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bpp::WordFromIndependentFrequenciesSet Class Referenceabstract

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. More...
 
 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. More...
 
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. More...
 
virtual std::string getName () const =0
 
std::string getName () const
 
virtual size_t getNumberOfFrequencies () const =0
 
size_t getNumberOfFrequencies () 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_ ()
 

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::AbstractAlphabet::getSize(), bpp::AbstractAlphabet::getSize(), bpp::AbstractWordFrequenciesSet::getSizeFromVector(), bpp::TextTools::toString(), bpp::TextTools::toString(), bpp::TextTools::toString(), updateFrequencies(), vFreq_, vFreq_, vNestedPrefix_, and vNestedPrefix_.

Referenced by clone().

WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet ( const WordFromIndependentFrequenciesSet &  iwfs)

Definition at line 102 of file WordFrequenciesSet.cpp.

References updateFrequencies(), vFreq_, vFreq_, and vFreq_.

WordFromIndependentFrequenciesSet::~WordFromIndependentFrequenciesSet ( )

Definition at line 114 of file WordFrequenciesSet.cpp.

References vFreq_, and vFreq_.

Member Function Documentation

WordFromIndependentFrequenciesSet* bpp::WordFromIndependentFrequenciesSet::clone ( ) const
inlinevirtual

Implements bpp::AbstractWordFrequenciesSet.

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(), vFreq_, and vFreq_.

const WordAlphabet* bpp::AbstractWordFrequenciesSet::getAlphabet ( ) const
inlinevirtualinherited
Returns
The alphabet associated to this set.

Reimplemented from bpp::AbstractFrequenciesSet.

Definition at line 118 of file WordFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::getAlphabet().

Referenced by bpp::CodonFromIndependentFrequenciesSet::getAlphabet(), bpp::CodonFromUniqueFrequenciesSet::getAlphabet(), bpp::AbstractWordFrequenciesSet::getLength(), setFrequencies(), setFrequencies(), bpp::WordFromUniqueFrequenciesSet::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(), vFreq_, vFreq_, and vFreq_.

double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t  i)
inlineprotectedinherited

Definition at line 161 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

const double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t  i) const
inlineprotectedinherited

Definition at line 162 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

virtual const std::vector<double>& bpp::FrequenciesSet::getFrequencies ( ) const
pure virtualinherited
Returns
The frequencies values of the set.

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate(), 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
inlinevirtualinherited
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_ ( )
inlineprotectedinherited

Definition at line 160 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

const FrequenciesSet& bpp::WordFromIndependentFrequenciesSet::getFrequenciesSetForLetter ( size_t  i) const
inlinevirtual

@ 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 virtualinherited

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::BppOFrequenciesSetFormat::read(), bpp::FullPerAACodonFrequenciesSet::setNamespace(), and bpp::BppOFrequenciesSetFormat::write().

std::string bpp::AbstractFrequenciesSet::getName ( ) const
inlinevirtualinherited

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 virtualinherited
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
inlinevirtualinherited
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(), bpp::FullFrequenciesSet::setFrequencies(), bpp::FixedFrequenciesSet::setFrequencies(), and bpp::FixedFrequenciesSet::setFrequencies().

size_t AbstractWordFrequenciesSet::getSizeFromVector ( const std::vector< FrequenciesSet * > &  freqVector)
protectedvirtualinherited

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 bpp::AbstractWordFrequenciesSet::operator=(), updateFrequencies(), vFreq_, vFreq_, vFreq_, vFreq_, vFreq_, vFreq_, vFreq_, vNestedPrefix_, and vNestedPrefix_.

Referenced by bpp::CodonFromIndependentFrequenciesSet::operator=().

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::AbstractWordFrequenciesSet::getAlphabet(), bpp::TextTools::toString(), updateFrequencies(), vFreq_, vFreq_, vFreq_, and vFreq_.

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

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 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.

Parameters
frequenciesThe 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)
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.

Parameters
frequenciesThe set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

void WordFromIndependentFrequenciesSet::setNamespace ( const std::string &  prefix)

Definition at line 231 of file WordFrequenciesSet.cpp.

References bpp::AbstractParametrizable::setNamespace(), bpp::TextTools::toString(), vFreq_, 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::AbstractFrequenciesSet::getFreq_(), vFreq_, vFreq_, and vFreq_.

Referenced by fireParameterChanged(), operator=(), setFrequencies(), bpp::CodonFromIndependentFrequenciesSet::updateFrequencies(), WordFromIndependentFrequenciesSet(), and WordFromIndependentFrequenciesSet().

Member Data Documentation

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_MILLI
staticinherited

Definition at line 101 of file FrequenciesSet.h.

Referenced by bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(), and bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet().

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_SMALL
staticinherited

Definition at line 100 of file FrequenciesSet.h.

Referenced by bpp::F84::F84(), bpp::F84::F84(), bpp::F84::F84(), bpp::FullFrequenciesSet::FullFrequenciesSet(), bpp::FullFrequenciesSet::FullFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::GTR::GTR(), bpp::GTR::GTR(), bpp::GTR::GTR(), bpp::HKY85::HKY85(), bpp::HKY85::HKY85(), bpp::HKY85::HKY85(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::TN93::TN93(), and bpp::TN93::TN93().

std::vector<FrequenciesSet*> bpp::WordFromIndependentFrequenciesSet::vFreq_
protected

Definition at line 143 of file WordFrequenciesSet.h.

Referenced by fireParameterChanged(), fireParameterChanged(), getDescription(), getDescription(), getDescription(), getFrequenciesSetForLetter(), getLength(), operator=(), operator=(), operator=(), operator=(), operator=(), operator=(), operator=(), setFrequencies(), setFrequencies(), setFrequencies(), setFrequencies(), setNamespace(), setNamespace(), updateFrequencies(), updateFrequencies(), updateFrequencies(), WordFromIndependentFrequenciesSet(), WordFromIndependentFrequenciesSet(), WordFromIndependentFrequenciesSet(), WordFromIndependentFrequenciesSet(), WordFromIndependentFrequenciesSet(), WordFromIndependentFrequenciesSet(), ~WordFromIndependentFrequenciesSet(), and ~WordFromIndependentFrequenciesSet().

std::vector<std::string> bpp::WordFromIndependentFrequenciesSet::vNestedPrefix_
protected

Definition at line 144 of file WordFrequenciesSet.h.

Referenced by operator=(), operator=(), setNamespace(), WordFromIndependentFrequenciesSet(), and WordFromIndependentFrequenciesSet().

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