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/FrequenciesSet/MvaFrequenciesSet.h>

Inheritance diagram for bpp::MvaFrequenciesSet:

Collaboration diagram for bpp::MvaFrequenciesSet:

Public Member Functions
	MvaFrequenciesSet (const ProteicAlphabet *alpha)
	Constructor. More...

MvaFrequenciesSet *	clone () const

MvaFrequenciesSet &	operator= (const MvaFrequenciesSet &mfs)

const ProteicAlphabet *	getAlphabet () const

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) throw (DimensionException, Exception)
	Set the parameters in order to match a given set of frequencies. More...

void	defineParameters ()

void	fireParameterChanged (const ParameterList &parameters)

void	updateFrequencies () throw (Exception)

void	initSet (CoalaCore *coala)

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

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

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

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

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	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

const StateMap &	getStateMap () const

const std::vector< double >	getFrequencies () const

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

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...

size_t	getNumberOfFrequencies () const

std::string	getName () const

void	normalize ()

Static Public Attributes
static IntervalConstraint	FREQUENCE_CONSTRAINT_SMALL

static IntervalConstraint	FREQUENCE_CONSTRAINT_MILLI

Protected Member Functions
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
RowMatrix< double >	tPpalAxes_

RowMatrix< double >	rowCoords_

size_t	nbrOfAxes_

std::string	model_

std::vector< double >	columnWeights_

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

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 57 of file MvaFrequenciesSet.h.

Constructor & Destructor Documentation

◆ MvaFrequenciesSet()

MvaFrequenciesSet::MvaFrequenciesSet ( const ProteicAlphabet * alpha )

Constructor.

Definition at line 46 of file MvaFrequenciesSet.cpp.

Referenced by clone().

Member Function Documentation

◆ clone()

MvaFrequenciesSet* bpp::MvaFrequenciesSet::clone ( ) const

inlinevirtual

Implements bpp::AbstractFrequenciesSet.

Definition at line 72 of file MvaFrequenciesSet.h.

References MvaFrequenciesSet().

◆ computeCoordsFirstSpaceCOA()

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

Definition at line 144 of file MvaFrequenciesSet.cpp.

Referenced by updateFrequencies().

◆ computeCoordsFirstSpacePCA()

void bpp::MvaFrequenciesSet::computeCoordsFirstSpacePCA	(	std::vector< double > &	tmpFreqs,
		std::vector< double > &	freqs
	)
throw	(	Exception
	)

◆ computeReverseCOA()

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

Definition at line 133 of file MvaFrequenciesSet.cpp.

Referenced by updateFrequencies().

◆ computeReversePCA()

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

◆ defineParameters()

void MvaFrequenciesSet::defineParameters ( )

Definition at line 66 of file MvaFrequenciesSet.cpp.

References nbrOfAxes_, paramValues_, and rowCoords_.

Referenced by initSet().

◆ fireParameterChanged()

void MvaFrequenciesSet::fireParameterChanged ( const ParameterList & parameters )

Definition at line 82 of file MvaFrequenciesSet.cpp.

References updateFrequencies().

◆ getAlphabet()

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

inlinevirtual

Returns: The alphabet associated to this set.

Reimplemented from bpp::AbstractFrequenciesSet.

Definition at line 96 of file MvaFrequenciesSet.h.

References bpp::AbstractFrequenciesSet::getAlphabet().

◆ 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.

◆ 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_(), updateFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), bpp::WordFromUniqueFrequenciesSet::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(), bpp::WordFromUniqueFrequenciesSet::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 updateFrequencies().

◆ getFrequencies_()

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

inlineprotectedinherited

Definition at line 202 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getName() [1/2]

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

pure virtualinherited

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().

◆ 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 bpp::WordFromUniqueFrequenciesSet::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().

◆ 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().

◆ initSet()

void MvaFrequenciesSet::initSet ( CoalaCore * coala )

Definition at line 56 of file MvaFrequenciesSet.cpp.

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

MvaFrequenciesSet& bpp::MvaFrequenciesSet::operator= ( const MvaFrequenciesSet & mfs )

inline

Definition at line 74 of file MvaFrequenciesSet.h.

References columnWeights_, model_, nbrOfAxes_, bpp::AbstractFrequenciesSet::operator=(), paramValues_, rowCoords_, and tPpalAxes_.

