Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...

#include <Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h>

Inheritance diagram for bpp::CodonDistancePhaseFrequenciesSubstitutionModel:

Collaboration diagram for bpp::CodonDistancePhaseFrequenciesSubstitutionModel:

Public Member Functions
	CodonDistancePhaseFrequenciesSubstitutionModel (const GeneticCode palph, NucleotideSubstitutionModel pmod, FrequenciesSet pfreq, const AlphabetIndex2 pdist=0)
	Build a new CodonDistancePhaseFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones. More...

	CodonDistancePhaseFrequenciesSubstitutionModel (const GeneticCode palph, NucleotideSubstitutionModel pmod1, NucleotideSubstitutionModel pmod2, NucleotideSubstitutionModel pmod3, FrequenciesSet pfreq, const AlphabetIndex2 pdist=0)
	Build a new CodonDistancePhaseFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones. More...

	CodonDistancePhaseFrequenciesSubstitutionModel (const CodonDistancePhaseFrequenciesSubstitutionModel &model)

CodonDistancePhaseFrequenciesSubstitutionModel &	operator= (const CodonDistancePhaseFrequenciesSubstitutionModel &model)

	~CodonDistancePhaseFrequenciesSubstitutionModel ()

CodonDistancePhaseFrequenciesSubstitutionModel *	clone () const

void	fireParameterChanged (const ParameterList &parameterlist)

std::string	getName () const
	Get the name of the model. More...

double	getCodonsMulRate (size_t i, size_t j) const
	Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More...

void	setNamespace (const std::string &)

void	setFreq (std::map< int, double > &frequencies)
	Set equilibrium frequencies. More...

void	updateMatrices ()
	Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...

virtual const std::vector< int > &	getAlphabetChars () const =0

const std::vector< int > &	getAlphabetChars () const

virtual int	getAlphabetChar (size_t i) const =0
	Get the char in the alphabet corresponding to a given state in the model. More...

int	getAlphabetChar (size_t i) const
	Get the char in the alphabet corresponding to a given state in the model. More...

virtual std::vector< size_t >	getModelStates (int i) const =0
	Get the state in the model corresponding to a particular char in the alphabet. More...

std::vector< size_t >	getModelStates (int i) const
	Get the state in the model corresponding to a particular char in the alphabet. More...

virtual double	freq (size_t i) const =0

virtual double	freq (size_t i) const

virtual double	Qij (size_t i, size_t j) const =0

virtual double	Qij (size_t i, size_t j) const

virtual double	Pij_t (size_t i, size_t j, double t) const =0

virtual double	Pij_t (size_t i, size_t j, double t) const

virtual double	dPij_dt (size_t i, size_t j, double t) const =0

virtual double	dPij_dt (size_t i, size_t j, double t) const

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const =0

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const

virtual const Vdouble &	getFrequencies () const =0

virtual const Vdouble &	getFrequencies () const

virtual const Matrix< double > &	getGenerator () const =0

const Matrix< double > &	getGenerator () const

virtual const Matrix< double > &	getExchangeabilityMatrix () const =0

const Matrix< double > &	getExchangeabilityMatrix () const

virtual double	Sij (size_t i, size_t j) const =0

double	Sij (size_t i, size_t j) const

virtual const Matrix< double > &	getPij_t (double t) const =0

virtual const Matrix< double > &	getPij_t (double t) const

virtual const Matrix< double > &	getdPij_dt (double t) const =0

virtual const Matrix< double > &	getdPij_dt (double t) const

virtual const Matrix< double > &	getd2Pij_dt2 (double t) const =0

virtual const Matrix< double > &	getd2Pij_dt2 (double t) const

virtual void	enableEigenDecomposition (bool yn)=0
	Set if eigenValues and Vectors must be computed. More...

virtual bool	enableEigenDecomposition ()=0
	Tell if eigenValues and Vectors must be computed. More...

void	enableEigenDecomposition (bool yn)
	Set if eigenValues and Vectors must be computed. More...

