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

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

Inheritance diagram for bpp::FullFrequenciesSet:

Collaboration diagram for bpp::FullFrequenciesSet:

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

	FullFrequenciesSet (StateMap *stateMap, const std::vector< double > &initFreqs, bool allowNullFreqs=false, unsigned short method=1, const std::string &name="Full.")

FullFrequenciesSet *	clone () const

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

unsigned short	getMethod () const

void	setNamespace (const std::string &nameSpace)

const Alphabet *	getAlphabet () const

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)

Private Member Functions
void	updateFreq_ ()

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

Detailed Description

A generic FrequenciesSet allowing for the estimation of all frequencies.

The FrequenciesSet 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 220 of file FrequenciesSet.h.

Constructor & Destructor Documentation

◆ FullFrequenciesSet() [1/2]

FullFrequenciesSet::FullFrequenciesSet	(	StateMap *	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 91 of file FrequenciesSet.cpp.

References bpp::StateMap::getNumberOfModelStates(), sFreq_, and updateFreq_().

Referenced by clone().

◆ FullFrequenciesSet() [2/2]

FullFrequenciesSet::FullFrequenciesSet	(	StateMap *	stateMap,
		const std::vector< double > &	initFreqs,
		bool	allowNullFreqs = `false`,
		unsigned short	method = `1`,
		const std::string &	name = `"Full."`
	)

Definition at line 106 of file FrequenciesSet.cpp.

References sFreq_, and updateFreq_().

Member Function Documentation

◆ clone()

FullFrequenciesSet* bpp::FullFrequenciesSet::clone ( ) const

inlinevirtual

Implements bpp::AbstractFrequenciesSet.

Reimplemented in bpp::FullProteinFrequenciesSet.

Definition at line 237 of file FrequenciesSet.h.

References FullFrequenciesSet().

◆ fireParameterChanged()

void FullFrequenciesSet::fireParameterChanged ( const ParameterList & parameters )

protected

Definition at line 130 of file FrequenciesSet.cpp.

References sFreq_, and updateFreq_().

◆ getAlphabet()

const Alphabet* bpp::AbstractFrequenciesSet::getAlphabet ( ) const

inlinevirtualinherited

Returns: The alphabet associated to this set.

Implements bpp::FrequenciesSet.

Reimplemented in bpp::FixedNucleotideFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FixedProteinFrequenciesSet, bpp::AbstractWordFrequenciesSet, bpp::MvaFrequenciesSet, bpp::GCFrequenciesSet, and bpp::FullProteinFrequenciesSet.

Definition at line 170 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::alphabet_.

Referenced by bpp::FullProteinFrequenciesSet::getAlphabet(), bpp::GCFrequenciesSet::getAlphabet(), bpp::MvaFrequenciesSet::getAlphabet(), bpp::AbstractWordFrequenciesSet::getAlphabet(), bpp::FixedProteinFrequenciesSet::getAlphabet(), bpp::FullNucleotideFrequenciesSet::getAlphabet(), bpp::FullCodonFrequenciesSet::getAlphabet(), bpp::FixedNucleotideFrequenciesSet::getAlphabet(), bpp::FixedCodonFrequenciesSet::getAlphabet(), bpp::FullPerAACodonFrequenciesSet::getAlphabet(), and updateFreq_().

◆ getAlphabetStatesFrequencies()

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_.

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_(), updateFreq_(), bpp::MvaFrequenciesSet::updateFrequencies(), bpp::WordFromIndependentFrequenciesSet::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()

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_.

◆ getMethod()

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

inline

Definition at line 242 of file FrequenciesSet.h.

References sFreq_.

◆ getName()

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()

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()

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()

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

virtual

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 115 of file FrequenciesSet.cpp.

References sFreq_, and updateFreq_().

◆ 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()

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 FullFrequenciesSet::setNamespace ( const std::string & nameSpace )

Definition at line 124 of file FrequenciesSet.cpp.

References sFreq_.

◆ updateFreq_()

void FullFrequenciesSet::updateFreq_ ( )

private

Definition at line 136 of file FrequenciesSet.cpp.

References bpp::AbstractFrequenciesSet::getAlphabet(), bpp::AbstractFrequenciesSet::getFreq_(), and sFreq_.

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

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().

◆ sFreq_

Simplex bpp::FullFrequenciesSet::sFreq_

private

Simplex to handle the probabilities and the parameters.

Definition at line 227 of file FrequenciesSet.h.

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

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

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FullFrequenciesSet() [1/2]

◆ FullFrequenciesSet() [2/2]

Member Function Documentation

◆ clone()

◆ fireParameterChanged()

◆ getAlphabet()

◆ getAlphabetStatesFrequencies()

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies()

◆ getFrequencies_()

◆ getMethod()

◆ getName()

◆ getNumberOfFrequencies()

◆ getStateMap()

◆ normalize()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies()

◆ setNamespace()

◆ updateFreq_()

Member Data Documentation

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ sFreq_