bpp-phyl  2.1.0
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bpp::MixtureOfASubstitutionModel Class Reference

Substitution models defined as a mixture of nested substitution models. More...

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

+ Inheritance diagram for bpp::MixtureOfASubstitutionModel:
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List of all members.

Public Member Functions

 MixtureOfASubstitutionModel (const Alphabet *alpha, SubstitutionModel *model, std::map< std::string, DiscreteDistribution * > parametersDistributionsList, int ffrom=-1, int tto=-1) throw (Exception)
 MixtureOfASubstitutionModel (const MixtureOfASubstitutionModel &)
MixtureOfASubstitutionModel & operator= (const MixtureOfASubstitutionModel &)
 ~MixtureOfASubstitutionModel ()
MixtureOfASubstitutionModel * clone () const
std::string getName () const
 Get the name of the model.
void updateMatrices ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.
Vint getSubmodelNumbers (std::string &desc) const
void setFreq (std::map< int, double > &)
 sets the eq frequencies of the first nested model, and adapts the parameters at best to it (surely there is a better way to manage this).
const DiscreteDistribution * getDistribution (std::string &parName) const
 returns the DiscreteDistribution associated with a given parameter name.
int from () const
 Numbers of the states between which the substitution rates of all the submodels must be equal. If they are set to -1, this constraint does not exist among the submodels.
int to () const
virtual size_t getNumberOfModels () const
 returns the number of models in the mixture
virtual const SubstitutionModel * getNModel (size_t i) const
 Returns a specific model from the mixture.
virtual SubstitutionModel * getNModel (size_t i)
double getNRate (size_t i) const
 Returns the rate of a specific model from the mixture.
virtual void setRate (double rate)
 Set the rate of the model and the submodels.
virtual void setVRates (const Vdouble &vd)
 Sets the rates of the submodels to be proportional to a given vector, with the constraint that the mean rate of the mixture equals rate_.
virtual void normalizeVRates ()
 Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.
const std::vector< double > & getVRates () const
 Returns the vector of all the rates of the mixture.
virtual double getNProbability (size_t i) const
 Returns the probability of a specific model from the mixture.
virtual const std::vector
< double > & 		getProbabilities () const
 Returns the vector of probabilities.
virtual void setNProbability (size_t i, double prob)
 Sets the probability of a specific model from the mixture.
double Qij (size_t i, size_t j) const
 This function can not be applied here, so it is defined to prevent wrong usage.
virtual size_t getNumberOfStates () const
 From SubstitutionModel interface.
virtual const Matrix< double > & getPij_t (double t) const
virtual const Matrix< double > & getdPij_dt (double t) const
virtual const Matrix< double > & getd2Pij_dt2 (double t) const
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.
int getAlphabetChar (size_t i) const
 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.
std::vector< size_t > getModelStates (int i) const
 Get the state in the model corresponding to a particular char in the alphabet.
virtual double freq (size_t i) const =0
virtual double freq (size_t i) 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 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.
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed.
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed.
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 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.
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.
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.
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 =0
 Get the rate.
virtual double getRate () const
 Get the rate.
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.
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data.
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
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
virtual bool hasParameter (const std::string &name) const =0
bool hasParameter (const std::string &name) const
virtual const ParameterList & getParameters () const =0
const ParameterList & getParameters () const
virtual const Parameter & getParameter (const std::string &name) const =0
const Parameter & getParameter (const std::string &name) const
virtual double getParameterValue (const std::string &name) const =0
double getParameterValue (const std::string &name) const
virtual void setAllParametersValues (const ParameterList &parameters)=0
void setAllParametersValues (const ParameterList &parameters)
virtual void setParameterValue (const std::string &name, double value)=0
void setParameterValue (const std::string &name, double value)
virtual void setParametersValues (const ParameterList &parameters)=0
void setParametersValues (const ParameterList &parameters)
virtual bool matchParametersValues (const ParameterList &parameters)=0
bool matchParametersValues (const ParameterList &parameters)
virtual size_t getNumberOfParameters () const =0
size_t getNumberOfParameters () const
virtual void setNamespace (const std::string &prefix)=0
void setNamespace (const std::string &prefix)
virtual std::string getNamespace () const =0
std::string getNamespace () const
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
std::string getParameterNameWithoutNamespace (const std::string &name) const
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed.
std::string getFrom (const std::string &name) const

