The Jukes-Cantor substitution model for nucleotides. More...

#include <Bpp/Phyl/Model/Nucleotide/JCnuc.h>

Inheritance diagram for bpp::JCnuc:

Collaboration diagram for bpp::JCnuc:

Public Member Functions
	JCnuc (const NucleicAlphabet *alpha)
virtual	~JCnuc ()
JCnuc *	clone () const
double	Pij_t (size_t i, size_t j, double d) const
double	dPij_dt (size_t i, size_t j, double d) const
double	d2Pij_dt2 (size_t i, size_t j, double d) const
const Matrix< double > &	getPij_t (double d) const
const Matrix< double > &	getdPij_dt (double d) const
const Matrix< double > &	getd2Pij_dt2 (double d) const
std::string	getName () const
	Get the name of the model.
void	setFreqFromData (const SequenceContainer &data)
	This method is disabled in this model since frequencies are not free parameters.
virtual size_t	getNumberOfStates () const
	Get the number of states.
virtual const std::vector< int > &	getAlphabetChars () const =0
virtual int	getAlphabetChar (size_t i) const =0
	Get the char in the alphabet corresponding to a given state in the model.
virtual std::vector< size_t >	getModelStates (int i) const =0
	Get the state in the model corresponding to a particular char in the alphabet.
virtual double	freq (size_t i) const =0
virtual double	Qij (size_t i, size_t j) const =0
virtual const Vdouble &	getFrequencies () const =0
virtual const Matrix< double > &	getGenerator () const =0
virtual const Matrix< double > &	getExchangeabilityMatrix () const =0
virtual double	Sij (size_t i, size_t j) const =0
virtual void	enableEigenDecomposition (bool yn)=0
	Set if eigenValues and Vectors must be computed.
virtual bool	enableEigenDecomposition ()=0
	Tell if eigenValues and Vectors must be computed.
virtual const Vdouble &	getEigenValues () const =0
virtual const Vdouble &	getIEigenValues () const =0
virtual bool	isDiagonalizable () const =0
virtual bool	isNonSingular () const =0
virtual const Matrix< double > &	getRowLeftEigenVectors () const =0
virtual const Matrix< double > &	getColumnRightEigenVectors () const =0
virtual const Alphabet *	getAlphabet () const =0
virtual double	getInitValue (size_t i, int state) const =0 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.
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.
virtual double	getRate () const =0
	Get the rate.
virtual void	setRate (double rate)=0
	Set the rate of the model (must be positive).
virtual void	addRateParameter ()=0
virtual void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
	Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual void	setFreq (std::map< int, double > &frequencies)
	Set equilibrium frequencies.
virtual const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
virtual size_t	getNumberOfIndependentParameters () const =0
virtual void	aliasParameters (const std::string &p1, const std::string &p2)=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 bool	hasParameter (const std::string &name) const =0
virtual const ParameterList &	getParameters () const =0
virtual const Parameter &	getParameter (const std::string &name) const =0
virtual double	getParameterValue (const std::string &name) const =0
virtual void	setAllParametersValues (const ParameterList &parameters)=0
virtual void	setParameterValue (const std::string &name, double value)=0
virtual void	setParametersValues (const ParameterList &parameters)=0
virtual bool	matchParametersValues (const ParameterList &parameters)=0
virtual size_t	getNumberOfParameters () const =0
virtual void	setNamespace (const std::string &prefix)=0
virtual std::string	getNamespace () const =0
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
const Alphabet *	getAlphabet () const
const std::vector< int > &	getAlphabetChars () const
int	getAlphabetChar (size_t i) const
	Get the char in the alphabet corresponding to a given state in the model.
std::vector< size_t >	getModelStates (int i) const
	Get the state in the model corresponding to a particular char in the alphabet.
virtual const Vdouble &	getFrequencies () const
const Matrix< double > &	getGenerator () const
const Matrix< double > &	getExchangeabilityMatrix () const
double	Sij (size_t i, size_t j) const
const Vdouble &	getEigenValues () const
const Vdouble &	getIEigenValues () const
bool	isDiagonalizable () const
bool	isNonSingular () const
const Matrix< double > &	getRowLeftEigenVectors () const
const Matrix< double > &	getColumnRightEigenVectors () const
virtual double	freq (size_t i) const
virtual double	Qij (size_t i, size_t j) const
double	getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
	Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual void	setFreq (std::map< int, double > &)
	Set equilibrium frequencies.
void	enableEigenDecomposition (bool yn)
	Set if eigenValues and Vectors must be computed.
bool	enableEigenDecomposition ()
	Tell if eigenValues and Vectors must be computed.
virtual void	fireParameterChanged (const ParameterList &parameters)
	Tells the model that a parameter value has changed.
void	addRateParameter ()
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.
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.
virtual double	getRate () const
	Get the rate.
virtual void	setRate (double rate)
	Set the rate of the model (must be positive).
size_t	getNumberOfIndependentParameters () const
void	aliasParameters (const std::string &p1, const std::string &p2)
void	unaliasParameters (const std::string &p1, const std::string &p2)
const ParameterList &	getIndependentParameters () const
std::vector< std::string >	getAlias (const std::string &name) 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
void	setNamespace (const std::string &prefix)
std::string	getNamespace () const
std::string	getParameterNameWithoutNamespace (const std::string &name) const
std::string	getFrom (const std::string &name) const
Protected Member Functions
void	updateMatrices ()
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_ ()
Protected Attributes
const Alphabet *	alphabet_
	The alphabet relevant to this model.
size_t	size_
	The size of the generator, i.e. the number of states.
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.
std::vector< int >	chars_
	The list of supported chars.
RowMatrix< double >	generator_
	The generator matrix of the model.
Vdouble	freq_
	The vector $\pi_e$ of equilibrium frequencies.
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.
RowMatrix< double >	pijt_
	These ones are for bookkeeping:
RowMatrix< double >	dpijt_
RowMatrix< double >	d2pijt_
bool	eigenDecompose_
	Tell if the eigen decomposition should be performed.
Vdouble	eigenValues_
	The vector of eigen values.
Vdouble	iEigenValues_
	The vector of the imaginary part of the eigen values.
bool	isDiagonalizable_
	boolean value for diagonalizability in R of the generator_
RowMatrix< double >	rightEigenVectors_
	The matrix made of right eigen vectors (by column).
bool	isNonSingular_
	boolean value for non-singularity of rightEigenVectors_
RowMatrix< double >	leftEigenVectors_
	The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.
std::vector< RowMatrix< double > >	vPowGen_
	vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).
RowMatrix< double >	tmpMat_
	For computational issues.
Private Attributes
double	exp_
RowMatrix< double >	p_
Friends
class	AbstractBiblioSubstitutionModel