◆ setFrequencies()

void MvaFrequenciesSet::setFrequencies	(	const std::vector< double > &	frequencies	)
throw	(	DimensionException,
		Exception
	)

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.

Implements bpp::FrequenciesSet.

Definition at line 130 of file MvaFrequenciesSet.cpp.

◆ 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 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

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().

◆ 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

frequencies The set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

◆ setMatrixOfRowCoords()

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

inline

Definition at line 99 of file MvaFrequenciesSet.h.

References rowCoords_.

Referenced by initSet().

◆ setModelName()

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

inline

Definition at line 101 of file MvaFrequenciesSet.h.

References model_.

◆ setNbrOfAxes()

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

inline

Definition at line 100 of file MvaFrequenciesSet.h.

References nbrOfAxes_.

Referenced by initSet().

◆ setParamValues()

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

inline

Definition at line 103 of file MvaFrequenciesSet.h.

References paramValues_.

◆ setTransposeMatrixOfPpalAxes()

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

inline

Definition at line 98 of file MvaFrequenciesSet.h.

References tPpalAxes_.

Referenced by initSet().

◆ setVectorOfColumnWeights()

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

inline

Definition at line 102 of file MvaFrequenciesSet.h.

References columnWeights_.

Referenced by initSet().

◆ updateFrequencies()

void MvaFrequenciesSet::updateFrequencies	(		)
throw	(	Exception
	)

Definition at line 87 of file MvaFrequenciesSet.cpp.

References computeCoordsFirstSpaceCOA(), computeReverseCOA(), bpp::AbstractFrequenciesSet::getFreq_(), bpp::AbstractFrequenciesSet::getFrequencies(), nbrOfAxes_, and bpp::AbstractFrequenciesSet::setFrequencies_().

Referenced by fireParameterChanged(), and initSet().

Member Data Documentation

◆ columnWeights_

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

protected

Definition at line 92 of file MvaFrequenciesSet.h.

Referenced by operator=(), and setVectorOfColumnWeights().

◆ 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().

◆ model_

std::string bpp::MvaFrequenciesSet::model_

protected

Definition at line 91 of file MvaFrequenciesSet.h.

Referenced by operator=(), and setModelName().

◆ nbrOfAxes_

size_t bpp::MvaFrequenciesSet::nbrOfAxes_

protected

Definition at line 90 of file MvaFrequenciesSet.h.

Referenced by defineParameters(), operator=(), setNbrOfAxes(), and updateFrequencies().

◆ paramValues_

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

protected

Definition at line 93 of file MvaFrequenciesSet.h.

Referenced by defineParameters(), operator=(), and setParamValues().

◆ rowCoords_

RowMatrix<double> bpp::MvaFrequenciesSet::rowCoords_

protected

Definition at line 89 of file MvaFrequenciesSet.h.

Referenced by defineParameters(), operator=(), and setMatrixOfRowCoords().

◆ tPpalAxes_

RowMatrix<double> bpp::MvaFrequenciesSet::tPpalAxes_

protected

Definition at line 88 of file MvaFrequenciesSet.h.

Referenced by operator=(), and setTransposeMatrixOfPpalAxes().

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

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MvaFrequenciesSet()

Member Function Documentation

◆ clone()

◆ computeCoordsFirstSpaceCOA()

◆ computeCoordsFirstSpacePCA()

◆ computeReverseCOA()

◆ computeReversePCA()

◆ defineParameters()

◆ fireParameterChanged()

◆ getAlphabet()

◆ 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]

◆ getStateMap() [1/2]

◆ getStateMap() [2/2]

◆ initSet()

◆ normalize()

◆ operator=()

◆ setFrequencies()

◆ setFrequencies_()

◆ setFrequenciesFromAlphabetStatesFrequencies() [1/2]

◆ setFrequenciesFromAlphabetStatesFrequencies() [2/2]

◆ setMatrixOfRowCoords()

◆ setModelName()

◆ setNbrOfAxes()

◆ setParamValues()

◆ setTransposeMatrixOfPpalAxes()

◆ setVectorOfColumnWeights()

◆ updateFrequencies()

Member Data Documentation

◆ columnWeights_

◆ FREQUENCE_CONSTRAINT_MILLI

◆ FREQUENCE_CONSTRAINT_SMALL

◆ model_

◆ nbrOfAxes_

◆ paramValues_

◆ rowCoords_

◆ tPpalAxes_