Protected Member Functions

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

std::vector< SubstitutionModel * > modelsContainer_
std::vector< double > vProbas_
std::vector< double > vRates_
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 $Q$ of the model.
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies.
RowMatrix< double > exchangeability_
 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.
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 $U^-1$ matrix made of right eigen vectors (by column).
bool isNonSingular_
 boolean value for non-singularity of rightEigenVectors_
RowMatrix< double > leftEigenVectors_
 The $U$ 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

std::map< std::string,
DiscreteDistribution * > 		distributionMap_
int from_
int to_

Friends

class AbstractBiblioSubstitutionModel

Detailed Description

Substitution models defined as a mixture of nested substitution models.

Author:
Laurent Guéguen

All the nested models are of the same type (for example T92 or GY94), and their parameter values can follow discrete distributions.

In this kind of model, there is no generator.

There is a map with connection from parameter names to discrete distributions, and then a related vector of "simple" substitution models for all the combinations of parameter values.

For example: HKY85(kappa=Gamma(n=3,alpha=2,beta=5), theta=TruncExponential(n=4,lambda=0.2,tp=1), theta1=0.4, theta2=TruncExponential(n=5,lambda=0.6,tp=1))

defines 3*4*5=60 different HKY85 nested models with rate one.

Optionnal arguments are used to homogeneize the rates of the nested models. Default values sets all the rates to 1, and given values are the two letters (from_ & to_) between which the substitution rates are the same in all nested models.

For example: HKY85(kappa=Gamma(n=3,alpha=2,beta=5), theta=TruncExponential(n=4,lambda=0.2,tp=1), theta1=0.4, theta2=TruncExponential(n=5,lambda=0.6,tp=1), from=A, to=C)

defines 3*4*5=60 different HKY85 nested models with the same A->C substitution rate.

If a distribution parameter does not respect the constraints of this parameter, there is an Exception at the creation of the wrong model, if any.

When used through a MixedTreeLikelihood objets, all the models have a specific probability, defined through the probabilities of the several parameter distributions. The computing of the likelihoods and probabilities are the expectation of the "simple" models values.

Definition at line 103 of file MixtureOfASubstitutionModel.h.

Constructor & Destructor Documentation

MixtureOfASubstitutionModel::MixtureOfASubstitutionModel ( const Alphabet *  alpha,
SubstitutionModel *  model,
std::map< std::string, DiscreteDistribution * >  parametersDistributionsList,
int  ffrom = -1,
int  tto = -1 
) throw (Exception)

Definition at line 53 of file MixtureOfASubstitutionModel.cpp.

References bpp::Constraint::clone(), bpp::DiscreteDistribution::getCategory(), bpp::Parameter::getConstraint(), bpp::DiscreteDistribution::getParameter(), bpp::DiscreteDistribution::getParameters(), bpp::Parameter::hasConstraint(), bpp::DiscreteDistribution::restrictToConstraint(), and bpp::ConstantDistribution::setNamespace().

Referenced by clone().

MixtureOfASubstitutionModel::MixtureOfASubstitutionModel ( const MixtureOfASubstitutionModel &  msm)

Definition at line 141 of file MixtureOfASubstitutionModel.cpp.

References distributionMap_.

MixtureOfASubstitutionModel::~MixtureOfASubstitutionModel ( )

Definition at line 176 of file MixtureOfASubstitutionModel.cpp.

References distributionMap_.

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().

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

Implements bpp::AbstractMixedSubstitutionModel.