Detailed Description

The Jukes-Cantor substitution model for nucleotides.

All rates equal:

$S = \begin{pmatrix} \cdots & r & r & r \\ r & \cdots & r & r \\ r & r & \cdots & r \\ r & r & r & \cdots \\ \end{pmatrix}$

$\pi = diag\left(\frac{1}{4}, \frac{1}{4}, \frac{1}{4}, \frac{1}{4}\right)$

Normalization: $r$ is set so that $\sum_i Q_{i,i}\pi_i = -1$ :

$S = \begin{pmatrix} -4 & \frac{4}{3} & \frac{4}{3} & \frac{4}{3} \\ \frac{4}{3} & -4 & \frac{4}{3} & \frac{4}{3} \\ \frac{4}{3} & \frac{4}{3} & -4 & \frac{4}{3} \\ \frac{4}{3} & \frac{4}{3} & \frac{4}{3} & -4 \\ \end{pmatrix}$

The normalized generator is obtained by taking the dot product of $S$ and $pi$ :

$Q = S . \pi = \begin{pmatrix} -1 & \frac{1}{3} & \frac{1}{3} & \frac{1}{3} \\ \frac{1}{3} & -1 & \frac{1}{3} & \frac{1}{3} \\ \frac{1}{3} & \frac{1}{3} & -1 & \frac{1}{3} \\ \frac{1}{3} & \frac{1}{3} & \frac{1}{3} & -1 \\ \end{pmatrix}$

The eigen values are $\left(0, -\frac{4}{3}, -\frac{4}{3}, -\frac{4}{3}\right)$ , the left eigen vectors are, by row:

$U = \begin{pmatrix} \frac{1}{4} & \frac{1}{4} & \frac{1}{4} & \frac{1}{4} \\ -\frac{1}{4} & -\frac{1}{4} & \frac{3}{4} & -\frac{1}{4} \\ -\frac{1}{4} & \frac{3}{4} & -\frac{1}{4} & -\frac{1}{4} \\ \frac{3}{4} & -\frac{1}{4} & -\frac{1}{4} & -\frac{1}{4} \\ \end{pmatrix}$

and the right eigen vectors are, by column:

$U^-1 = \begin{pmatrix} 1 & 0 & 0 & 1 \\ 1 & 0 & 1 & 0 \\ 1 & 1 & 0 & 0 \\ 1 & -1 & -1 & -1 \\ \end{pmatrix}$

In addition, a rate_ factor defines the mean rate of the model.

The probabilities of changes are computed analytically using the formulas:

$P_{i,j}(t) = \begin{cases} \frac{1}{4} + \frac{3}{4}e^{-rate\_*\frac{4}{3}t} & \text{if $i=j$}, \\ \frac{1}{4} - \frac{1}{4}e^{-rate\_*\frac{4}{3}t} & \text{otherwise}. \end{cases}$

First and second order derivatives are also computed analytically using the formulas:

$\frac{\partial P_{i,j}(t)}{\partial t} = rate\_ * \begin{cases} -e^{-rate\_*\frac{4}{3}t} & \text{if $i=j$}, \\ \frac{1}{3}e^{-rate*\frac{4}{3}t} & \text{otherwise}. \end{cases}$

$\frac{\partial^2 P_{i,j}(t)}{\partial t^2} = rate\_^2 *\begin{cases} \frac{4}{3}e^{-rate\_*\frac{4}{3}t} & \text{if $i=j$}, \\ -\frac{4}{9}e^{-rate\_*\frac{4}{3}t} & \text{otherwise}. \end{cases}$

Reference:

Jukes TH and Cantor CR (1969), Evolution_ of proteins molecules_, 121-123, in Mammalian_ protein metabolism_.

Definition at line 129 of file JCnuc.h.

Constructor & Destructor Documentation

JCnuc::JCnuc ( const NucleicAlphabet * alpha )

Definition at line 50 of file JCnuc.cpp.

References updateMatrices().

Referenced by clone().

virtual bpp::JCnuc::~JCnuc ( ) [inline, virtual]

Definition at line 140 of file JCnuc.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( ) [virtual, inherited]

Implements bpp::SubstitutionModel.

Definition at line 434 of file AbstractSubstitutionModel.cpp.

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

virtual void bpp::SubstitutionModel::addRateParameter ( ) [pure virtual, inherited]

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

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

JCnuc* bpp::JCnuc::clone ( ) const [inline, virtual]

Implements bpp::AbstractReversibleSubstitutionModel.

Definition at line 147 of file JCnuc.h.

References JCnuc().

double JCnuc::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const `[virtual]`

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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 139 of file JCnuc.cpp.

References bpp::AbstractSubstitutionModel::rate_.

double JCnuc::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const `[virtual]`

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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 129 of file JCnuc.cpp.

References bpp::AbstractSubstitutionModel::rate_.

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool yn ) [inline, virtual, inherited]

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 ( ) [inline, virtual, inherited]

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 290 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool yn ) [pure virtual, inherited]

Set if eigenValues and Vectors must be computed.

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

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

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( ) [pure virtual, inherited]

Tell if eigenValues and Vectors must be computed.

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

virtual void bpp::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList & parameters ) [inline, virtual, inherited]

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::JCprot, bpp::YpR, bpp::RE08, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::gBGC, bpp::CodonRateFrequenciesSubstitutionModel, and bpp::CodonRateSubstitutionModel.

Definition at line 297 of file AbstractSubstitutionModel.h.

References bpp::SubstitutionModel::getName(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::size(), and bpp::AbstractSubstitutionModel::updateMatrices().

virtual double bpp::SubstitutionModel::freq ( size_t i ) const [pure virtual, inherited]

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::dPij_dt(), bpp::AbstractBiblioSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getPij_t(), bpp::RE08::Pij_t(), and bpp::RE08::updateMatrices().

virtual double bpp::AbstractSubstitutionModel::freq ( size_t i ) const [inline, virtual, inherited]

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 [inline, virtual, inherited]

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 virtual, inherited]

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 virtual, inherited]

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(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

int bpp::AbstractSubstitutionModel::getAlphabetChar ( size_t i ) const [inline, virtual, inherited]

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 virtual, inherited]

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 [inline, virtual, inherited]

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_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getColumnRightEigenVectors ( ) const [inline, virtual, inherited]

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 virtual, inherited]

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 > & JCnuc::getd2Pij_dt2 ( double t ) const [virtual]

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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 175 of file JCnuc.cpp.

References exp_, p_, bpp::AbstractSubstitutionModel::rate_, and bpp::AbstractSubstitutionModel::size_.

const Matrix< double > & JCnuc::getdPij_dt ( double t ) const [virtual]

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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 162 of file JCnuc.cpp.

References exp_, p_, bpp::AbstractSubstitutionModel::rate_, and bpp::AbstractSubstitutionModel::size_.

const Vdouble& bpp::AbstractSubstitutionModel::getEigenValues ( ) const [inline, virtual, inherited]

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 virtual, inherited]

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 [inline, virtual, inherited]

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 virtual, inherited]

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 [inline, virtual, inherited]

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_.

