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

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

Inheritance diagram for bpp::FixedProteinFrequenciesSet:

Collaboration diagram for bpp::FixedProteinFrequenciesSet:

Public Member Functions
	FixedProteinFrequenciesSet (const ProteicAlphabet *alphabet, const std::vector< double > &initFreqs, const std::string &name="Fixed")

	FixedProteinFrequenciesSet (const ProteicAlphabet *alphabet, const std::string &name="Fixed")
	Construction with uniform frequencies on the letters of the alphabet. More...

FixedProteinFrequenciesSet *	clone () const

const ProteicAlphabet *	getAlphabet () 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	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

void	setFrequencies (const std::vector< double > &frequencies)
	Set the parameters in order to match a given set of frequencies. More...

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 Attributes
static IntervalConstraint	FREQUENCE_CONSTRAINT_SMALL

static IntervalConstraint	FREQUENCE_CONSTRAINT_MILLI

Protected Member Functions
void	fireParameterChanged (const ParameterList &parameters)

std::vector< double > &	getFrequencies_ ()

double &	getFreq_ (size_t i)

const double &	getFreq_ (size_t i) const

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

Detailed Description

FrequenciesSet useful for homogeneous and stationary models, protein implementation.

This set contains no parameter.

Definition at line 105 of file ProteinFrequenciesSet.h.

Constructor & Destructor Documentation

◆ FixedProteinFrequenciesSet() [1/2]

bpp::FixedProteinFrequenciesSet::FixedProteinFrequenciesSet	(	const ProteicAlphabet *	alphabet,
		const std::vector< double > &	initFreqs,
		const std::string &	name = `"Fixed"`
	)

inline

Definition at line 110 of file ProteinFrequenciesSet.h.

Referenced by clone().

◆ FixedProteinFrequenciesSet() [2/2]

bpp::FixedProteinFrequenciesSet::FixedProteinFrequenciesSet	(	const ProteicAlphabet *	alphabet,
		const std::string &	name = `"Fixed"`
	)

inline

Construction with uniform frequencies on the letters of the alphabet.

Definition at line 117 of file ProteinFrequenciesSet.h.

Member Function Documentation

◆ clone()

FixedProteinFrequenciesSet* bpp::FixedProteinFrequenciesSet::clone ( ) const

inlinevirtual

Reimplemented from bpp::FixedFrequenciesSet.

Definition at line 125 of file ProteinFrequenciesSet.h.

References FixedProteinFrequenciesSet().

◆ fireParameterChanged()

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

inlineprotectedinherited

Definition at line 340 of file FrequenciesSet.h.

◆ getAlphabet()

const ProteicAlphabet* bpp::FixedProteinFrequenciesSet::getAlphabet ( ) const

inlinevirtual

Returns: The alphabet associated to this set.

Implements bpp::ProteinFrequenciesSet.

Definition at line 128 of file ProteinFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::getAlphabet().

◆ getAlphabetStatesFrequencies() [1/2]

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

pure virtualinherited

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

Implemented in bpp::AbstractFrequenciesSet.

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

◆ getAlphabetStatesFrequencies() [2/2]

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

virtualinherited

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

Implements bpp::FrequenciesSet.

Definition at line 79 of file FrequenciesSet.cpp.

◆ getFreq_() [1/2]

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

inlineprotectedinherited

Definition at line 203 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getFreq_() [2/2]

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

inlineprotectedinherited

Definition at line 204 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getFrequencies() [1/2]

virtual const std::vector<double> bpp::FrequenciesSet::getFrequencies ( ) const

pure virtualinherited

Returns: The frequencies values of the set.

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::WAG01::WAG01(), and bpp::BppOFrequenciesSetFormat::write().

◆ getFrequencies() [2/2]

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

inlinevirtualinherited

Returns: The frequencies values of the set.

Implements bpp::FrequenciesSet.

Definition at line 174 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

◆ getFrequencies_()

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

inlineprotectedinherited

Definition at line 202 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ 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().

◆ setFrequencies() [1/2]

virtual void bpp::FrequenciesSet::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::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::FullFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::MvaFrequenciesSet, and bpp::GCFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::BppOFrequenciesSetFormat::initialize_(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::LG08::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::WordFromUniqueFrequenciesSet::setFrequencies(), bpp::MarkovModulatedFrequenciesSet::setFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

◆ setFrequencies() [2/2]

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

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.

Implements bpp::FrequenciesSet.

Definition at line 163 of file FrequenciesSet.cpp.

References bpp::AbstractFrequenciesSet::getNumberOfFrequencies(), and bpp::AbstractFrequenciesSet::setFrequencies_().

◆ setFrequencies_()

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

inlineprotectedinherited

Definition at line 205 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

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

pure virtualinherited

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

Parameters

frequencies The set of frequencies to match.

Implemented in bpp::AbstractFrequenciesSet.

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

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

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

virtualinherited

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

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

Parameters

frequencies The set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

Member Data Documentation

◆ 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().

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

Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h

Public Member Functions

Static Public Attributes

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ FixedProteinFrequenciesSet() [1/2]

◆ FixedProteinFrequenciesSet() [2/2]

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_()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ normalize()

◆ setFrequencies() [1/2]

◆ setFrequencies() [2/2]

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

Member Data Documentation

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL