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.
	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 std::vector < double > &	getFrequencies () const =0
const std::vector< double > &	getFrequencies () const
virtual void	setFrequenciesFromMap (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.
void	setFrequenciesFromMap (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.
virtual std::string	getName () const =0
std::string	getName () const
virtual size_t	getNumberOfFrequencies () const =0
size_t	getNumberOfFrequencies () const
virtual bool	hasParameter (const std::string &name) const =0
bool	hasParameter (const std::string &name) const
virtual const ParameterList &	getParameters () const =0
const ParameterList &	getParameters () const
virtual const Parameter &	getParameter (const std::string &name) const =0
const Parameter &	getParameter (const std::string &name) const
virtual double	getParameterValue (const std::string &name) const =0
double	getParameterValue (const std::string &name) const
virtual void	setAllParametersValues (const ParameterList &parameters)=0
void	setAllParametersValues (const ParameterList &parameters)
virtual void	setParameterValue (const std::string &name, double value)=0
void	setParameterValue (const std::string &name, double value)
virtual void	setParametersValues (const ParameterList &parameters)=0
void	setParametersValues (const ParameterList &parameters)
virtual bool	matchParametersValues (const ParameterList &parameters)=0
bool	matchParametersValues (const ParameterList &parameters)
virtual size_t	getNumberOfParameters () const =0
size_t	getNumberOfParameters () const
virtual std::string	getNamespace () const =0
std::string	getNamespace () const
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
std::string	getParameterNameWithoutNamespace (const std::string &name) const
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)
void	addParameter_ (Parameter *parameter)
void	addParameters_ (const ParameterList &parameters)
void	deleteParameter_ (size_t index)
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_ ()
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::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::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getParameters(), bpp::WordAlphabet::getSize(), bpp::AbstractWordFrequenciesSet::getSizeFromVector(), bpp::TextTools::toString(), updateFrequencies(), vFreq_, and vNestedPrefix_.

Referenced by clone().

WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet ( const WordFromIndependentFrequenciesSet & iwfs )

Definition at line 102 of file WordFrequenciesSet.cpp.

References updateFrequencies(), and vFreq_.

WordFromIndependentFrequenciesSet::~WordFromIndependentFrequenciesSet ( )

Definition at line 114 of file WordFrequenciesSet.cpp.

References vFreq_.

Member Function Documentation

WordFromIndependentFrequenciesSet* bpp::WordFromIndependentFrequenciesSet::clone ( ) const [inline, virtual]

Implements bpp::AbstractWordFrequenciesSet.

Reimplemented in bpp::CodonFromIndependentFrequenciesSet.

Definition at line 159 of file WordFrequenciesSet.h.

References WordFromIndependentFrequenciesSet().

void WordFromIndependentFrequenciesSet::fireParameterChanged ( const ParameterList & pl ) [virtual]

Implements bpp::AbstractParametrizable.

Definition at line 143 of file WordFrequenciesSet.cpp.

References updateFrequencies(), and vFreq_.

const WordAlphabet* bpp::AbstractWordFrequenciesSet::getAlphabet ( ) const [inline, virtual, inherited]

Returns:: The alphabet associated to this set.

Reimplemented from bpp::AbstractFrequenciesSet.

Reimplemented in bpp::CodonFromUniqueFrequenciesSet, and bpp::CodonFromIndependentFrequenciesSet.

Definition at line 118 of file WordFrequenciesSet.h.

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

std::string WordFromIndependentFrequenciesSet::getDescription ( ) const

Definition at line 240 of file WordFrequenciesSet.cpp.

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

double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t i ) [inline, protected, inherited]

Definition at line 161 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::GCFrequenciesSet::fireParameterChanged(), bpp::FullCodonFrequenciesSet::fireParameterChanged(), bpp::FullNucleotideFrequenciesSet::fireParameterChanged(), bpp::FullFrequenciesSet::fireParameterChanged(), bpp::FixedCodonFrequenciesSet::FixedCodonFrequenciesSet(), bpp::FixedFrequenciesSet::FixedFrequenciesSet(), bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(), bpp::FullFrequenciesSet::FullFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::GCFrequenciesSet::GCFrequenciesSet(), bpp::GCFrequenciesSet::setFrequencies(), bpp::FullCodonFrequenciesSet::setFrequencies(), bpp::FixedCodonFrequenciesSet::setFrequencies(), bpp::MvaFrequenciesSet::updateFrequencies(), updateFrequencies(), bpp::FullPerAACodonFrequenciesSet::updateFrequencies(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::CodonFromIndependentFrequenciesSet::updateFrequencies(), and bpp::CodonFromUniqueFrequenciesSet::updateFrequencies().