Definition at line 122 of file MixtureOfASubstitutionModel.h.

References MixtureOfASubstitutionModel().

virtual double bpp::SubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const [pure virtual, inherited]
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 [inline, virtual, inherited]
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 virtual, inherited]
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 [inline, virtual, inherited]
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) [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_.

int bpp::MixtureOfASubstitutionModel::from ( ) const [inline]

Numbers of the states between which the substitution rates of all the submodels must be equal. If they are set to -1, this constraint does not exist among the submodels.

Definition at line 164 of file MixtureOfASubstitutionModel.h.

References from_.

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

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.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

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:
iThe 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:
iThe 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 > & AbstractMixedSubstitutionModel::getd2Pij_dt2 ( double  t) const [virtual, inherited]
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 153 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, and bpp::AbstractMixedSubstitutionModel::vProbas_.

const DiscreteDistribution * MixtureOfASubstitutionModel::getDistribution ( std::string &  parName) const

returns the DiscreteDistribution associated with a given parameter name.

Parameters:
parNamename of the parameter

Definition at line 186 of file MixtureOfASubstitutionModel.cpp.

References distributionMap_.

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

const Matrix< double > & AbstractMixedSubstitutionModel::getdPij_dt ( double  t) const [virtual, inherited]
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 133 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, and bpp::AbstractMixedSubstitutionModel::vProbas_.

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 $t$ 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 $t$ 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:
ithe index of the state in the model.
stateAn observed state in the sequence/site.
Returns:
1 or 0 depending if the two states are compatible.
Exceptions:
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif 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:
ithe index of the state in the model.
stateAn observed state in the sequence/site.
Returns:
1 or 0 depending if the two states are compatible.
Exceptions:
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif 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:
iThe 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:
iThe 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::MixtureOfASubstitutionModel::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 125 of file MixtureOfASubstitutionModel.h.

virtual const SubstitutionModel* bpp::AbstractMixedSubstitutionModel::getNModel ( size_t  i) const [inline, virtual, inherited]

Returns a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 131 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_.

Referenced by bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

virtual SubstitutionModel* bpp::AbstractMixedSubstitutionModel::getNModel ( size_t  i) [inline, virtual, inherited]

Implements bpp::MixedSubstitutionModel.

Definition at line 136 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_.

virtual double bpp::AbstractMixedSubstitutionModel::getNProbability ( size_t  i) const [inline, virtual, inherited]

Returns the probability of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 190 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::vProbas_.

double bpp::AbstractMixedSubstitutionModel::getNRate ( size_t  i) const [inline, virtual, inherited]

Returns the rate of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 145 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::vRates_.

virtual size_t bpp::AbstractMixedSubstitutionModel::getNumberOfModels ( ) const [inline, virtual, inherited]

returns the number of models in the mixture

Implements bpp::MixedSubstitutionModel.

Definition at line 123 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_.

Referenced by bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

size_t AbstractMixedSubstitutionModel::getNumberOfStates ( ) const [virtual, inherited]

From SubstitutionModel interface.

Implements bpp::SubstitutionModel.

Definition at line 108 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_.

Referenced by bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getPij_t(), updateMatrices(), and bpp::MixtureOfSubstitutionModels::updateMatrices().

const Matrix< double > & AbstractMixedSubstitutionModel::getPij_t ( double  t) const [virtual, inherited]
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 113 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractSubstitutionModel::pijt_, and bpp::AbstractMixedSubstitutionModel::vProbas_.

virtual const std::vector<double>& bpp::AbstractMixedSubstitutionModel::getProbabilities ( ) const [inline, virtual, inherited]

Returns the vector of probabilities.

Implements bpp::MixedSubstitutionModel.

Definition at line 200 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::vProbas_.

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().

Vint MixtureOfASubstitutionModel::getSubmodelNumbers ( std::string &  desc) const [virtual]

Implements bpp::MixedSubstitutionModel.

