Basal class for words of reversible substitution models. More...

#include <Bpp/Phyl/Model/WordSubstitutionModel.h>

Inheritance diagram for bpp::WordSubstitutionModel:

Collaboration diagram for bpp::WordSubstitutionModel:

Public Member Functions
	WordSubstitutionModel (const std::vector< SubstitutionModel * > &modelVector, const std::string &st="")
	Build a new WordSubstitutionModel object from a Vector of pointers to SubstitutionModels. More...

	WordSubstitutionModel (SubstitutionModel *pmodel, unsigned int num, const std::string &st="")
	Build a new WordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models. More...

virtual	~WordSubstitutionModel ()

WordSubstitutionModel *	clone () const

virtual const RowMatrix< double > &	getPij_t (double d) const

virtual const RowMatrix< double > &	getdPij_dt (double d) const

virtual const RowMatrix< double > &	getd2Pij_dt2 (double d) const

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

void	setNamespace (const std::string &prefix)

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

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

virtual void	setFreq (std::map< int, double > &freqs)
	Estimation of the parameters of the models so that the *equilibrium frequencies match the given ones. More...

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. 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 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

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

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) 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. 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 void	fireParameterChanged (const ParameterList &parameters)
	Tells the model that a parameter value has changed. More...

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. 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
	Get the rate. More...

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

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

Protected Member Functions
	WordSubstitutionModel (const Alphabet *alph, const std::string &="")
	Constructor for the derived classes only. More...

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

virtual void	completeMatrices ()
	Called by updateMatrices to handle specific modifications for inheriting classes. 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

Basal class for words of reversible substitution models.

Author: Laurent Guéguen

Only substitutions with one letter changed are accepted. Hence the equilibrium frequency of each word is the product of the equilibrium frequencies of the letters.

If there are $n$ models, $\rho_i$ is the rate of model i ( $\sum_{i=1}^{n} \rho_i = 1$ ) and the rates are defined by relative rates parameters $r_i$ (called "relratei") with:

$1 <= i < n, \rho_i = (1-r_1).(1-r_2)...(1-r_{i-1}).r_{i}$

$\rho_n = (1-r_1).(1-r_2)...(1-r_{n-1})$

and

$\forall 1 <= i < n, r_i = \frac{\rho_i}{1-(\rho_1+...\rho_{i-1})}$

where $\rho_i$ stands for the rate of position $i$ .

Definition at line 74 of file WordSubstitutionModel.h.

Constructor & Destructor Documentation

WordSubstitutionModel::WordSubstitutionModel	(	const std::vector< SubstitutionModel * > &	modelVector,
		const std::string &	st = `""`
	)

Build a new WordSubstitutionModel object from a Vector of pointers to SubstitutionModels.

Parameters

modelVector	the Vector of substitution models to use, in the order of the positions in the words from left to right. All the models must be different objects to avoid parameters redundancy, otherwise only the first model is used. The used models are owned by the instance.
st	the Namespace.

Definition at line 59 of file WordSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::TextTools::toString(), updateMatrices(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by clone().

WordSubstitutionModel::WordSubstitutionModel	(	SubstitutionModel *	pmodel,
		unsigned int	num,
		const std::string &	st = `""`
	)

Build a new WordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models.

Parameters

pmodel	pointer to the substitution model to use in all the positions. It is owned by the instance.
num	The number of models involved.
st	the Namespace.

Definition at line 89 of file WordSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::TextTools::toString(), and updateMatrices().

virtual bpp::WordSubstitutionModel::~WordSubstitutionModel ( )

inlinevirtual

Definition at line 103 of file WordSubstitutionModel.h.

WordSubstitutionModel::WordSubstitutionModel	(	const Alphabet *	alph,
		const std::string &	st = `""`
	)

protected

Constructor for the derived classes only.

Definition at line 79 of file WordSubstitutionModel.cpp.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )

virtualinherited

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

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

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 $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation