bpp::FrequenciesSet Class Reference

Parametrize a set of state frequencies. More...

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

Inheritance diagram for bpp::FrequenciesSet:

Collaboration diagram for bpp::FrequenciesSet:

Public Member Functions
FrequenciesSet *	clone () const =0
virtual const Alphabet *	getAlphabet () const =0
virtual const StateMap &	getStateMap () const =0
virtual const std::vector< double >	getFrequencies () const =0
virtual const std::map< int, double >	getAlphabetStatesFrequencies () const =0
virtual void	setFrequencies (const std::vector< double > &frequencies)=0
	Set the parameters in order to match a given set of frequencies. More...
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...
virtual std::string	getName () const =0
virtual size_t	getNumberOfFrequencies () const =0

Static Public Attributes
static IntervalConstraint	FREQUENCE_CONSTRAINT_SMALL
static IntervalConstraint	FREQUENCE_CONSTRAINT_MILLI

Detailed Description

Parametrize a set of state frequencies.

Frequencies are ordered according to alphabet states.

Definition at line 62 of file FrequenciesSet.h.

Member Function Documentation

clone()

FrequenciesSet* bpp::FrequenciesSet::clone ( ) const

pure virtual

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::FullFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::FixedNucleotideFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::AbstractFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::FixedProteinFrequenciesSet, bpp::AbstractWordFrequenciesSet, bpp::GCFrequenciesSet, bpp::FullProteinFrequenciesSet, bpp::MvaFrequenciesSet, bpp::WordFrequenciesSet, bpp::CodonFrequenciesSet, bpp::NucleotideFrequenciesSet, and bpp::ProteinFrequenciesSet.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::operator=(), bpp::AbstractCodonFrequenciesSubstitutionModel::operator=(), bpp::WordFromUniqueFrequenciesSet::operator=(), and bpp::MarkovModulatedFrequenciesSet::operator=().

getAlphabet()

virtual const Alphabet* bpp::FrequenciesSet::getAlphabet ( ) const

pure virtual

Returns

The alphabet associated to this set.

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::FixedNucleotideFrequenciesSet, bpp::AbstractFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FixedProteinFrequenciesSet, bpp::AbstractWordFrequenciesSet, bpp::MvaFrequenciesSet, bpp::GCFrequenciesSet, bpp::FullProteinFrequenciesSet, bpp::WordFrequenciesSet, bpp::CodonFrequenciesSet, bpp::NucleotideFrequenciesSet, and bpp::ProteinFrequenciesSet.

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

getAlphabetStatesFrequencies()

virtual const std::map<int, double> bpp::FrequenciesSet::getAlphabetStatesFrequencies ( ) const

pure virtual

Returns

The frequencies of each alphabet states according to this model.

Implemented in bpp::AbstractFrequenciesSet.

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

getFrequencies()

virtual const std::vector<double> bpp::FrequenciesSet::getFrequencies ( ) const

pure virtual

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

getName()

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

pure virtual

Implemented in bpp::AbstractFrequenciesSet.

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

getNumberOfFrequencies()

virtual size_t bpp::FrequenciesSet::getNumberOfFrequencies ( ) const

pure virtual

Returns

The number of frequencies in the set. This is equivalent to getStateMap().getNumberOfModelStates().

Implemented in bpp::AbstractFrequenciesSet.

getStateMap()

virtual const StateMap& bpp::FrequenciesSet::getStateMap ( ) const

pure virtual

Returns

The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequenciesSet.

setFrequencies()

virtual void bpp::FrequenciesSet::setFrequencies ( const std::vector< double > &  frequencies )

pure 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.

Implemented in bpp::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::FullFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::MvaFrequenciesSet, and bpp::GCFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::BppOFrequenciesSetFormat::initialize_(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::LG08::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::WordFromUniqueFrequenciesSet::setFrequencies(), bpp::MarkovModulatedFrequenciesSet::setFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

setFrequenciesFromAlphabetStatesFrequencies()

virtual void bpp::FrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > &  frequencies )

pure virtual

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().

Member Data Documentation

FREQUENCE_CONSTRAINT_MILLI

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_MILLI

static

Definition at line 118 of file FrequenciesSet.h.

FREQUENCE_CONSTRAINT_SMALL

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_SMALL

static

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().

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

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