Parametrize a set of state frequencies for proteins. More...

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

Inheritance diagram for bpp::ProteinFrequenciesSet:

Collaboration diagram for bpp::ProteinFrequenciesSet:

Public Member Functions
ProteinFrequenciesSet *	clone () const =0

const ProteicAlphabet *	getAlphabet () const =0

virtual const std::vector < double > &	getFrequencies () 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	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...

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 for proteins.

Definition at line 52 of file ProteinFrequenciesSet.h.

Member Function Documentation

ProteinFrequenciesSet* bpp::ProteinFrequenciesSet::clone ( ) const

pure virtual

Implements bpp::FrequenciesSet.

Implemented in bpp::FixedProteinFrequenciesSet, bpp::FullProteinFrequenciesSet, and bpp::MvaFrequenciesSet.

Referenced by bpp::LG08::operator=(), bpp::DSO78::operator=(), bpp::JTT92::operator=(), bpp::WAG01::operator=(), bpp::UserProteinSubstitutionModel::operator=(), bpp::JCprot::operator=(), bpp::FullPerAACodonFrequenciesSet::operator=(), bpp::LG08::setFrequenciesSet(), bpp::JTT92::setFrequenciesSet(), bpp::DSO78::setFrequenciesSet(), bpp::WAG01::setFrequenciesSet(), bpp::UserProteinSubstitutionModel::setFrequenciesSet(), and bpp::JCprot::setFrequenciesSet().

const ProteicAlphabet* bpp::ProteinFrequenciesSet::getAlphabet ( ) const

pure virtual

Returns: The alphabet associated to this set.

Implements bpp::FrequenciesSet.

Implemented in bpp::FixedProteinFrequenciesSet, bpp::MvaFrequenciesSet, and bpp::FullProteinFrequenciesSet.

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().

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().

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.

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

pure virtualinherited

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::WordFromUniqueFrequenciesSet, bpp::FullFrequenciesSet, bpp::FixedCodonFrequenciesSet, 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::FullPerAACodonFrequenciesSet::setFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

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

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().