A frequencies set used to estimate frequencies at the root with the COaLA model. Frequencies at the root are optimized in the same way than the equlibrium frequencies on branches. Hyperparameters are used, which represent positions along the principal axes obtained from a preliminary Correspondence Analysis. From the optimized positions, the 20 frequencies are calculated. More...

#include <Bpp/Phyl/Model/FrequencySet/MvaFrequencySet.h>

Inheritance diagram for bpp::MvaFrequencySet:

Collaboration diagram for bpp::MvaFrequencySet:

Public Member Functions
	MvaFrequencySet (std::shared_ptr< const ProteicAlphabet > alpha)
	Constructor. More...

MvaFrequencySet *	clone () const override

std::shared_ptr< const ProteicAlphabet >	getProteicAlphabet () const override

void	setTransposeMatrixOfPpalAxes (const RowMatrix< double > &matrix)

void	setMatrixOfRowCoords (const RowMatrix< double > &matrix)

void	setNbrOfAxes (const size_t &nAxes)

void	setModelName (const std::string &modelName)

void	setVectorOfColumnWeights (const std::vector< double > &cw)

void	setParamValues (std::map< std::string, std::string > &valuesSettings)

void	setFrequencies (const std::vector< double > &frequencies) override
	Set the parameters in order to match a given set of frequencies. More...

void	defineParameters ()

void	fireParameterChanged (const ParameterList &parameters) override

void	updateFrequencies ()

void	initSet (const CoalaCore &coala)

void	computeReversePCA (const std::vector< double > &positions, std::vector< double > &tmpFreqs)

void	computeCoordsFirstSpacePCA (std::vector< double > &tmpFreqs, std::vector< double > &freqs)

void	computeReverseCOA (const std::vector< double > &positions, std::vector< double > &tmpFreqs)

void	computeCoordsFirstSpaceCOA (std::vector< double > &tmpFreqs, std::vector< double > &freqs)

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0

virtual const Alphabet &	alphabet () const =0

virtual const StateMapInterface &	stateMap () const =0

virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0

virtual const Vdouble &	getFrequencies () const =0

virtual const std::map< int, double >	getAlphabetStatesFrequencies () const =0

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

virtual size_t	getNumberOfIndependentParameters () const=0

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

virtual const ParameterList &	getIndependentParameters () const=0

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

virtual std::map< std::string, std::string >	getAliases () const=0

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (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 void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=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

std::shared_ptr< const Alphabet >	getAlphabet () const override

const Alphabet &	alphabet () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

const Vdouble &	getFrequencies () const override

const std::map< int, double >	getAlphabetStatesFrequencies () const override

void	setFrequenciesFromAlphabetStatesFrequencies (const std::map< int, double > &frequencies) override
	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...

size_t	getNumberOfFrequencies () const override

std::string	getName () const override

void	normalize ()

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

void	unaliasParameters (const std::string &p1, const std::string &p2)

const ParameterList &	getIndependentParameters () const

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

void	setNamespace (const std::string &prefix)

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

bool	hasIndependentParameter (const std::string &name) const

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

std::string	getFrom (const std::string &name) const

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

Static Public Attributes
static std::shared_ptr< IntervalConstraint >	FREQUENCE_CONSTRAINT_SMALL

static std::shared_ptr< IntervalConstraint >	FREQUENCE_CONSTRAINT_MILLI

static std::shared_ptr< IntervalConstraint >	FREQUENCE_CONSTRAINT_CENTI

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

std::vector< double > &	getFrequencies_ ()

double &	getFreq_ (size_t i)

const double &	getFreq_ (size_t i) const

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

ParameterList &	getParameters_ () override

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

Protected Attributes
RowMatrix< double >	tPpalAxes_

RowMatrix< double >	rowCoords_

size_t	nbrOfAxes_

std::string	model_

std::vector< double >	columnWeights_

std::map< std::string, std::string >	paramValues_

Private Attributes
std::shared_ptr< const Alphabet >	alphabet_

std::shared_ptr< const StateMapInterface >	stateMap_

std::vector< double >	freq_

std::string	name_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Detailed Description

A frequencies set used to estimate frequencies at the root with the COaLA model. Frequencies at the root are optimized in the same way than the equlibrium frequencies on branches. Hyperparameters are used, which represent positions along the principal axes obtained from a preliminary Correspondence Analysis. From the optimized positions, the 20 frequencies are calculated.

