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

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

Inheritance diagram for bpp::WordFromIndependentFrequenciesSet:

Collaboration diagram for bpp::WordFromIndependentFrequenciesSet:

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

	WordFromIndependentFrequenciesSet (const WordFromIndependentFrequenciesSet &iwfs)

	~WordFromIndependentFrequenciesSet ()

WordFromIndependentFrequenciesSet &	operator= (const WordFromIndependentFrequenciesSet &iwfs)

WordFromIndependentFrequenciesSet *	clone () const

void	fireParameterChanged (const ParameterList &pl)

virtual void	updateFrequencies ()

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

const FrequenciesSet &	getFrequenciesSetForLetter (size_t i) const

virtual size_t	getLength () const

void	setNamespace (const std::string &prefix)

std::string	getDescription () const

const WordAlphabet *	getAlphabet () const

virtual const StateMap &	getStateMap () const =0

const StateMap &	getStateMap () const

virtual const std::vector< double >	getFrequencies () const =0

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

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

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

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)
	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

virtual size_t	getNumberOfFrequencies () const =0

size_t	getNumberOfFrequencies () const

void	normalize ()

Static Public Attributes
static IntervalConstraint	FREQUENCE_CONSTRAINT_SMALL

static IntervalConstraint	FREQUENCE_CONSTRAINT_MILLI

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

std::vector< double > &	getFrequencies_ ()

double &	getFreq_ (size_t i)

const double &	getFreq_ (size_t i) const

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

Protected Attributes
std::vector< FrequenciesSet * >	vFreq_

std::vector< std::string >	vNestedPrefix_

Detailed Description

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

Author: Laurent Guéguen

Definition at line 139 of file WordFrequenciesSet.h.

Constructor & Destructor Documentation

◆ WordFromIndependentFrequenciesSet() [1/2]

WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet	(	const WordAlphabet *	pWA,
		const std::vector< FrequenciesSet *> &	freqVector,
		const std::string &	prefix = `""`,
		const std::string &	name = `"WordFromIndependent"`
	)

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

Definition at line 77 of file WordFrequenciesSet.cpp.

References bpp::AbstractWordFrequenciesSet::getSizeFromVector(), updateFrequencies(), vFreq_, and vNestedPrefix_.

Referenced by clone().

◆ WordFromIndependentFrequenciesSet() [2/2]

WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet ( const WordFromIndependentFrequenciesSet & iwfs )

Definition at line 102 of file WordFrequenciesSet.cpp.

References updateFrequencies(), and vFreq_.

◆ ~WordFromIndependentFrequenciesSet()

WordFromIndependentFrequenciesSet::~WordFromIndependentFrequenciesSet ( )

Definition at line 114 of file WordFrequenciesSet.cpp.

References vFreq_.

Member Function Documentation

◆ clone()

WordFromIndependentFrequenciesSet* bpp::WordFromIndependentFrequenciesSet::clone ( ) const

inlinevirtual

Implements bpp::AbstractWordFrequenciesSet.

Definition at line 159 of file WordFrequenciesSet.h.

References WordFromIndependentFrequenciesSet().

◆ fireParameterChanged()

void WordFromIndependentFrequenciesSet::fireParameterChanged ( const ParameterList & pl )

Definition at line 143 of file WordFrequenciesSet.cpp.

References updateFrequencies(), and vFreq_.

◆ getAlphabet()

const WordAlphabet* bpp::AbstractWordFrequenciesSet::getAlphabet ( ) const

inlinevirtualinherited

Returns: The alphabet associated to this set.

Reimplemented from bpp::AbstractFrequenciesSet.

Definition at line 118 of file WordFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::getAlphabet().

Referenced by bpp::CodonFromIndependentFrequenciesSet::getAlphabet(), bpp::CodonFromUniqueFrequenciesSet::getAlphabet(), bpp::AbstractWordFrequenciesSet::getLength(), setFrequencies(), bpp::WordFromUniqueFrequenciesSet::setFrequencies(), updateFrequencies(), and bpp::WordFromUniqueFrequenciesSet::updateFrequencies().

◆ getAlphabetStatesFrequencies() [1/2]

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

pure virtualinherited

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

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel::setFreq().

◆ getAlphabetStatesFrequencies() [2/2]

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

virtualinherited

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

Implements bpp::FrequenciesSet.

Definition at line 79 of file FrequenciesSet.cpp.

◆ getDescription()

std::string WordFromIndependentFrequenciesSet::getDescription ( ) const

Definition at line 239 of file WordFrequenciesSet.cpp.

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

◆ getFreq_() [1/2]

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

inlineprotectedinherited

Definition at line 203 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::GCFrequenciesSet::fireParameterChanged(), bpp::FullNucleotideFrequenciesSet::fireParameterChanged(), bpp::FixedCodonFrequenciesSet::FixedCodonFrequenciesSet(), bpp::FixedFrequenciesSet::FixedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::GCFrequenciesSet::GCFrequenciesSet(), bpp::GCFrequenciesSet::setFrequencies(), bpp::FixedCodonFrequenciesSet::setFrequencies(), bpp::FullCodonFrequenciesSet::updateFreq_(), bpp::FullFrequenciesSet::updateFreq_(), bpp::MvaFrequenciesSet::updateFrequencies(), 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_.