bool	enableEigenDecomposition ()
	Tell if eigenValues and Vectors must be computed. More...

virtual const Vdouble &	getEigenValues () const =0

const Vdouble &	getEigenValues () const

virtual const Vdouble &	getIEigenValues () const =0

const Vdouble &	getIEigenValues () const

virtual bool	isDiagonalizable () const =0

bool	isDiagonalizable () const

virtual bool	isNonSingular () const =0

bool	isNonSingular () const

virtual const Matrix< double > &	getRowLeftEigenVectors () const =0

const Matrix< double > &	getRowLeftEigenVectors () const

virtual const Matrix< double > &	getColumnRightEigenVectors () const =0

const Matrix< double > &	getColumnRightEigenVectors () const

virtual const Alphabet *	getAlphabet () const =0

const Alphabet *	getAlphabet () const

virtual size_t	getNumberOfStates () const =0
	Get the number of states. More...

virtual size_t	getNumberOfStates () const
	Get the number of states. More...

virtual double	getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)

double	getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)

virtual double	getScale () const =0
	Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...

double	getScale () const
	Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...

virtual void	setScale (double scale)=0
	Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector. More...

void	setScale (double scale)
	Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector. More...

virtual double	getRate () const =0
	Get the rate. More...

virtual double	getRate () const
	Get the rate. More...

virtual void	setRate (double rate)=0
	Set the rate of the model (must be positive). More...

virtual void	setRate (double rate)
	Set the rate of the model (must be positive). More...

virtual void	addRateParameter ()=0

void	addRateParameter ()

virtual void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

virtual const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...

virtual size_t	getNumberOfIndependentParameters () const =0

size_t	getNumberOfIndependentParameters () const

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

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

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

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

virtual const ParameterList &	getIndependentParameters () const =0

const ParameterList &	getIndependentParameters () const

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

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

const SubstitutionModel *	getNModel (size_t i) const
	returns the ith model, or Null if i is not a valid number. More...

size_t	getNumberOfModels () const

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

const ParameterList &	getParameters () const

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

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

void	setAllParametersValues (const ParameterList &parameters)

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

void	setParametersValues (const ParameterList &parameters)

bool	matchParametersValues (const ParameterList &parameters)

size_t	getNumberOfParameters () const

std::string	getNamespace () const

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

const GeneticCode *	getGeneticCode () const

const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...

Protected Member Functions
void	completeMatrices ()
	Method inherited from AbstractWordSubstitutionModel. More...

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

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

ParameterList &	getParameters_ ()

Static Protected Member Functions
static Alphabet *	extractAlph (const std::vector< SubstitutionModel * > &modelVector)

Protected Attributes
std::vector< SubstitutionModel * >	VSubMod_

std::vector< std::string >	VnestedPrefix_

std::vector< double >	Vrate_

const Alphabet *	alphabet_
	The alphabet relevant to this model. More...

size_t	size_
	The size of the generator, i.e. the number of states. More...

double	rate_
	The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...

std::vector< int >	chars_
	The list of supported chars. More...

RowMatrix< double >	generator_
	The generator matrix of the model. More...

Vdouble	freq_
	The vector $\pi_e$ of equilibrium frequencies. More...

RowMatrix< double >	exchangeability_
	The exchangeability matrix of the model, defined as $S_{ij}=\frac{Q_{ij}}{\pi_j}$ . When the model is reversible, this matrix is symetric. More...

RowMatrix< double >	pijt_
	These ones are for bookkeeping: More...

RowMatrix< double >	dpijt_

RowMatrix< double >	d2pijt_

bool	eigenDecompose_
	Tell if the eigen decomposition should be performed. More...

Vdouble	eigenValues_
	The vector of eigen values. More...

Vdouble	iEigenValues_
	The vector of the imaginary part of the eigen values. More...

bool	isDiagonalizable_
	boolean value for diagonalizability in R of the generator_ More...

