the Frequencies in words are the product of Independent Frequencies in letters More...

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

Inheritance diagram for bpp::WordFromIndependentFrequencySet:

Collaboration diagram for bpp::WordFromIndependentFrequencySet:

Public Member Functions
	WordFromIndependentFrequencySet (std::shared_ptr< const WordAlphabet > pWA, std::vector< std::unique_ptr< FrequencySetInterface >> &freqVector, const std::string &prefix="", const std::string &name="WordFromIndependent")
	Constructor from a WordAlphabet* and a vector of different std::shared_ptr<FrequencySet>. Throws an Exception if their lengths do not match. More...

	WordFromIndependentFrequencySet (std::shared_ptr< const CodonAlphabet > pWA, std::vector< std::unique_ptr< FrequencySetInterface >> &freqVector, const std::string &prefix="", const std::string &name="WordFromIndependent")

	WordFromIndependentFrequencySet (const WordFromIndependentFrequencySet &iwfs)

virtual	~WordFromIndependentFrequencySet ()

WordFromIndependentFrequencySet &	operator= (const WordFromIndependentFrequencySet &iwfs)

WordFromIndependentFrequencySet *	clone () const override

void	fireParameterChanged (const ParameterList &pl) override

virtual void	updateFrequencies ()

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

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

virtual size_t	getLength () const override
	Return the length of the words. More...

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

std::string	getDescription () const

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

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0

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

virtual const Alphabet &	alphabet () const =0

const Alphabet &	alphabet () const override

virtual const StateMapInterface &	stateMap () const =0

const StateMapInterface &	stateMap () const override

virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0

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

virtual const Vdouble &	getFrequencies () const =0

const Vdouble &	getFrequencies () const override

virtual const std::map< int, double >	getAlphabetStatesFrequencies () const =0

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

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...

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...

virtual std::string	getName () const =0

std::string	getName () const override

virtual size_t	getNumberOfFrequencies () const =0

size_t	getNumberOfFrequencies () const override

virtual size_t	getNumberOfIndependentParameters () const=0

size_t	getNumberOfIndependentParameters () const

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

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

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

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

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

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

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

virtual std::map< std::string, std::string >	getAliases () const=0

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

virtual bool	hasParameter (const std::string &name) const=0

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

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

virtual const Parameter &	parameter (const std::string &name) const=0

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

virtual double	getParameterValue (const std::string &name) const=0

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

virtual void	setParameterValue (const std::string &name, double value)=0

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

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

virtual void	removeConstraint (const std::string &name)=0

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

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

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

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

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

virtual ParameterList &	getParameters_ ()=0

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::vector< std::unique_ptr< FrequencySetInterface > >	vFreq_

std::vector< std::string >	vNestedPrefix_

Private Attributes
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 words are the product of Independent Frequencies in letters

Author: Laurent Guéguen

Definition at line 91 of file WordFrequencySet.h.

Constructor & Destructor Documentation

◆ WordFromIndependentFrequencySet() [1/3]

WordFromIndependentFrequencySet::WordFromIndependentFrequencySet	(	std::shared_ptr< const WordAlphabet >	pWA,
		std::vector< std::unique_ptr< FrequencySetInterface >> &	freqVector,
		const std::string &	prefix = `""`,
		const std::string &	name = `"WordFromIndependent"`
	)

Constructor from a WordAlphabet* and a vector of different std::shared_ptr<FrequencySet>. Throws an Exception if their lengths do not match.

Definition at line 41 of file WordFrequencySet.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractWordFrequencySet::getSizeFromVector(), bpp::TextTools::toString(), updateFrequencies(), vFreq_, and vNestedPrefix_.

Referenced by clone().

◆ WordFromIndependentFrequencySet() [2/3]

WordFromIndependentFrequencySet::WordFromIndependentFrequencySet	(	std::shared_ptr< const CodonAlphabet >	pWA,
		std::vector< std::unique_ptr< FrequencySetInterface >> &	freqVector,
		const std::string &	prefix = `""`,
		const std::string &	name = `"WordFromIndependent"`
	)

Definition at line 69 of file WordFrequencySet.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractWordFrequencySet::getSizeFromVector(), bpp::TextTools::toString(), updateFrequencies(), vFreq_, and vNestedPrefix_.

◆ WordFromIndependentFrequencySet() [3/3]

WordFromIndependentFrequencySet::WordFromIndependentFrequencySet ( const WordFromIndependentFrequencySet & iwfs )

Definition at line 98 of file WordFrequencySet.cpp.

References updateFrequencies(), and vFreq_.

◆ ~WordFromIndependentFrequencySet()

WordFromIndependentFrequencySet::~WordFromIndependentFrequencySet ( )

virtual

Definition at line 110 of file WordFrequencySet.cpp.

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()

WordFromIndependentFrequencySet* bpp::WordFromIndependentFrequencySet::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractWordFrequencySet.

Definition at line 121 of file WordFrequencySet.h.

References WordFromIndependentFrequencySet().

◆ fireParameterChanged()

void WordFromIndependentFrequencySet::fireParameterChanged ( const ParameterList & pl )

overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 129 of file WordFrequencySet.cpp.

References updateFrequencies(), and vFreq_.

◆ frequencySetForLetter()

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

inlineoverridevirtual

Return the n-th FrequencySet&.

Implements bpp::WordFrequencySetInterface.

Definition at line 142 of file WordFrequencySet.h.

References vFreq_.

◆ 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.

◆ getDescription()

std::string WordFromIndependentFrequencySet::getDescription ( ) const

Definition at line 225 of file WordFrequencySet.cpp.

References bpp::AbstractFrequencySet::getName(), and vFreq_.

◆ 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(), updateFrequencies(), bpp::WordFromUniqueFrequencySet::updateFrequencies(), bpp::CodonFromIndependentFrequencySet::updateFrequencies(), bpp::CodonFromUniqueFrequencySet::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_().

◆ getLength()

size_t WordFromIndependentFrequencySet::getLength ( ) const

overridevirtual

Return the length of the words.

Reimplemented from bpp::AbstractWordFrequencySet.

Definition at line 211 of file WordFrequencySet.cpp.

References vFreq_.

◆ 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 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 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 bpp::CodonFromUniqueFrequencySet::getCodonAlphabet(), bpp::AbstractWordFrequencySet::getLength(), setFrequencies(), bpp::WordFromUniqueFrequencySet::setFrequencies(), 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=()

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

Definition at line 113 of file WordFrequencySet.cpp.

References bpp::AbstractWordFrequencySet::operator=(), updateFrequencies(), vFreq_, and vNestedPrefix_.

Referenced by bpp::CodonFromIndependentFrequencySet::operator=().

◆ setFrequencies()

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

overridevirtual

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::FrequencySetInterface.

Definition at line 169 of file WordFrequencySet.cpp.

References bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractWordFrequencySet::getWordAlphabet(), bpp::AbstractParameterAliasable::matchParametersValues(), bpp::TextTools::toString(), updateFrequencies(), and vFreq_.

◆ 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 WordFromIndependentFrequencySet::setNamespace ( const std::string & prefix )

overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 216 of file WordFrequencySet.cpp.

References bpp::AbstractParameterAliasable::setNamespace(), bpp::TextTools::toString(), vFreq_, and vNestedPrefix_.

◆ 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 WordFromIndependentFrequencySet::updateFrequencies ( )

virtual

Reimplemented in bpp::CodonFromIndependentFrequencySet.

Definition at line 143 of file WordFrequencySet.cpp.

References bpp::AbstractFrequencySet::getFreq_(), bpp::AbstractWordFrequencySet::getWordAlphabet(), and vFreq_.

Referenced by fireParameterChanged(), operator=(), setFrequencies(), bpp::CodonFromIndependentFrequencySet::updateFrequencies(), and WordFromIndependentFrequencySet().

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=().

◆ 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().

◆ name_

std::string bpp::AbstractFrequencySet::name_

privateinherited

Definition at line 107 of file FrequencySet.h.

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

◆ 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().

◆ vFreq_

std::vector<std::unique_ptr<FrequencySetInterface> > bpp::WordFromIndependentFrequencySet::vFreq_

protected

Definition at line 95 of file WordFrequencySet.h.

Referenced by fireParameterChanged(), frequencySetForLetter(), getDescription(), getLength(), operator=(), setFrequencies(), setNamespace(), updateFrequencies(), and WordFromIndependentFrequencySet().

◆ vNestedPrefix_

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

protected

Definition at line 96 of file WordFrequencySet.h.

Referenced by operator=(), setNamespace(), and WordFromIndependentFrequencySet().

The documentation for this class was generated from the following files:

Bpp/Phyl/Model/FrequencySet/WordFrequencySet.h
Bpp/Phyl/Model/FrequencySet/WordFrequencySet.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ WordFromIndependentFrequencySet() [1/3]

◆ WordFromIndependentFrequencySet() [2/3]

◆ WordFromIndependentFrequencySet() [3/3]

◆ ~WordFromIndependentFrequencySet()

Member Function Documentation

◆ alphabet() [1/2]

◆ alphabet() [2/2]

◆ clone()

◆ fireParameterChanged()

◆ frequencySetForLetter()

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getAlphabetStatesFrequencies() [1/2]

◆ getAlphabetStatesFrequencies() [2/2]

◆ getDescription()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_()

◆ getLength()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getSizeFromVector()

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ getWordAlphabet()

◆ normalize()

◆ operator=()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

◆ setNamespace()

◆ stateMap() [1/2]

◆ stateMap() [2/2]

◆ updateFrequencies()

Member Data Documentation

◆ alphabet_

◆ freq_

◆ FREQUENCE_CONSTRAINT_CENTI

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ name_

◆ stateMap_

◆ vFreq_

◆ vNestedPrefix_