Author: Mathieu Groussin

Definition at line 21 of file MvaFrequencySet.h.

Constructor & Destructor Documentation

◆ MvaFrequencySet()

MvaFrequencySet::MvaFrequencySet ( std::shared_ptr< const ProteicAlphabet > alpha )

Constructor.

Definition at line 12 of file MvaFrequencySet.cpp.

Referenced by clone().

Member Function Documentation

◆ alphabet() [1/2]

virtual const Alphabet& bpp::FrequencySetInterface::alphabet ( ) const

pure virtualinherited

Returns: The alphabet associated to this set.

Implemented in bpp::AbstractFrequencySet.

◆ alphabet() [2/2]

const Alphabet& bpp::AbstractFrequencySet::alphabet ( ) const

inlineoverridevirtualinherited

Returns: The alphabet associated to this set.

Implements bpp::FrequencySetInterface.

Definition at line 142 of file FrequencySet.h.

References bpp::AbstractFrequencySet::alphabet_.

◆ clone()

MvaFrequencySet* bpp::MvaFrequencySet::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteinFrequencySetInterface.

Definition at line 31 of file MvaFrequencySet.h.

References MvaFrequencySet().

◆ computeCoordsFirstSpaceCOA()

void MvaFrequencySet::computeCoordsFirstSpaceCOA	(	std::vector< double > &	tmpFreqs,
		std::vector< double > &	freqs
	)

Definition at line 113 of file MvaFrequencySet.cpp.

References columnWeights_.

Referenced by updateFrequencies().

◆ computeCoordsFirstSpacePCA()

void bpp::MvaFrequencySet::computeCoordsFirstSpacePCA	(	std::vector< double > &	tmpFreqs,
		std::vector< double > &	freqs
	)

◆ computeReverseCOA()

void MvaFrequencySet::computeReverseCOA	(	const std::vector< double > &	positions,
		std::vector< double > &	tmpFreqs
	)

Definition at line 102 of file MvaFrequencySet.cpp.

References nbrOfAxes_, and tPpalAxes_.

Referenced by updateFrequencies().

◆ computeReversePCA()

void bpp::MvaFrequencySet::computeReversePCA	(	const std::vector< double > &	positions,
		std::vector< double > &	tmpFreqs
	)

◆ defineParameters()

void MvaFrequencySet::defineParameters ( )

Definition at line 35 of file MvaFrequencySet.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), RowMatrix< double >::col(), bpp::AbstractParameterAliasable::getNamespace(), bpp::VectorTools::max(), bpp::VectorTools::min(), nbrOfAxes_, paramValues_, rowCoords_, bpp::TextTools::toDouble(), and bpp::TextTools::toString().

Referenced by initSet().

◆ fireParameterChanged()

void MvaFrequencySet::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 51 of file MvaFrequencySet.cpp.

References updateFrequencies().

◆ getAlphabet() [1/2]

virtual std::shared_ptr<const Alphabet> bpp::FrequencySetInterface::getAlphabet ( ) const

pure virtualinherited

Returns: The alphabet associated to this set.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::UserCodonFrequencySet::getCodonAlphabet(), bpp::FixedNucleotideFrequencySet::getNucleicAlphabet(), bpp::UserNucleotideFrequencySet::getNucleicAlphabet(), bpp::FullProteinFrequencySet::getProteicAlphabet(), bpp::FixedProteinFrequencySet::getProteicAlphabet(), and bpp::UserProteinFrequencySet::getProteicAlphabet().

◆ getAlphabet() [2/2]

std::shared_ptr<const Alphabet> bpp::AbstractFrequencySet::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns: The alphabet associated to this set.

Implements bpp::FrequencySetInterface.

Definition at line 140 of file FrequencySet.h.

References bpp::AbstractFrequencySet::alphabet_.

Referenced by bpp::FullCodonFrequencySet::getCodonAlphabet(), bpp::FixedCodonFrequencySet::getCodonAlphabet(), bpp::FullPerAACodonFrequencySet::getCodonAlphabet(), bpp::CodonFromIndependentFrequencySet::getCodonAlphabet(), bpp::GCFrequencySet::getNucleicAlphabet(), bpp::FullNucleotideFrequencySet::getNucleicAlphabet(), getProteicAlphabet(), bpp::AbstractWordFrequencySet::getWordAlphabet(), bpp::UserFrequencySet::readFromFile_(), bpp::FullCodonFrequencySet::setFrequencies(), and bpp::FullFrequencySet::updateFreq_().

◆ getAlphabetStatesFrequencies() [1/2]

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

pure virtualinherited

Returns: The frequencies of each alphabet states according to this model.

Implemented in bpp::AbstractFrequencySet.

◆ getAlphabetStatesFrequencies() [2/2]

const std::map< int, double > AbstractFrequencySet::getAlphabetStatesFrequencies ( ) const

overridevirtualinherited

Returns: The frequencies of each alphabet states according to this model.

Implements bpp::FrequencySetInterface.

Definition at line 57 of file FrequencySet.cpp.

◆ getFreq_() [1/2]

double& bpp::AbstractFrequencySet::getFreq_ ( size_t i )

inlineprotectedinherited

Definition at line 179 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::GCFrequencySet::fireParameterChanged(), bpp::FullNucleotideFrequencySet::fireParameterChanged(), bpp::FixedCodonFrequencySet::FixedCodonFrequencySet(), bpp::FullNucleotideFrequencySet::FullNucleotideFrequencySet(), bpp::GCFrequencySet::GCFrequencySet(), bpp::UserFrequencySet::readFromFile_(), bpp::FixedCodonFrequencySet::setFrequencies(), bpp::UserCodonFrequencySet::setFrequencies(), bpp::GCFrequencySet::setFrequencies(), bpp::FullCodonFrequencySet::updateFreq_(), bpp::FullFrequencySet::updateFreq_(), updateFrequencies(), bpp::WordFromIndependentFrequencySet::updateFrequencies(), bpp::WordFromUniqueFrequencySet::updateFrequencies(), bpp::CodonFromIndependentFrequencySet::updateFrequencies(), bpp::CodonFromUniqueFrequencySet::updateFrequencies(), and bpp::FullPerAACodonFrequencySet::updateFrequencies_().

◆ getFreq_() [2/2]

const double& bpp::AbstractFrequencySet::getFreq_ ( size_t i ) const

inlineprotectedinherited

Definition at line 180 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

◆ getFrequencies() [1/2]

virtual const Vdouble& bpp::FrequencySetInterface::getFrequencies ( ) const

pure virtualinherited

Returns: The frequencies values of the set.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::NonHomogeneousSubstitutionProcess::getRootFrequencies(), bpp::CodonDistanceFrequenciesSubstitutionModel::setFreq(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq(), bpp::DFPDistanceFrequenciesSubstitutionModel::setFreq(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

◆ getFrequencies() [2/2]

const Vdouble& bpp::AbstractFrequencySet::getFrequencies ( ) const

inlineoverridevirtualinherited

Returns: The frequencies values of the set.

Implements bpp::FrequencySetInterface.

Definition at line 148 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by updateFrequencies().

◆ getFrequencies_()

std::vector<double>& bpp::AbstractFrequencySet::getFrequencies_ ( )

inlineprotectedinherited

Definition at line 178 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::UserFrequencySet::readFromFile_().

◆ getName() [1/2]

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

pure virtualinherited

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::BppOFrequencySetFormat::writeFrequencySet().

◆ getName() [2/2]

std::string bpp::AbstractFrequencySet::getName ( ) const

inlineoverridevirtualinherited

Implements bpp::FrequencySetInterface.

Definition at line 165 of file FrequencySet.h.

References bpp::AbstractFrequencySet::name_.

Referenced by bpp::WordFromIndependentFrequencySet::getDescription(), and bpp::WordFromUniqueFrequencySet::getDescription().

◆ getNumberOfFrequencies() [1/2]

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

pure virtualinherited

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

Implemented in bpp::AbstractFrequencySet.

◆ getNumberOfFrequencies() [2/2]

size_t bpp::AbstractFrequencySet::getNumberOfFrequencies ( ) const

inlineoverridevirtualinherited

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

Implements bpp::FrequencySetInterface.

Definition at line 163 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::FromModelFrequencySet::setFrequencies(), bpp::FixedFrequencySet::setFrequencies(), and bpp::UserFrequencySet::setFrequencies().

◆ getProteicAlphabet()

std::shared_ptr<const ProteicAlphabet> bpp::MvaFrequencySet::getProteicAlphabet ( ) const

inlineoverridevirtual

Implements bpp::ProteinFrequencySetInterface.

Definition at line 56 of file MvaFrequencySet.h.

References bpp::AbstractFrequencySet::getAlphabet().

◆ getStateMap() [1/2]

virtual std::shared_ptr<const StateMapInterface> bpp::FrequencySetInterface::getStateMap ( ) const

pure virtualinherited

Returns: A shared_ptr toward the mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequencySet.

◆ getStateMap() [2/2]

std::shared_ptr<const StateMapInterface> bpp::AbstractFrequencySet::getStateMap ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr toward the mapping of model states with alphabet states.

Implements bpp::FrequencySetInterface.

Definition at line 146 of file FrequencySet.h.

References bpp::AbstractFrequencySet::stateMap_.

◆ initSet()

void MvaFrequencySet::initSet ( const CoalaCore & coala )

Definition at line 25 of file MvaFrequencySet.cpp.

References defineParameters(), bpp::CoalaCore::getColumnWeights(), bpp::CoalaCore::getNbrOfAxes(), bpp::CoalaCore::getRowCoordinates(), bpp::CoalaCore::getTppalAxesMatrix(), setMatrixOfRowCoords(), setNbrOfAxes(), setTransposeMatrixOfPpalAxes(), setVectorOfColumnWeights(), and updateFrequencies().

◆ normalize()

void bpp::AbstractFrequencySet::normalize ( )

inlineinherited

Definition at line 167 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::FullPerAACodonFrequencySet::updateFrequencies_().

◆ setFrequencies()

void MvaFrequencySet::setFrequencies ( const std::vector< double > & frequencies )

overridevirtual

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.

Implements bpp::FrequencySetInterface.

Definition at line 99 of file MvaFrequencySet.cpp.

◆ setFrequencies_()

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

inlineprotectedinherited

Definition at line 181 of file FrequencySet.h.

References bpp::AbstractFrequencySet::freq_.

Referenced by bpp::FromModelFrequencySet::fireParameterChanged(), bpp::MarkovModulatedFrequencySet::fireParameterChanged(), bpp::FixedFrequencySet::FixedFrequencySet(), bpp::FromModelFrequencySet::FromModelFrequencySet(), bpp::MarkovModulatedFrequencySet::MarkovModulatedFrequencySet(), bpp::FixedFrequencySet::setFrequencies(), bpp::UserFrequencySet::setFrequencies(), bpp::FullNucleotideFrequencySet::setFrequencies(), and updateFrequencies().

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

void AbstractFrequencySet::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > & frequencies )

overridevirtualinherited

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

frequencies The set of frequencies to match.

