bpp-phyl  2.2.0
Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | List of all members
bpp::WordFromUniqueFrequenciesSet Class Referenceabstract

#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. More...
 
 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 StateMap & getStateMap () const =0
 
const StateMap & getStateMap () const
 
virtual const std::vector< double > getFrequencies () const =0
 
const std::vector< double > getFrequencies () const
 
virtual const std::map< int, double > getAlphabetStatesFrequencies () const =0
 
const std::map< int, double > getAlphabetStatesFrequencies () const
 
virtual void setFrequenciesFromAlphabetStatesFrequencies (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 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...
 
virtual std::string getName () const =0
 
std::string getName () const
 
virtual size_t getNumberOfFrequencies () const =0
 
size_t getNumberOfFrequencies () const
 
void normalize ()
 

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)
 

Protected Attributes

FrequenciesSet * pFreq_
 
std::string NestedPrefix_
 
size_t length_
 

Detailed Description

Definition at line 190 of file WordFrequenciesSet.h.

Constructor & Destructor Documentation

◆ WordFromUniqueFrequenciesSet() [1/2]

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 253 of file WordFrequenciesSet.cpp.

References length_, NestedPrefix_, pFreq_, and updateFrequencies().

Referenced by clone().

◆ WordFromUniqueFrequenciesSet() [2/2]

WordFromUniqueFrequenciesSet::WordFromUniqueFrequenciesSet ( const WordFromUniqueFrequenciesSet &  iwfs)

Definition at line 277 of file WordFrequenciesSet.cpp.

References updateFrequencies().

◆ ~WordFromUniqueFrequenciesSet()

WordFromUniqueFrequenciesSet::~WordFromUniqueFrequenciesSet ( )

Definition at line 299 of file WordFrequenciesSet.cpp.

References pFreq_.

Member Function Documentation

◆ clone()

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

Implements bpp::AbstractWordFrequenciesSet.

Definition at line 211 of file WordFrequenciesSet.h.

References WordFromUniqueFrequenciesSet().

◆ fireParameterChanged()

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

Definition at line 306 of file WordFrequenciesSet.cpp.

References pFreq_, and updateFrequencies().

◆ getAlphabet()

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

◆ getAlphabetStatesFrequencies() [1/2]

virtual const std::map<int, double> bpp::FrequenciesSet::getAlphabetStatesFrequencies ( ) const
pure virtualinherited
Returns
The frequencies of each alphabet states according to this model.

Implemented in bpp::AbstractFrequenciesSet.

Referenced by bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel::setFreq().

◆ getAlphabetStatesFrequencies() [2/2]

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.

◆ getDescription()

string WordFromUniqueFrequenciesSet::getDescription ( ) const

Definition at line 390 of file WordFrequenciesSet.cpp.

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

◆ 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_(), bpp::FullFrequenciesSet::updateFreq_(), bpp::MvaFrequenciesSet::updateFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), 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() [1/2]

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

◆ getFrequencies() [2/2]

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_.

◆ getFrequenciesSetForLetter()

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

@ brief Return the n-th FrequenciesSet&

Implements bpp::WordFrequenciesSet.

Definition at line 230 of file WordFrequenciesSet.h.

References pFreq_.

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

◆ getLength()

size_t bpp::WordFromUniqueFrequenciesSet::getLength ( ) const
inlinevirtual

@ 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().

◆ getName() [1/2]

virtual std::string bpp::FrequenciesSet::getName ( ) const
pure virtualinherited

Implemented in bpp::AbstractFrequenciesSet.

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

◆ getName() [2/2]

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 getDescription().

◆ getNumberOfFrequencies() [1/2]

virtual size_t bpp::FrequenciesSet::getNumberOfFrequencies ( ) const
pure virtualinherited
Returns
The number of frequencies in the set. This is equivalent to getStateMap().getNumberOfModelStates().

Implemented in bpp::AbstractFrequenciesSet.

◆ getNumberOfFrequencies() [2/2]

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().

◆ getSizeFromVector()

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

Implements bpp::WordFrequenciesSet.

Definition at line 48 of file WordFrequenciesSet.cpp.

Referenced by bpp::WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet().

◆ getStateMap() [1/2]

virtual const StateMap& bpp::FrequenciesSet::getStateMap ( ) const
pure virtualinherited
Returns
The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequenciesSet.

◆ getStateMap() [2/2]

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().

◆ operator=()

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

Definition at line 287 of file WordFrequenciesSet.cpp.

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

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

◆ setFrequencies()

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(), length_, pFreq_, bpp::FrequenciesSet::setFrequencies(), and updateFrequencies().

◆ 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() [1/2]

virtual void bpp::FrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies ( 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().

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

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
frequenciesThe set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

◆ setNamespace()

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

Definition at line 378 of file WordFrequenciesSet.cpp.

References length_, NestedPrefix_, and pFreq_.

◆ updateFrequencies()

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(), length_, and pFreq_.

Referenced by fireParameterChanged(), operator=(), setFrequencies(), bpp::CodonFromUniqueFrequenciesSet::updateFrequencies(), and WordFromUniqueFrequenciesSet().

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().

◆ length_

size_t bpp::WordFromUniqueFrequenciesSet::length_
protected

Definition at line 196 of file WordFrequenciesSet.h.

Referenced by getDescription(), getLength(), operator=(), setFrequencies(), setNamespace(), updateFrequencies(), and WordFromUniqueFrequenciesSet().

◆ NestedPrefix_

std::string bpp::WordFromUniqueFrequenciesSet::NestedPrefix_
protected

Definition at line 195 of file WordFrequenciesSet.h.

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

◆ pFreq_

FrequenciesSet* bpp::WordFromUniqueFrequenciesSet::pFreq_
protected

Definition at line 194 of file WordFrequenciesSet.h.

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

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