Basic implementation of the FrequencySet interface. More...

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

Inheritance diagram for bpp::AbstractFrequencySet:

Collaboration diagram for bpp::AbstractFrequencySet:

Public Member Functions
	AbstractFrequencySet (std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix, const std::string &name)

	AbstractFrequencySet (const AbstractFrequencySet &af)

AbstractFrequencySet &	operator= (const AbstractFrequencySet &af)

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...

size_t	getNumberOfFrequencies () const override

std::string	getName () const override

void	normalize ()

FrequencySetInterface *	clone () 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 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

void	setNamespace (const std::string &prefix)

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

const ParameterList &	getIndependentParameters () const

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)

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

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

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

const ParameterList &	getParameters () const override

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

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

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

virtual void	fireParameterChanged (const ParameterList &parameters)

virtual Clonable *	clone () const=0

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
std::vector< double > &	getFrequencies_ ()

double &	getFreq_ (size_t i)

const double &	getFreq_ (size_t i) const

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

virtual ParameterList &	getParameters_ ()=0

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

ParameterList &	getParameters_ () override

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

Basic implementation of the FrequencySet interface.

Definition at line 99 of file FrequencySet.h.

Constructor & Destructor Documentation

◆ AbstractFrequencySet() [1/2]

bpp::AbstractFrequencySet::AbstractFrequencySet	(	std::shared_ptr< const StateMapInterface >	stateMap,
		const std::string &	prefix,
		const std::string &	name
	)

inline

Definition at line 110 of file FrequencySet.h.

◆ AbstractFrequencySet() [2/2]

bpp::AbstractFrequencySet::AbstractFrequencySet ( const AbstractFrequencySet & af )

inline

Definition at line 121 of file FrequencySet.h.

Member Function Documentation

◆ alphabet()

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

inlineoverridevirtual

Returns: The alphabet associated to this set.

Implements bpp::FrequencySetInterface.

Definition at line 142 of file FrequencySet.h.

References alphabet_.

◆ clone()

FrequencySetInterface* bpp::FrequencySetInterface::clone ( ) const

pure virtualinherited

Implements bpp::ParameterAliasable.

Referenced by bpp::EquiprobableSubstitutionModel::setFrequencySet().

◆ getAlphabet()

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

inlineoverridevirtual

Returns: The alphabet associated to this set.

Implements bpp::FrequencySetInterface.

Definition at line 140 of file FrequencySet.h.

References 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()

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

overridevirtual

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

Implements bpp::FrequencySetInterface.

Definition at line 57 of file FrequencySet.cpp.

◆ getFreq_() [1/2]

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

inlineprotected

Definition at line 179 of file FrequencySet.h.

References freq_.

◆ getFreq_() [2/2]

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

inlineprotected

Definition at line 180 of file FrequencySet.h.

References freq_.

◆ getFrequencies()

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

inlineoverridevirtual

Returns: The frequencies values of the set.

Implements bpp::FrequencySetInterface.

Definition at line 148 of file FrequencySet.h.

References freq_.

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

◆ getFrequencies_()

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

inlineprotected

Definition at line 178 of file FrequencySet.h.

References freq_.

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

◆ getName()

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

inlineoverridevirtual

Implements bpp::FrequencySetInterface.

Definition at line 165 of file FrequencySet.h.

References name_.

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

◆ getNumberOfFrequencies()

size_t bpp::AbstractFrequencySet::getNumberOfFrequencies ( ) const

inlineoverridevirtual

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 freq_.

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

◆ getStateMap()

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

inlineoverridevirtual

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 stateMap_.

◆ normalize()

void bpp::AbstractFrequencySet::normalize ( )

inline

Definition at line 167 of file FrequencySet.h.

References freq_.

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

◆ operator=()

AbstractFrequencySet& bpp::AbstractFrequencySet::operator= ( const AbstractFrequencySet & af )

inline

Definition at line 129 of file FrequencySet.h.

References alphabet_, freq_, name_, bpp::AbstractParameterAliasable::operator=(), and stateMap_.

Referenced by bpp::AbstractWordFrequencySet::operator=(), bpp::FixedCodonFrequencySet::operator=(), bpp::FromModelFrequencySet::operator=(), bpp::FullCodonFrequencySet::operator=(), bpp::FullPerAACodonFrequencySet::operator=(), bpp::MarkovModulatedFrequencySet::operator=(), and bpp::UserFrequencySet::operator=().

◆ setFrequencies()

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 )

inlineprotected

Definition at line 181 of file FrequencySet.h.

References 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()

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

overridevirtual

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.

◆ stateMap()

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

inlineoverridevirtual

Returns: The mapping of model states with alphabet states.

Implements bpp::FrequencySetInterface.

Definition at line 144 of file FrequencySet.h.

References stateMap_.

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

Member Data Documentation

◆ alphabet_

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

private

Definition at line 104 of file FrequencySet.h.

Referenced by alphabet(), getAlphabet(), and operator=().

◆ freq_

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

private

Definition at line 106 of file FrequencySet.h.

Referenced by getFreq_(), getFrequencies(), getFrequencies_(), getNumberOfFrequencies(), normalize(), operator=(), and 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_

private

Definition at line 107 of file FrequencySet.h.

Referenced by getName(), and operator=().

◆ stateMap_

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

private

Definition at line 105 of file FrequencySet.h.

Referenced by getStateMap(), operator=(), and stateMap().

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

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractFrequencySet() [1/2]

◆ AbstractFrequencySet() [2/2]

Member Function Documentation

◆ alphabet()

◆ clone()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies()

◆ getFrequencies_()

◆ getName()

◆ getNumberOfFrequencies()

◆ getStateMap()

◆ normalize()

◆ operator=()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies()

◆ stateMap()

Member Data Documentation

◆ alphabet_

◆ freq_

◆ FREQUENCE_CONSTRAINT_CENTI

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ name_

◆ stateMap_