◆ getFrequenciesSetForLetter()

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

inlinevirtual

@ brief Return the n-th FrequenciesSet&

Implements bpp::WordFrequenciesSet.

Definition at line 177 of file WordFrequenciesSet.h.

References vFreq_.

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

◆ getLength()

size_t WordFromIndependentFrequenciesSet::getLength ( ) const

virtual

@ brief Return the length of the words

Reimplemented from bpp::AbstractWordFrequenciesSet.

Definition at line 225 of file WordFrequenciesSet.cpp.

References vFreq_.

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

◆ getName() [1/2]

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

pure virtualinherited

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::AbstractCodonFrequenciesSubstitutionModel::AbstractCodonFrequenciesSubstitutionModel(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::WordFromUniqueFrequenciesSet::getDescription(), bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(), bpp::BppOFrequenciesSetFormat::read(), and bpp::BppOFrequenciesSetFormat::write().

◆ getName() [2/2]

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

inlinevirtualinherited

Implements bpp::FrequenciesSet.

Definition at line 191 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::name_.

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

◆ getNumberOfFrequencies() [1/2]

virtual size_t bpp::FrequenciesSet::getNumberOfFrequencies ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractFrequenciesSet.

◆ getNumberOfFrequencies() [2/2]

size_t bpp::AbstractFrequenciesSet::getNumberOfFrequencies ( ) const

inlinevirtualinherited

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

Implements bpp::FrequenciesSet.

Definition at line 189 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

◆ getSizeFromVector()

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

protectedvirtualinherited

Implements bpp::WordFrequenciesSet.

Definition at line 48 of file WordFrequenciesSet.cpp.

Referenced by WordFromIndependentFrequenciesSet().

◆ getStateMap() [1/2]

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

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequenciesSet.

◆ getStateMap() [2/2]

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

inlinevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::FrequenciesSet.

Definition at line 172 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::stateMap_.

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

◆ normalize()

void bpp::AbstractFrequenciesSet::normalize ( )

inlineinherited

Definition at line 193 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

◆ operator=()

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

Definition at line 122 of file WordFrequenciesSet.cpp.

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

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

◆ setFrequencies()

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

virtual

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

Implements bpp::FrequenciesSet.

Definition at line 183 of file WordFrequenciesSet.cpp.

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

◆ setFrequencies_()

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

inlineprotectedinherited

Definition at line 205 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

virtual void bpp::FrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > & frequencies )

pure virtualinherited

Set the Frequencies from the one of the map which keys match with a letter of the Alphabet. The frequencies are normalized so that the matching values sum 1.

Parameters

frequencies The set of frequencies to match.

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::BppOFrequenciesSetFormat::initialize_(), bpp::AbstractCodonFitnessSubstitutionModel::setFreq(), bpp::AbstractCodonFrequenciesSubstitutionModel::setFreq(), and bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::setFreq().

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

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

virtualinherited

Set the Frequencies from the one of the map which keys match with a letter of the Alphabet. The frequencies are normalized so that the matching values sum 1.

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

Parameters

frequencies The set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

◆ setNamespace()

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

Definition at line 230 of file WordFrequenciesSet.cpp.

References vFreq_, and vNestedPrefix_.

◆ updateFrequencies()

void WordFromIndependentFrequenciesSet::updateFrequencies ( )

virtual

Reimplemented in bpp::CodonFromIndependentFrequenciesSet.

Definition at line 157 of file WordFrequenciesSet.cpp.

References bpp::AbstractWordFrequenciesSet::getAlphabet(), bpp::AbstractFrequenciesSet::getFreq_(), and vFreq_.

Referenced by fireParameterChanged(), operator=(), setFrequencies(), bpp::CodonFromIndependentFrequenciesSet::updateFrequencies(), and WordFromIndependentFrequenciesSet().

Member Data Documentation

◆ 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().

◆ vFreq_

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

protected

Definition at line 143 of file WordFrequenciesSet.h.

Referenced by fireParameterChanged(), getDescription(), getFrequenciesSetForLetter(), getLength(), operator=(), setFrequencies(), setNamespace(), updateFrequencies(), WordFromIndependentFrequenciesSet(), and ~WordFromIndependentFrequenciesSet().

◆ vNestedPrefix_

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

protected

Definition at line 144 of file WordFrequenciesSet.h.

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

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

Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h
Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ WordFromIndependentFrequenciesSet() [1/2]

◆ WordFromIndependentFrequenciesSet() [2/2]

◆ ~WordFromIndependentFrequenciesSet()

Member Function Documentation

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies() [1/2]

◆ getAlphabetStatesFrequencies() [2/2]

◆ getDescription()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_()

◆ getFrequenciesSetForLetter()

◆ getLength()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getSizeFromVector()

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ normalize()

◆ operator=()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

◆ setNamespace()

◆ updateFrequencies()

Member Data Documentation

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ vFreq_

◆ vNestedPrefix_