const double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t i ) const [inline, protected, inherited]

Definition at line 162 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

virtual const std::vector<double>& bpp::FrequenciesSet::getFrequencies ( ) const [pure virtual, inherited]

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::FullPerAACodonFrequenciesSet::updateFrequencies(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::WAG01::WAG01(), and bpp::BppOFrequenciesSetFormat::write().

const std::vector<double>& bpp::AbstractFrequenciesSet::getFrequencies ( ) const [inline, virtual, inherited]

Returns:: The frequencies values of the set.

Implements bpp::FrequenciesSet.

Definition at line 151 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

std::vector<double>& bpp::AbstractFrequenciesSet::getFrequencies_ ( ) [inline, protected, inherited]

Definition at line 160 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

const FrequenciesSet& bpp::WordFromIndependentFrequenciesSet::getFrequenciesSetForLetter ( size_t i ) const [inline, virtual]

@ brief Return the n-th FrequenciesSet&

Implements bpp::WordFrequenciesSet.

Definition at line 177 of file WordFrequenciesSet.h.

References vFreq_.

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

size_t WordFromIndependentFrequenciesSet::getLength ( ) const [virtual]

@ brief Return the length of the words

Reimplemented from bpp::AbstractWordFrequenciesSet.

Definition at line 226 of file WordFrequenciesSet.cpp.

References vFreq_.

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

virtual std::string bpp::FrequenciesSet::getName ( ) const [pure virtual, inherited]

Implemented in bpp::AbstractFrequenciesSet.

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

std::string bpp::AbstractFrequenciesSet::getName ( ) const [inline, virtual, inherited]

Implements bpp::FrequenciesSet.

Definition at line 157 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::name_.

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

virtual size_t bpp::FrequenciesSet::getNumberOfFrequencies ( ) const [pure virtual, inherited]

Returns:: The number of frequencies in the set. In most cases this will correspond to the size of the alphabet, but it needs not be.

Implemented in bpp::AbstractFrequenciesSet.

size_t bpp::AbstractFrequenciesSet::getNumberOfFrequencies ( ) const [inline, virtual, inherited]

Returns:: The number of frequencies in the set. In most cases this will correspond to the size of the alphabet, but it needs not be.

Implements bpp::FrequenciesSet.

Definition at line 155 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::FullFrequenciesSet::setFrequencies(), and bpp::FixedFrequenciesSet::setFrequencies().

size_t AbstractWordFrequenciesSet::getSizeFromVector ( const std::vector< FrequenciesSet * > & freqVector ) [protected, virtual, inherited]

Implements bpp::WordFrequenciesSet.

Definition at line 48 of file WordFrequenciesSet.cpp.

Referenced by WordFromIndependentFrequenciesSet().

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

Definition at line 122 of file WordFrequenciesSet.cpp.

References updateFrequencies(), vFreq_, and vNestedPrefix_.

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(), bpp::AbstractParametrizable::getParameters(), bpp::WordAlphabet::getSize(), bpp::AbstractParametrizable::matchParametersValues(), bpp::TextTools::toString(), updateFrequencies(), and vFreq_.

void bpp::AbstractFrequenciesSet::setFrequencies_ ( const std::vector< double > & frequencies ) [inline, protected, inherited]

Definition at line 163 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

virtual void bpp::FrequenciesSet::setFrequenciesFromMap ( const std::map< int, double > & frequencies ) [pure virtual, inherited]

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().

void AbstractFrequenciesSet::setFrequenciesFromMap ( const std::map< int, double > & frequencies ) [virtual, inherited]

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.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

void WordFromIndependentFrequenciesSet::setNamespace ( const std::string & prefix ) [virtual]

Reimplemented from bpp::AbstractParametrizable.

Definition at line 231 of file WordFrequenciesSet.cpp.

References bpp::TextTools::toString(), vFreq_, and vNestedPrefix_.

void WordFromIndependentFrequenciesSet::updateFrequencies ( ) [virtual]

Reimplemented in bpp::CodonFromIndependentFrequenciesSet.

Definition at line 157 of file WordFrequenciesSet.cpp.

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