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

Inheritance diagram for bpp::WordFromUniqueFrequenciesSet:

Collaboration diagram for bpp::WordFromUniqueFrequenciesSet:

Public Member Functions
	WordFromUniqueFrequenciesSet (const WordAlphabet pWA, FrequenciesSet pabsfreq, const std::string &prefix="", const std::string &name="WordFromUnique")
	Constructor from a WordAlphabet* and a FrequenciesSet* repeated as many times as the length of the words.
	WordFromUniqueFrequenciesSet (const WordFromUniqueFrequenciesSet &iwfs)
WordFromUniqueFrequenciesSet &	operator= (const WordFromUniqueFrequenciesSet &iwfs)
	~WordFromUniqueFrequenciesSet ()
WordFromUniqueFrequenciesSet *	clone () const
virtual void	fireParameterChanged (const ParameterList &pl)
virtual void	setFrequencies (const std::vector< double > &frequencies)
virtual void	updateFrequencies ()
const FrequenciesSet &	getFrequenciesSetForLetter (size_t i) const
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
FrequenciesSet *	pFreq_
std::string	NestedPrefix_
size_t	length_

Detailed Description

Definition at line 190 of file WordFrequenciesSet.h.

Constructor & Destructor Documentation

WordFromUniqueFrequenciesSet::WordFromUniqueFrequenciesSet	(	const WordAlphabet *	pWA,
		FrequenciesSet *	pabsfreq,
		const std::string &	prefix = `""`,
		const std::string &	name = `"WordFromUnique"`
	)

Constructor from a WordAlphabet* and a FrequenciesSet* repeated as many times as the length of the words.

Definition at line 254 of file WordFrequenciesSet.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::Parametrizable::getParameters(), length_, NestedPrefix_, pFreq_, bpp::Parametrizable::setNamespace(), bpp::TextTools::toString(), and updateFrequencies().

Referenced by clone().

WordFromUniqueFrequenciesSet::WordFromUniqueFrequenciesSet ( const WordFromUniqueFrequenciesSet & iwfs )

Definition at line 277 of file WordFrequenciesSet.cpp.

References updateFrequencies().

WordFromUniqueFrequenciesSet::~WordFromUniqueFrequenciesSet ( )

Definition at line 299 of file WordFrequenciesSet.cpp.

References pFreq_.

Member Function Documentation

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

Implements bpp::AbstractWordFrequenciesSet.

Reimplemented in bpp::CodonFromUniqueFrequenciesSet.

Definition at line 211 of file WordFrequenciesSet.h.

References WordFromUniqueFrequenciesSet().

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

Implements bpp::AbstractParametrizable.

Definition at line 306 of file WordFrequenciesSet.cpp.

References bpp::Parametrizable::matchParametersValues(), pFreq_, and updateFrequencies().

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(), bpp::WordFromIndependentFrequenciesSet::setFrequencies(), setFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), and updateFrequencies().

string WordFromUniqueFrequenciesSet::getDescription ( ) const

Definition at line 391 of file WordFrequenciesSet.cpp.

References bpp::FrequenciesSet::getName(), bpp::AbstractFrequenciesSet::getName(), length_, pFreq_, and bpp::TextTools::toString().

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(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), bpp::FullPerAACodonFrequenciesSet::updateFrequencies(), 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(), 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::WordFromUniqueFrequenciesSet::getFrequenciesSetForLetter ( size_t i ) const [inline, virtual]

@ brief Return the n-th FrequenciesSet&

Implements bpp::WordFrequenciesSet.

Definition at line 230 of file WordFrequenciesSet.h.

References pFreq_.

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

size_t bpp::WordFromUniqueFrequenciesSet::getLength ( ) const [inline, virtual]

@ brief Return the length of the words

Reimplemented from bpp::AbstractWordFrequenciesSet.

Definition at line 232 of file WordFrequenciesSet.h.

References length_.

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(), 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 bpp::WordFromIndependentFrequenciesSet::getDescription(), and 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 bpp::WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet().

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

Definition at line 287 of file WordFrequenciesSet.cpp.

References bpp::FrequenciesSet::clone(), length_, NestedPrefix_, pFreq_, and updateFrequencies().

void WordFromUniqueFrequenciesSet::setFrequencies ( const std::vector< double > & frequencies ) [virtual]

@ brief 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. The frequencies of each letter is the average of the frequencies of that letter at all positions.

Implements bpp::FrequenciesSet.

Definition at line 334 of file WordFrequenciesSet.cpp.

References bpp::FrequenciesSet::getAlphabet(), bpp::AbstractWordFrequenciesSet::getAlphabet(), bpp::Parametrizable::getParameters(), bpp::WordAlphabet::getSize(), bpp::Alphabet::getSize(), length_, bpp::AbstractParametrizable::matchParametersValues(), pFreq_, bpp::FrequenciesSet::setFrequencies(), bpp::TextTools::toString(), and updateFrequencies().

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 379 of file WordFrequenciesSet.cpp.

References length_, NestedPrefix_, pFreq_, bpp::Parametrizable::setNamespace(), and bpp::TextTools::toString().

void WordFromUniqueFrequenciesSet::updateFrequencies ( ) [virtual]

Reimplemented in bpp::CodonFromUniqueFrequenciesSet.

Definition at line 312 of file WordFrequenciesSet.cpp.

References bpp::FrequenciesSet::getAlphabet(), bpp::AbstractWordFrequenciesSet::getAlphabet(), bpp::AbstractFrequenciesSet::getFreq_(), bpp::FrequenciesSet::getFrequencies(), bpp::Alphabet::getSize(), bpp::WordAlphabet::getSize(), length_, and pFreq_.