Implements bpp::FrequencySetInterface.

Definition at line 28 of file FrequencySet.cpp.

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

virtual void bpp::FrequencySetInterface::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

frequencies The set of frequencies to match.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::BppOFrequencySetFormat::initialize_().

◆ setMatrixOfRowCoords()

void bpp::MvaFrequencySet::setMatrixOfRowCoords ( const RowMatrix< double > & matrix )

inline

Definition at line 62 of file MvaFrequencySet.h.

References rowCoords_.

Referenced by initSet().

◆ setModelName()

void bpp::MvaFrequencySet::setModelName ( const std::string & modelName )

inline

Definition at line 64 of file MvaFrequencySet.h.

References model_.

◆ setNbrOfAxes()

void bpp::MvaFrequencySet::setNbrOfAxes ( const size_t & nAxes )

inline

Definition at line 63 of file MvaFrequencySet.h.

References nbrOfAxes_.

Referenced by initSet().

◆ setParamValues()

void bpp::MvaFrequencySet::setParamValues ( std::map< std::string, std::string > & valuesSettings )

inline

Definition at line 66 of file MvaFrequencySet.h.

References paramValues_.

◆ setTransposeMatrixOfPpalAxes()

void bpp::MvaFrequencySet::setTransposeMatrixOfPpalAxes ( const RowMatrix< double > & matrix )

inline

Definition at line 61 of file MvaFrequencySet.h.

References tPpalAxes_.

Referenced by initSet().

◆ setVectorOfColumnWeights()

void bpp::MvaFrequencySet::setVectorOfColumnWeights ( const std::vector< double > & cw )

inline

Definition at line 65 of file MvaFrequencySet.h.

References columnWeights_.

Referenced by initSet().

◆ stateMap() [1/2]

virtual const StateMapInterface& bpp::FrequencySetInterface::stateMap ( ) const

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequencySet.

◆ stateMap() [2/2]

const StateMapInterface& bpp::AbstractFrequencySet::stateMap ( ) const

inlineoverridevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::FrequencySetInterface.

Definition at line 144 of file FrequencySet.h.

References bpp::AbstractFrequencySet::stateMap_.

Referenced by bpp::FixedFrequencySet::FixedFrequencySet(), bpp::FullFrequencySet::FullFrequencySet(), bpp::FromModelFrequencySet::setFrequencies(), and bpp::FullPerAACodonFrequencySet::updateFrequencies_().

◆ updateFrequencies()

void MvaFrequencySet::updateFrequencies ( )

Definition at line 56 of file MvaFrequencySet.cpp.

References computeCoordsFirstSpaceCOA(), computeReverseCOA(), bpp::AbstractFrequencySet::getFreq_(), bpp::AbstractFrequencySet::getFrequencies(), bpp::AbstractParameterAliasable::getParameterValue(), nbrOfAxes_, bpp::AbstractFrequencySet::setFrequencies_(), bpp::VectorTools::sum(), and bpp::TextTools::toString().

Referenced by fireParameterChanged(), and initSet().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractFrequencySet::alphabet_

privateinherited

Definition at line 104 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::alphabet(), bpp::AbstractFrequencySet::getAlphabet(), and bpp::AbstractFrequencySet::operator=().

◆ columnWeights_

std::vector<double> bpp::MvaFrequencySet::columnWeights_

protected

Definition at line 52 of file MvaFrequencySet.h.

Referenced by computeCoordsFirstSpaceCOA(), and setVectorOfColumnWeights().

◆ freq_

std::vector<double> bpp::AbstractFrequencySet::freq_

privateinherited

Definition at line 106 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::getFreq_(), bpp::AbstractFrequencySet::getFrequencies(), bpp::AbstractFrequencySet::getFrequencies_(), bpp::AbstractFrequencySet::getNumberOfFrequencies(), bpp::AbstractFrequencySet::normalize(), bpp::AbstractFrequencySet::operator=(), and bpp::AbstractFrequencySet::setFrequencies_().

◆ FREQUENCE_CONSTRAINT_CENTI

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_CENTI

staticinherited

Definition at line 92 of file FrequencySet.h.

Referenced by bpp::FullNucleotideFrequencySet::FullNucleotideFrequencySet().

◆ FREQUENCE_CONSTRAINT_MILLI

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_MILLI

staticinherited

Definition at line 91 of file FrequencySet.h.

◆ FREQUENCE_CONSTRAINT_SMALL

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_SMALL

staticinherited

Definition at line 90 of file FrequencySet.h.

Referenced by bpp::F81::F81(), bpp::F84::F84(), bpp::GTR::GTR(), bpp::HKY85::HKY85(), bpp::T92::T92(), and bpp::TN93::TN93().

◆ model_

std::string bpp::MvaFrequencySet::model_

protected

Definition at line 51 of file MvaFrequencySet.h.

Referenced by setModelName().

◆ name_

std::string bpp::AbstractFrequencySet::name_

privateinherited

Definition at line 107 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::getName(), and bpp::AbstractFrequencySet::operator=().

◆ nbrOfAxes_

size_t bpp::MvaFrequencySet::nbrOfAxes_

protected

Definition at line 50 of file MvaFrequencySet.h.

Referenced by computeReverseCOA(), defineParameters(), setNbrOfAxes(), and updateFrequencies().

◆ paramValues_

std::map<std::string, std::string> bpp::MvaFrequencySet::paramValues_

protected

Definition at line 53 of file MvaFrequencySet.h.

Referenced by defineParameters(), and setParamValues().

◆ rowCoords_

RowMatrix<double> bpp::MvaFrequencySet::rowCoords_

protected

Definition at line 49 of file MvaFrequencySet.h.

Referenced by defineParameters(), and setMatrixOfRowCoords().

◆ stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractFrequencySet::stateMap_

privateinherited

Definition at line 105 of file FrequencySet.h.

Referenced by bpp::AbstractFrequencySet::getStateMap(), bpp::AbstractFrequencySet::operator=(), and bpp::AbstractFrequencySet::stateMap().

◆ tPpalAxes_

RowMatrix<double> bpp::MvaFrequencySet::tPpalAxes_

protected

Definition at line 48 of file MvaFrequencySet.h.

Referenced by computeReverseCOA(), and setTransposeMatrixOfPpalAxes().

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

Bpp/Phyl/Model/FrequencySet/MvaFrequencySet.h
Bpp/Phyl/Model/FrequencySet/MvaFrequencySet.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MvaFrequencySet()

Member Function Documentation

◆ alphabet() [1/2]

◆ alphabet() [2/2]

◆ clone()

◆ computeCoordsFirstSpaceCOA()

◆ computeCoordsFirstSpacePCA()

◆ computeReverseCOA()

◆ computeReversePCA()

◆ defineParameters()

◆ fireParameterChanged()

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getAlphabetStatesFrequencies() [1/2]

◆ getAlphabetStatesFrequencies() [2/2]

◆ getFreq_() [1/2]

◆ getFreq_() [2/2]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrequencies_()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfFrequencies() [1/2]

◆ getNumberOfFrequencies() [2/2]

◆ getProteicAlphabet()

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ initSet()

◆ normalize()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

◆ setMatrixOfRowCoords()

◆ setModelName()

◆ setNbrOfAxes()

◆ setParamValues()

◆ setTransposeMatrixOfPpalAxes()

◆ setVectorOfColumnWeights()

◆ stateMap() [1/2]

◆ stateMap() [2/2]

◆ updateFrequencies()

Member Data Documentation

◆ alphabet_

◆ columnWeights_

◆ freq_

◆ FREQUENCE_CONSTRAINT_CENTI

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ model_

◆ name_

◆ nbrOfAxes_

◆ paramValues_

◆ rowCoords_

◆ stateMap_

◆ tPpalAxes_