 28 of file FrequencySet.cpp.

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

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_().

◆ setNamespace()

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

overridevirtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 391 of file WordFrequencySet.cpp.

References bpp::WordFromUniqueFrequencySet::length_, bpp::WordFromUniqueFrequencySet::NestedPrefix_, bpp::WordFromUniqueFrequencySet::pFreq_, bpp::AbstractParameterAliasable::setNamespace(), and bpp::TextTools::toString().

◆ stateMap() [1/2]

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

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequencySet.

◆ stateMap() [2/2]

const StateMapInterface& bpp::AbstractFrequencySet::stateMap ( ) const

inlineoverridevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::FrequencySetInterface.

Definition at line 144 of file FrequencySet.h.

References bpp::AbstractFrequencySet::stateMap_.

Referenced by bpp::FixedFrequencySet::FixedFrequencySet(), bpp::FullFrequencySet::FullFrequencySet(), bpp::FromModelFrequencySet::setFrequencies(), and bpp::FullPerAACodonFrequencySet::updateFrequencies_().

◆ updateFrequencies()

void CodonFromUniqueFrequencySet::updateFrequencies ( )

overridevirtual

Update the frequencies given the parameters.

Reimplemented from bpp::WordFromUniqueFrequencySet.

Definition at line 586 of file CodonFrequencySet.cpp.

References getCodonAlphabet(), bpp::AbstractFrequencySet::getFreq_(), mgmtStopCodon_, mStopNeigh_, pgc_, bpp::pow(), and bpp::WordFromUniqueFrequencySet::updateFrequencies().

Referenced by CodonFromUniqueFrequencySet().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractFrequencySet::alphabet_

privateinherited

Definition at line 104 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::alphabet(), bpp::AbstractFrequencySet::getAlphabet(), and bpp::AbstractFrequencySet::operator=().

◆ F0

const short CodonFrequencySetInterface::F0 = 0

staticinherited

Definition at line 62 of file CodonFrequencySet.h.

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

◆ F1X4

const short CodonFrequencySetInterface::F1X4 = 1

staticinherited

Definition at line 63 of file CodonFrequencySet.h.

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

◆ F3X4

const short CodonFrequencySetInterface::F3X4 = 2

staticinherited

Definition at line 64 of file CodonFrequencySet.h.

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

◆ F61

const short CodonFrequencySetInterface::F61 = 3

staticinherited

Definition at line 65 of file CodonFrequencySet.h.

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

◆ freq_

std::vector<double> bpp::AbstractFrequencySet::freq_

privateinherited

Definition at line 106 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::getFreq_(), bpp::AbstractFrequencySet::getFrequencies(), bpp::AbstractFrequencySet::getFrequencies_(), bpp::AbstractFrequencySet::getNumberOfFrequencies(), bpp::AbstractFrequencySet::normalize(), bpp::AbstractFrequencySet::operator=(), and bpp::AbstractFrequencySet::setFrequencies_().

◆ 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().

◆ length_

size_t bpp::WordFromUniqueFrequencySet::length_

protectedinherited

Definition at line 163 of file WordFrequencySet.h.

Referenced by bpp::WordFromUniqueFrequencySet::getDescription(), bpp::WordFromUniqueFrequencySet::getLength(), bpp::WordFromUniqueFrequencySet::operator=(), bpp::WordFromUniqueFrequencySet::setFrequencies(), bpp::WordFromUniqueFrequencySet::setNamespace(), bpp::WordFromUniqueFrequencySet::updateFrequencies(), and bpp::WordFromUniqueFrequencySet::WordFromUniqueFrequencySet().

◆ mgmtStopCodon_

unsigned short bpp::CodonFromUniqueFrequencySet::mgmtStopCodon_

private

Definition at line 435 of file CodonFrequencySet.h.

Referenced by CodonFromUniqueFrequencySet(), getMgmtStopCodon(), operator=(), and updateFrequencies().

◆ mStopNeigh_

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

private

Definition at line 433 of file CodonFrequencySet.h.

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

◆ name_

std::string bpp::AbstractFrequencySet::name_

privateinherited

Definition at line 107 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::getName(), and bpp::AbstractFrequencySet::operator=().

◆ NestedPrefix_

std::string bpp::WordFromUniqueFrequencySet::NestedPrefix_

protectedinherited

Definition at line 162 of file WordFrequencySet.h.

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

◆ pFreq_

std::unique_ptr<FrequencySetInterface> bpp::WordFromUniqueFrequencySet::pFreq_

protectedinherited

Definition at line 161 of file WordFrequencySet.h.

◆ pgc_

std::shared_ptr<const GeneticCode> bpp::CodonFromUniqueFrequencySet::pgc_

private

Definition at line 437 of file CodonFrequencySet.h.

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

◆ stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractFrequencySet::stateMap_

privateinherited

Definition at line 105 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::getStateMap(), bpp::AbstractFrequencySet::operator=(), and bpp::AbstractFrequencySet::stateMap().

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

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CodonFromUniqueFrequencySet() [1/2]

◆ CodonFromUniqueFrequencySet() [2/2]

◆ ~CodonFromUniqueFrequencySet()

Member Function Documentation

◆ alphabet() [1/2]

◆ alphabet() [2/2]

◆ clone()

◆ fireParameterChanged()

◆ frequencySetForLetter()

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getAlphabetStatesFrequencies() [1/2]

◆ getAlphabetStatesFrequencies() [2/2]

◆ getCodonAlphabet()

◆ getDescription()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_()

◆ getFrequencySetForCodons()

◆ getGeneticCode()

◆ getLength()

◆ getMgmtStopCodon()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getSizeFromVector()

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ getWordAlphabet()

◆ normalize()

◆ operator=()

◆ setFrequencies() [1/2]

◆ setFrequencies() [2/2]

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

◆ setNamespace()

◆ stateMap() [1/2]

◆ stateMap() [2/2]

◆ updateFrequencies()

Member Data Documentation

◆ alphabet_

◆ F0

◆ F1X4

◆ F3X4

◆ F61

◆ freq_

◆ FREQUENCE_CONSTRAINT_CENTI

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ length_

◆ mgmtStopCodon_

◆ mStopNeigh_

◆ name_

◆ NestedPrefix_

◆ pFreq_

◆ pgc_

◆ stateMap_