A generic FrequencySet allowing for the estimation of all frequencies. More...

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

Inheritance diagram for bpp::FullFrequencySet:

Collaboration diagram for bpp::FullFrequencySet:

Public Member Functions
	FullFrequencySet (std::shared_ptr< const StateMapInterface > stateMap, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")
	Construction with uniform frequencies on the states of the alphabet. More...

	FullFrequencySet (std::shared_ptr< const StateMapInterface > stateMap, const std::vector< double > &initFreqs, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full")

FullFrequencySet *	clone () const override

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

unsigned short	getMethod () const

void	setNamespace (const std::string &nameSpace) 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...

size_t	getNumberOfFrequencies () const override

std::string	getName () const override

void	normalize ()

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

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
void	fireParameterChanged (const ParameterList &parameters) override

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

ParameterList &	getParameters_ () override

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

Private Member Functions
void	updateFreq_ ()

Private Attributes
Simplex	sFreq_
	Simplex to handle the probabilities and the parameters. More...

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

A generic FrequencySet allowing for the estimation of all frequencies.

The FrequencySet has hence n-1 parameters, where n is the size of the input alphabet.

The parametrization depends on the method used. Default method is 1 (ie global ratio).

See also: Simplex

Definition at line 196 of file FrequencySet.h.

Constructor & Destructor Documentation

◆ FullFrequencySet() [1/2]

FullFrequencySet::FullFrequencySet	(	std::shared_ptr< const StateMapInterface >	stateMap,
		bool	allowNullFreqs = `false`,
		unsigned short	method = `1`,
		const std::string &	name = `"Full"`
	)

Construction with uniform frequencies on the states of the alphabet.

Definition at line 70 of file FrequencySet.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::StateMapInterface::getNumberOfModelStates(), bpp::Simplex::getParameters(), bpp::Simplex::setFrequencies(), sFreq_, bpp::AbstractFrequencySet::stateMap(), and updateFreq_().

Referenced by clone().

◆ FullFrequencySet() [2/2]

FullFrequencySet::FullFrequencySet	(	std::shared_ptr< const StateMapInterface >	stateMap,
		const std::vector< double > &	initFreqs,
		bool	allowNullFreqs = `false`,
		unsigned short	method = `1`,
		const std::string &	name = `"Full"`
	)

Definition at line 94 of file FrequencySet.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::Simplex::getParameters(), bpp::Simplex::setFrequencies(), sFreq_, and updateFreq_().

Member Function Documentation

◆ alphabet()

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()

FullFrequencySet* bpp::FullFrequencySet::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Reimplemented in bpp::FullProteinFrequencySet.

Definition at line 223 of file FrequencySet.h.

References FullFrequencySet().

◆ fireParameterChanged()

void FullFrequencySet::fireParameterChanged ( const ParameterList & parameters )

overrideprotectedvirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 125 of file FrequencySet.cpp.

References bpp::Simplex::matchParametersValues(), sFreq_, and updateFreq_().

◆ getAlphabet()

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 updateFreq_().

◆ getAlphabetStatesFrequencies()

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.

◆ 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_(), updateFreq_(), bpp::MvaFrequencySet::updateFrequencies(), bpp::WordFromIndependentFrequencySet::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()

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_().

◆ getMethod()

unsigned short bpp::FullFrequencySet::getMethod ( ) const

inline

Definition at line 231 of file FrequencySet.h.

References bpp::Simplex::getMethod(), and sFreq_.

◆ getName()

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()

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().

◆ getStateMap()

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_.

◆ normalize()

void bpp::AbstractFrequencySet::normalize ( )

inlineinherited

Definition at line 167 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

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

◆ setFrequencies()

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

overridevirtual

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::FrequencySetInterface.

Definition at line 111 of file FrequencySet.cpp.

References bpp::Simplex::getParameters(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setParametersValues(), sFreq_, and updateFreq_().

◆ 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()

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.

◆ setNamespace()

void FullFrequencySet::setNamespace ( const std::string & nameSpace )

overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 119 of file FrequencySet.cpp.

References bpp::AbstractParameterAliasable::setNamespace(), bpp::Simplex::setNamespace(), and sFreq_.

◆ stateMap()

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

◆ updateFreq_()

void FullFrequencySet::updateFreq_ ( )

private

Definition at line 131 of file FrequencySet.cpp.

References bpp::AbstractFrequencySet::getAlphabet(), bpp::AbstractFrequencySet::getFreq_(), bpp::Simplex::prob(), and sFreq_.

Referenced by fireParameterChanged(), FullFrequencySet(), and setFrequencies().

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=().

◆ sFreq_

Simplex bpp::FullFrequencySet::sFreq_

private

Simplex to handle the probabilities and the parameters.

Definition at line 203 of file FrequencySet.h.

Referenced by fireParameterChanged(), FullFrequencySet(), getMethod(), setFrequencies(), setNamespace(), and updateFreq_().

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FullFrequencySet() [1/2]

◆ FullFrequencySet() [2/2]

Member Function Documentation

◆ alphabet()

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies()

◆ getFrequencies_()

◆ getMethod()

◆ getName()

◆ getNumberOfFrequencies()

◆ getStateMap()

◆ normalize()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies()

◆ setNamespace()

◆ stateMap()

◆ updateFreq_()

Member Data Documentation

◆ alphabet_

◆ freq_

◆ FREQUENCE_CONSTRAINT_CENTI

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ name_

◆ sFreq_

◆ stateMap_