Referenced by bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), and bpp::JCprot::setFreqFromData().

virtual const Vdouble& bpp::SubstitutionModel::getFrequencies ( ) const [pure virtual, inherited]

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(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const [inline, virtual, inherited]

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 [inline, virtual, inherited]

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 virtual, inherited]

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 Vdouble& bpp::AbstractSubstitutionModel::getIEigenValues ( ) const [inline, virtual, inherited]

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 virtual, inherited]

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) `[virtual, inherited]`

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 virtual, inherited]`

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 virtual, inherited]

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 [inline, virtual, inherited]

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::AbstractSubstitutionModel::chars_, and bpp::VectorTools::whichAll().

std::string bpp::JCnuc::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:: The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 157 of file JCnuc.h.

virtual size_t bpp::NucleotideSubstitutionModel::getNumberOfStates ( ) const [inline, virtual, inherited]

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.

Reimplemented in bpp::gBGC.

Definition at line 68 of file NucleotideSubstitutionModel.h.

const Matrix< double > & JCnuc::getPij_t ( double t ) const [virtual]

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

See also:: Pij_t()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 149 of file JCnuc.cpp.

References exp_, p_, bpp::AbstractSubstitutionModel::rate_, and bpp::AbstractSubstitutionModel::size_.

double AbstractSubstitutionModel::getRate ( ) const [virtual, inherited]

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 virtual, inherited]

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 [inline, virtual, inherited]

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 virtual, inherited]

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 [virtual, inherited]

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(), bpp::AbstractSubstitutionModel::freq_, and bpp::AbstractSubstitutionModel::generator_.

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

virtual double bpp::SubstitutionModel::getScale ( ) const [pure virtual, inherited]

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 [inline, virtual, inherited]

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 virtual, inherited]

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 [inline, virtual, inherited]

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 virtual, inherited]

Returns:: True is the model is non-singular.

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

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

double JCnuc::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const `[virtual]`

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

See also:: getPij_t(), getStates()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 119 of file JCnuc.cpp.

References bpp::AbstractSubstitutionModel::rate_.

virtual double bpp::SubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const `[pure virtual, inherited]`

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(), and bpp::YpR::updateMatrices().

virtual double bpp::AbstractSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const `[inline, virtual, inherited]`

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 AbstractSubstitutionModel::setFreq ( std::map< int, double > & frequencies ) [virtual, inherited]

Set equilibrium frequencies.

Parameters:

frequencies The map of the frequencies to use.

Reimplemented from bpp::SubstitutionModel.

Reimplemented in bpp::F84, bpp::HKY85, bpp::MixtureOfSubstitutionModels, bpp::T92, bpp::AbstractWordSubstitutionModel, bpp::GTR, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::RN95, bpp::TN93, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::RN95s, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::BinarySubstitutionModel, bpp::SSR, bpp::L95, and bpp::CodonRateFrequenciesSubstitutionModel.

Definition at line 389 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::size_, and bpp::AbstractSubstitutionModel::updateMatrices().

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

virtual void bpp::SubstitutionModel::setFreq ( std::map< int, double > & frequencies ) [inline, virtual, inherited]

Set equilibrium frequencies.

Parameters:

frequencies The map of the frequencies to use.

Definition at line 455 of file SubstitutionModel.h.

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

void bpp::JCnuc::setFreqFromData ( const SequenceContainer & data ) [inline]

This method is disabled in this model since frequencies are not free parameters.

Consider using the HKY85 model for instance if you want to set frequencies as parameters.

Parameters:

data	Useless parameter.

Definition at line 166 of file JCnuc.h.

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

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(), and bpp::AbstractSubstitutionModel::size_.

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

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 AbstractSubstitutionModel::setRate ( double rate ) [virtual, inherited]

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::AbstractParameterAliasable::setParameterValue(), and bpp::TextTools::toString().

virtual void bpp::SubstitutionModel::setRate ( double rate ) [pure virtual, inherited]

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 ) [virtual, inherited]

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::AbstractSubstitutionModel::generator_, and bpp::MatrixTools::scale().

virtual void bpp::SubstitutionModel::setScale ( double scale ) [pure virtual, inherited]

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 `[inline, virtual, inherited]`

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 virtual, inherited]`

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 JCnuc::updateMatrices ( ) [protected, virtual]

In the case of the model of Jukes & Cantor, this method is not usefull since the generator is fully determined. No matrice can be changed... This method is only used in the constructor of the class.

Reimplemented from bpp::AbstractReversibleSubstitutionModel.

Definition at line 62 of file JCnuc.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::leftEigenVectors_, and bpp::AbstractSubstitutionModel::rightEigenVectors_.

Referenced by JCnuc().