RowMatrix< double >	rightEigenVectors_
	The matrix made of right eigen vectors (by column). More...

bool	isNonSingular_
	boolean value for non-singularity of rightEigenVectors_ More...

RowMatrix< double >	leftEigenVectors_
	The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More...

std::vector< RowMatrix< double > >	vPowGen_
	vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More...

RowMatrix< double >	tmpMat_
	For computational issues. More...

Detailed Description

Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models.

Author: Laurent Guéguen

This class should be used with models which equilibrium distribution is fixed, ans does not depend on the parameters. Otherwise there may be problems of identifiability of the parameters.

See description in AbstractCodonDistanceSubstitutionModel and AbstractCodonPhaseFrequenciesSubstitutionModel class.

Only substitutions with one letter changed are accepted.

The additional parameter to CodonPhaseFrequenciesSubstitutionModel is the ratio of nonsynonymous over synonymous substitutions.

If a distance $d$ between amino-acids is defined, the ratio between non-synonymous and synonymous substitutions rates is, if the codied amino-acids are $x$ and $y$ , $\beta*\exp(-\alpha.d(x,y))$ with non-negative parameter "alpha" and positive parameter "beta".

If such a distance is not defined, the ratio between non-synonymous and synonymous substitutions rates is $\beta$ with positive parameter "beta".

Definition at line 78 of file CodonDistancePhaseFrequenciesSubstitutionModel.h.

Constructor & Destructor Documentation

CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel	(	const GeneticCode *	palph,
		NucleotideSubstitutionModel *	pmod,
		FrequenciesSet *	pfreq,
		const AlphabetIndex2 *	pdist = `0`
	)

Build a new CodonDistancePhaseFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones.

Parameters

palph	pointer to a GeneticCode
pmod	pointer to the NucleotideSubstitutionModel to use in the three positions. It is owned by the instance.
pfreq	pointer to the FrequenciesSet* equilibrium frequencies
pdist	optional pointer to the AlphabetIndex2 amino-acids distance object.

Definition at line 47 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractCodonSubstitutionModel::updateMatrices().

Referenced by clone().

CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel	(	const GeneticCode *	palph,
		NucleotideSubstitutionModel *	pmod1,
		NucleotideSubstitutionModel *	pmod2,
		NucleotideSubstitutionModel *	pmod3,
		FrequenciesSet *	pfreq,
		const AlphabetIndex2 *	pdist = `0`
	)

Build a new CodonDistancePhaseFrequenciesSubstitutionModel object from three pointers to AbstractSubstitutionModels. NEW AbstractSubstitutionModels are copied from the given ones.

Parameters

palph	pointer to a GeneticCode
pmod1,pmod2,pmod3	are pointers to the NucleotideSubstitutionModel to use in the three positions. All the models must be different objects to avoid redundant parameters. They are owned by the instance.
pfreq	pointer to the FrequenciesSet* equilibrium frequencies
pdist	optional pointer to the AlphabetIndex2 amino-acids distance object.

Definition at line 61 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractCodonSubstitutionModel::updateMatrices().

bpp::CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel ( const CodonDistancePhaseFrequenciesSubstitutionModel & model )

inline

Definition at line 120 of file CodonDistancePhaseFrequenciesSubstitutionModel.h.

bpp::CodonDistancePhaseFrequenciesSubstitutionModel::~CodonDistancePhaseFrequenciesSubstitutionModel ( )

inline

Definition at line 142 of file CodonDistancePhaseFrequenciesSubstitutionModel.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )

virtualinherited

Implements bpp::SubstitutionModel.

Definition at line 434 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::getNamespace(), and bpp::AbstractSubstitutionModel::rate_.

virtual void bpp::SubstitutionModel::addRateParameter ( )

pure virtualinherited

Implemented in bpp::AbstractSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter().

CodonDistancePhaseFrequenciesSubstitutionModel* bpp::CodonDistancePhaseFrequenciesSubstitutionModel::clone ( ) const

inlinevirtual

Implements bpp::AbstractCodonSubstitutionModel.

Definition at line 144 of file CodonDistancePhaseFrequenciesSubstitutionModel.h.

References CodonDistancePhaseFrequenciesSubstitutionModel().

void AbstractCodonSubstitutionModel::completeMatrices ( )

protectedvirtualinherited

Method inherited from AbstractWordSubstitutionModel.

This method sets the rates to/from stop codons to zero and performs the multiplication by the specific codon-codon rate.

Implements bpp::AbstractWordSubstitutionModel.

Definition at line 174 of file AbstractCodonSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::alphabet_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractCodonSubstitutionModel::getCodonsMulRate(), bpp::AbstractWordSubstitutionModel::getNumberOfStates(), bpp::CodonAlphabet::isStop(), and bpp::CodonAlphabet::isStop().

virtual double bpp::SubstitutionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The second order derivative of the probability of change from state i to state j with respect to time t, at time t.

See Also: getd2Pij_dt2(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(), and bpp::RE08::d2Pij_dt2().

virtual double bpp::AbstractSubstitutionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlinevirtualinherited

Returns: The second order derivative of the probability of change from state i to state j with respect to time t, at time t.

See Also: getd2Pij_dt2(), getStates()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 280 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_dt2().

virtual double bpp::SubstitutionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The first order derivative of the probability of change from state i to state j with respect to time t, at time t.

See Also: getdPij_dt(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::dPij_dt(), and bpp::RE08::dPij_dt().

virtual double bpp::AbstractSubstitutionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlinevirtualinherited

Returns: The first order derivative of the probability of change from state i to state j with respect to time t, at time t.

See Also: getdPij_dt(), getStates()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 279 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool yn )

inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 288 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )

inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 290 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool yn )

pure virtualinherited

Set if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), bpp::gBGC::gBGC(), and bpp::YpR::YpR().

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( )

pure virtualinherited

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Alphabet * AbstractWordSubstitutionModel::extractAlph ( const std::vector< SubstitutionModel * > & modelVector )

staticprotectedinherited

Definition at line 239 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::getAlphabet().

void CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged ( const ParameterList & parameterlist )

virtual

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 82 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::AbstractCodonDistanceSubstitutionModel::fireParameterChanged(), and bpp::AbstractSubstitutionModel::fireParameterChanged().

virtual double bpp::SubstitutionModel::freq ( size_t i ) const

pure virtualinherited

Returns: Equilibrium frequency associated to character i.

See Also: getFrequencies(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::AbstractBiblioSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::RE08::getPij_t(), bpp::RE08::getPij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), and bpp::RE08::updateMatrices().

virtual double bpp::AbstractSubstitutionModel::freq ( size_t i ) const

inlinevirtualinherited

Returns: Equilibrium frequency associated to character i.

See Also: getFrequencies(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 274 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

const Alphabet* bpp::AbstractSubstitutionModel::getAlphabet ( ) const

inlinevirtualinherited

Returns: Get the alphabet associated to this model.

Implements bpp::SubstitutionModel.

Definition at line 242 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::AbstractWordSubstitutionModel::extractAlph(), bpp::AbstractWordSubstitutionModel::getNumberOfStates(), and bpp::AbstractWordSubstitutionModel::operator=().

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

pure virtualinherited

Returns: Get the alphabet associated to this model.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

virtual int bpp::SubstitutionModel::getAlphabetChar ( size_t i ) const

pure virtualinherited

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters

i	The index of the state.

Returns: The corresponding state in the alphabet.

See Also: MarkovModulatedSubstitutionModel; getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

int bpp::AbstractSubstitutionModel::getAlphabetChar ( size_t i ) const

inlinevirtualinherited

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters

i	The index of the state.

Returns: The corresponding state in the alphabet.

See Also: MarkovModulatedSubstitutionModel; getStates()

Implements bpp::SubstitutionModel.

Definition at line 246 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetChars ( ) const

pure virtualinherited

Returns: The supported states of the model, as a vector of int codes.

See Also: Alphabet

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChars(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetChars ( ) const

inlinevirtualinherited

Returns: The supported states of the model, as a vector of int codes.

See Also: Alphabet

Implements bpp::SubstitutionModel.

Definition at line 244 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

double CodonDistancePhaseFrequenciesSubstitutionModel::getCodonsMulRate	(	size_t	,
		size_t
	)		const

virtual

Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides.

Reimplemented from bpp::AbstractCodonDistanceSubstitutionModel.

Definition at line 91 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), and bpp::AbstractCodonSubstitutionModel::getCodonsMulRate().

const Matrix<double>& bpp::AbstractSubstitutionModel::getColumnRightEigenVectors ( ) const

inlinevirtualinherited

Returns: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 272 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const

pure virtualinherited

Returns: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix< double > & AbstractSubstitutionModel::getd2Pij_dt2 ( double t ) const

virtualinherited

Returns: All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See Also: d2Pij_dt2()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 275 of file AbstractSubstitutionModel.cpp.

Referenced by bpp::AbstractSubstitutionModel::d2Pij_dt2().

virtual const Matrix<double>& bpp::SubstitutionModel::getd2Pij_dt2 ( double t ) const

pure virtualinherited

Returns: All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See Also: d2Pij_dt2()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(), and bpp::RE08::getd2Pij_dt2().

const Matrix< double > & AbstractSubstitutionModel::getdPij_dt ( double t ) const

virtualinherited

Returns: Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See Also: dPij_dt()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 206 of file AbstractSubstitutionModel.cpp.

Referenced by bpp::AbstractSubstitutionModel::dPij_dt().

virtual const Matrix<double>& bpp::SubstitutionModel::getdPij_dt ( double t ) const

pure virtualinherited

Returns: Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See Also: dPij_dt()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::getdPij_dt(), and bpp::RE08::getdPij_dt().

const Vdouble& bpp::AbstractSubstitutionModel::getEigenValues ( ) const

inlinevirtualinherited

Returns: A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 262 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const

pure virtualinherited

Returns: A vector with all real parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix<double>& bpp::AbstractSubstitutionModel::getExchangeabilityMatrix ( ) const

inlinevirtualinherited

Returns: The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$ .

Implements bpp::SubstitutionModel.

Definition at line 254 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const

pure virtualinherited

Returns: The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$ .

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

inlinevirtualinherited

Returns: A vector of all equilibrium frequencies.

See Also: freq()

Implements bpp::SubstitutionModel.

Definition at line 250 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

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

pure virtualinherited

Returns: A vector of all equilibrium frequencies.

See Also: freq()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const FrequenciesSet* bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getFrequenciesSet ( ) const

inlinevirtualinherited

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented from bpp::SubstitutionModel.

Definition at line 117 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::posfreqset_.

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const

inlinevirtualinherited

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 463 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().

const Matrix<double>& bpp::AbstractSubstitutionModel::getGenerator ( ) const

inlinevirtualinherited

Returns: The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $\forall i; \sum_j Q_{i,j} = 0$ , meaning that $ $\forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$ , and (ii) $\sum_i Q_{i,i} \times \pi_i = -1$ . This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time are measured in units of expected number of changes per site. Additionnaly, the rate_ attibute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See Also: Qij()

Implements bpp::SubstitutionModel.

Definition at line 252 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const

pure virtualinherited

Returns: The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $\forall i; \sum_j Q_{i,j} = 0$ , meaning that $ $\forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$ , and (ii) $\sum_i Q_{i,i} \times \pi_i = -1$ . This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time are measured in units of expected number of changes per site. Additionnaly, the rate_ attibute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See Also: Qij()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const GeneticCode* bpp::AbstractCodonDistanceSubstitutionModel::getGeneticCode ( ) const

inlineinherited

Definition at line 140 of file AbstractCodonDistanceSubstitutionModel.h.

References bpp::AbstractCodonDistanceSubstitutionModel::geneticCode_.

const Vdouble& bpp::AbstractSubstitutionModel::getIEigenValues ( ) const

inlinevirtualinherited

Returns: A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 264 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const

pure virtualinherited

Returns: A vector with all imaginary parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().

double AbstractSubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const throw (IndexOutOfBoundsException, BadIntException)

virtualinherited

This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See Also: getStates();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08.

Definition at line 350 of file AbstractSubstitutionModel.cpp.

virtual double bpp::SubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const throw (IndexOutOfBoundsException, BadIntException)

pure virtualinherited

This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See Also: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int i ) const

pure virtualinherited

Get the state in the model corresponding to a particular char in the alphabet.

Parameters

i	The alphabet char to check.

Returns: A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( int i ) const

inlinevirtualinherited

Get the state in the model corresponding to a particular char in the alphabet.

Parameters

i	The alphabet char to check.

Returns: A vector of indices of model states.

Implements bpp::SubstitutionModel.

Definition at line 248 of file AbstractSubstitutionModel.h.

References bpp::VectorTools::whichAll().

std::string CodonDistancePhaseFrequenciesSubstitutionModel::getName ( ) const

virtual

Get the name of the model.

Returns: The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 77 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

const SubstitutionModel* bpp::AbstractWordSubstitutionModel::getNModel ( size_t i ) const

inlineinherited

returns the ith model, or Null if i is not a valid number.

Definition at line 155 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::BppOSubstitutionModelFormat::write(), bpp::BppOSubstitutionModelFormat::write(), and bpp::BppOSubstitutionModelFormat::write().

size_t bpp::AbstractWordSubstitutionModel::getNumberOfModels ( ) const

inlineinherited

Definition at line 162 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

size_t AbstractWordSubstitutionModel::getNumberOfStates ( ) const

virtualinherited

Get the number of states.

For most models, this equals the size of the alphabet.

Returns: The number of different states in the model.

Implements bpp::SubstitutionModel.

Definition at line 234 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::getAlphabet().

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::setFreq(), bpp::AbstractWordSubstitutionModel::updateMatrices(), and bpp::AbstractWordSubstitutionModel::updateMatrices().

virtual size_t bpp::SubstitutionModel::getNumberOfStates ( ) const

pure virtualinherited

Get the number of states.

For most models, this equals the size of the alphabet.

Returns: The number of different states in the model.

Implemented in bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::getNumberOfStates(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix< double > & AbstractSubstitutionModel::getPij_t ( double t ) const

virtualinherited

Returns: All probabilities of change from state i to state j during time t.

See Also: Pij_t()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 135 of file AbstractSubstitutionModel.cpp.

Referenced by bpp::AbstractSubstitutionModel::Pij_t().

virtual const Matrix<double>& bpp::SubstitutionModel::getPij_t ( double t ) const

pure virtualinherited

Returns: All probabilities of change from state i to state j during time t.

See Also: Pij_t()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractBiblioSubstitutionModel::getPij_t(), and bpp::RE08::getPij_t().

double AbstractSubstitutionModel::getRate ( ) const

virtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 416 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

virtual double bpp::SubstitutionModel::getRate ( ) const

pure virtualinherited

Get the rate.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::getRate(), and bpp::MarkovModulatedSubstitutionModel::getRate().

const Matrix<double>& bpp::AbstractSubstitutionModel::getRowLeftEigenVectors ( ) const

inlinevirtualinherited

Returns: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 270 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const

pure virtualinherited

Returns: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

double AbstractSubstitutionModel::getScale ( ) const

virtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns: Minus the scalar product of diagonal elements and the frequencies vector.

Implements bpp::SubstitutionModel.

Definition at line 401 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::diag(), and bpp::AbstractSubstitutionModel::freq_.

Referenced by bpp::AbstractReversibleSubstitutionModel::updateMatrices().

virtual double bpp::SubstitutionModel::getScale ( ) const

pure virtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns: Minus the scalar product of diagonal elements and the frequencies vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const

inlinevirtualinherited

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 266 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const

pure virtualinherited

Returns: True if the model is diagonalizable in R.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isDiagonalizable().

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const

inlinevirtualinherited

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const

pure virtualinherited

Returns: True is the model is non-singular.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isNonSingular().

CodonDistancePhaseFrequenciesSubstitutionModel& bpp::CodonDistancePhaseFrequenciesSubstitutionModel::operator= ( const CodonDistancePhaseFrequenciesSubstitutionModel & model )

inline

Definition at line 130 of file CodonDistancePhaseFrequenciesSubstitutionModel.h.

References bpp::AbstractParameterAliasable::operator=(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::operator=(), bpp::AbstractCodonDistanceSubstitutionModel::operator=(), bpp::AbstractCodonSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::operator=(), and bpp::AbstractSubstitutionModel::operator=().

virtual double bpp::SubstitutionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The probability of change from state i to state j during time t.

See Also: getPij_t(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::Pij_t(), and bpp::RE08::Pij_t().

virtual double bpp::AbstractSubstitutionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlinevirtualinherited

Returns: The probability of change from state i to state j during time t.

See Also: getPij_t(), getStates()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 278 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_t().

virtual double bpp::SubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

pure virtualinherited

Returns: The rate in the generator of change from state i to state j.

See Also: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::gBGC::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), and bpp::YpR::updateMatrices().

virtual double bpp::AbstractSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

Returns: The rate in the generator of change from state i to state j.

See Also: getStates();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 276 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void CodonDistancePhaseFrequenciesSubstitutionModel::setFreq ( std::map< int, double > & frequencies )

virtual

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Reimplemented from bpp::AbstractCodonPhaseFrequenciesSubstitutionModel.

Definition at line 106 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::setFreq().

void AbstractSubstitutionModel::setFreqFromData	(	const SequenceContainer &	data,
		double	pseudoCount = `0`
	)

virtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters

data	The sequences to use.
pseudoCount	A quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Implements bpp::SubstitutionModel.

Definition at line 367 of file AbstractSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getCounts(), bpp::AbstractSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::size_, and bpp::AbstractSubstitutionModel::size_.

virtual void bpp::SubstitutionModel::setFreqFromData	(	const SequenceContainer &	data,
		double	pseudoCount = `0`
	)

pure virtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters

data	The sequences to use.
pseudoCount	A quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), and bpp::MarkovModulatedSubstitutionModel::setFreqFromData().

void CodonDistancePhaseFrequenciesSubstitutionModel::setNamespace ( const std::string & st )

Definition at line 98 of file CodonDistancePhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::setNamespace(), bpp::AbstractParameterAliasable::setNamespace(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::setNamespace(), and bpp::AbstractWordSubstitutionModel::setNamespace().

void AbstractSubstitutionModel::setRate ( double rate )

virtualinherited

Set the rate of the model (must be positive).

Parameters

rate	must be positive.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 423 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::hasParameter(), bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractParameterAliasable::setParameterValue(), and bpp::TextTools::toString().

Referenced by bpp::AbstractMixedSubstitutionModel::setRate().

virtual void bpp::SubstitutionModel::setRate ( double rate )

pure virtualinherited

Set the rate of the model (must be positive).

Parameters

rate	must be positive.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::setRate(), and bpp::MarkovModulatedSubstitutionModel::setRate().

void AbstractSubstitutionModel::setScale ( double scale )

virtualinherited

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implements bpp::SubstitutionModel.

Definition at line 410 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::scale().

virtual void bpp::SubstitutionModel::setScale ( double scale )

pure virtualinherited

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().

double bpp::AbstractSubstitutionModel::Sij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

Returns: The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implements bpp::SubstitutionModel.

Definition at line 256 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual double bpp::SubstitutionModel::Sij	(	size_t	i,
		size_t	j
	)		const

pure virtualinherited

Returns: The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::Sij().

void AbstractCodonSubstitutionModel::updateMatrices ( )

virtualinherited

Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The generator_ matrix and freq_ vector must be initialized.

Eigen values and vectors are computed from the generator and assigned to the eigenValues_ for the real part, iEigenValues_ for the imaginary part, rightEigenVectors_ and leftEigenVectors_ variables. isDiagonalizable_ checks if the generator_ is diagonalizable in R.

The optional rate parameter is not taken into account in this method to prevent unnecessary computation.

Reimplemented from bpp::AbstractWordSubstitutionModel.

Definition at line 151 of file AbstractCodonSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractCodonSubstitutionModel::hasParametrizedRates_, bpp::TextTools::toString(), bpp::TextTools::toString(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::Vrate_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Member Data Documentation

const Alphabet* bpp::AbstractSubstitutionModel::alphabet_

protectedinherited

The alphabet relevant to this model.

Definition at line 84 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractSubstitutionModel::getAlphabet(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), and bpp::AbstractWordSubstitutionModel::~AbstractWordSubstitutionModel().

std::vector<int> bpp::AbstractSubstitutionModel::chars_

protectedinherited

The list of supported chars.

Definition at line 102 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::AbstractSubstitutionModel::getAlphabetChar(), bpp::AbstractSubstitutionModel::getAlphabetChars(), bpp::AbstractSubstitutionModel::getModelStates(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), and bpp::RE08::RE08().

RowMatrix<double> bpp::AbstractSubstitutionModel::d2pijt_

mutableprotectedinherited

Definition at line 129 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::dpijt_

mutableprotectedinherited

Definition at line 128 of file AbstractSubstitutionModel.h.

bool bpp::AbstractSubstitutionModel::eigenDecompose_

protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 134 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), bpp::AbstractSubstitutionModel::operator=(), and bpp::AbstractSubstitutionModel::operator=().

Vdouble bpp::AbstractSubstitutionModel::eigenValues_

protectedinherited

The vector of eigen values.

Definition at line 139 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_

protectedinherited

The exchangeability matrix $S$ of the model, defined as $S_{ij}=\frac{Q_{ij}}{\pi_j}$ . When the model is reversible, this matrix is symetric.

Definition at line 122 of file AbstractSubstitutionModel.h.

Vdouble bpp::AbstractSubstitutionModel::freq_

protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_

protectedinherited

The generator matrix $Q$ of the model.

Definition at line 107 of file AbstractSubstitutionModel.h.

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_

protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 144 of file AbstractSubstitutionModel.h.

bool bpp::AbstractSubstitutionModel::isDiagonalizable_

protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 150 of file AbstractSubstitutionModel.h.

bool bpp::AbstractSubstitutionModel::isNonSingular_

protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 161 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_

protectedinherited

The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.

Definition at line 168 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_

mutableprotectedinherited

These ones are for bookkeeping:

Definition at line 127 of file AbstractSubstitutionModel.h.

double bpp::AbstractSubstitutionModel::rate_

protectedinherited

The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized.

Definition at line 97 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_

protectedinherited

The $U^-1$ matrix made of right eigen vectors (by column).

Definition at line 155 of file AbstractSubstitutionModel.h.

size_t bpp::AbstractSubstitutionModel::size_

protectedinherited

The size of the generator, i.e. the number of states.

Definition at line 89 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_

mutableprotectedinherited

For computational issues.

Definition at line 182 of file AbstractSubstitutionModel.h.

std::vector<std::string> bpp::AbstractWordSubstitutionModel::VnestedPrefix_

protectedinherited

Definition at line 86 of file AbstractWordSubstitutionModel.h.

std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_

protectedinherited

vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).

Definition at line 175 of file AbstractSubstitutionModel.h.

std::vector<double> bpp::AbstractWordSubstitutionModel::Vrate_

protectedinherited

Definition at line 88 of file AbstractWordSubstitutionModel.h.

std::vector<SubstitutionModel*> bpp::AbstractWordSubstitutionModel::VSubMod_

protectedinherited

Definition at line 85 of file AbstractWordSubstitutionModel.h.

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

Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h
Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation