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:

List of all members.

Public Member Functions
FrequenciesSet *	clone () const =0
virtual const Alphabet *	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.
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.
virtual std::string	getName () const =0
virtual size_t	getNumberOfFrequencies () const =0
virtual bool	hasParameter (const std::string &name) const =0
virtual const ParameterList &	getParameters () const =0
virtual const Parameter &	getParameter (const std::string &name) const =0
virtual double	getParameterValue (const std::string &name) const =0
virtual void	setAllParametersValues (const ParameterList &parameters)=0
virtual void	setParameterValue (const std::string &name, double value)=0
virtual void	setParametersValues (const ParameterList &parameters)=0
virtual bool	matchParametersValues (const ParameterList &parameters)=0
virtual size_t	getNumberOfParameters () const =0
virtual void	setNamespace (const std::string &prefix)=0
virtual std::string	getNamespace () const =0
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
Static Public Attributes
static IntervalConstraint	FREQUENCE_CONSTRAINT_SMALL
static IntervalConstraint	FREQUENCE_CONSTRAINT_MILLI

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Detailed Description

Parametrize a set of state frequencies.

Definition at line 54 of file FrequenciesSet.h.

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Member Function Documentation

FrequenciesSet* bpp::FrequenciesSet::clone

(

)

const [pure virtual]

Implements bpp::Parametrizable.

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::FixedNucleotideFrequenciesSet, bpp::FullFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::AbstractFrequenciesSet, 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=().

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::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, 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().

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().

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().

virtual size_t bpp::FrequenciesSet::getNumberOfFrequencies

(

)

const [pure virtual]

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 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::FullPerAACodonFrequenciesSet, bpp::FixedFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::FullFrequenciesSet, 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().

virtual void bpp::FrequenciesSet::setFrequenciesFromMap

(

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().

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Member Data Documentation

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_MILLI [static]

Definition at line 101 of file FrequenciesSet.h.

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

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_SMALL [static]

Definition at line 100 of file FrequenciesSet.h.

Referenced by bpp::F84::F84(), bpp::FullFrequenciesSet::FullFrequenciesSet(), 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