Definition at line 281 of file MixtureOfASubstitutionModel.cpp.

References distributionMap_, bpp::StringTokenizer::hasMoreToken(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::StringTokenizer::nextToken(), and bpp::TextTools::toInt().

const std::vector<double>& bpp::AbstractMixedSubstitutionModel::getVRates ( ) const [inline, virtual, inherited]

Returns the vector of all the rates of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 180 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::vRates_.

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().

void AbstractMixedSubstitutionModel::normalizeVRates ( ) [virtual, inherited]

Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.

Implements bpp::MixedSubstitutionModel.

Definition at line 202 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractMixedSubstitutionModel::vProbas_, and bpp::AbstractMixedSubstitutionModel::vRates_.

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

MixtureOfASubstitutionModel & MixtureOfASubstitutionModel::operator= ( const MixtureOfASubstitutionModel &  msm)

Definition at line 156 of file MixtureOfASubstitutionModel.cpp.

References distributionMap_, from_, and to_.

virtual double bpp::SubstitutionModel::Pij_t ( size_t  i,
size_t  j,
double  t 
) const [pure virtual, inherited]
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::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 [inline, virtual, inherited]
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().

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

This function can not be applied here, so it is defined to prevent wrong usage.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 220 of file AbstractMixedSubstitutionModel.h.

Referenced by updateMatrices().

void MixtureOfASubstitutionModel::setFreq ( std::map< int, double > &  m) [virtual]

sets the eq frequencies of the first nested model, and adapts the parameters at best to it (surely there is a better way to manage this).

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 275 of file MixtureOfASubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::AbstractMixedSubstitutionModel::modelsContainer_.

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

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

Parameters:
dataThe sequences to use.
pseudoCountA 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:
dataThe sequences to use.
pseudoCountA 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().

virtual void bpp::AbstractMixedSubstitutionModel::setNProbability ( size_t  i,
double  prob 
) [inline, virtual, inherited]

Sets the probability of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 209 of file AbstractMixedSubstitutionModel.h.

References bpp::AbstractMixedSubstitutionModel::vProbas_.

void AbstractMixedSubstitutionModel::setRate ( double  rate) [virtual, inherited]

Set the rate of the model and the submodels.

Parameters:
ratemust be positive.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 173 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractMixedSubstitutionModel::vProbas_, and bpp::AbstractMixedSubstitutionModel::vRates_.

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().

void AbstractMixedSubstitutionModel::setVRates ( const Vdouble &  vd) [virtual, inherited]

Sets the rates of the submodels to be proportional to a given vector, with the constraint that the mean rate of the mixture equals rate_.

Parameters:
vda vector of positive values such that the rates of the respective submodels are in the same proportions (ie this vector does not need to be normalized).

Implements bpp::MixedSubstitutionModel.

Reimplemented in bpp::MixtureOfSubstitutionModels.

Definition at line 191 of file AbstractMixedSubstitutionModel.cpp.

References bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractMixedSubstitutionModel::normalizeVRates(), and bpp::AbstractMixedSubstitutionModel::vRates_.

Referenced by updateMatrices().

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().

int bpp::MixtureOfASubstitutionModel::to ( ) const [inline]

Definition at line 165 of file MixtureOfASubstitutionModel.h.

References to_.

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

void MixtureOfASubstitutionModel::updateMatrices ( ) [virtual]

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::AbstractSubstitutionModel.

Definition at line 194 of file MixtureOfASubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), distributionMap_, bpp::AbstractSubstitutionModel::freq_, from_, bpp::AbstractMixedSubstitutionModel::getNModel(), bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractParameterAliasable::getParameter(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractMixedSubstitutionModel::Qij(), bpp::ParameterList::reset(), bpp::ParameterList::setParameterValue(), bpp::AbstractMixedSubstitutionModel::setVRates(), to_, and bpp::AbstractMixedSubstitutionModel::vProbas_.

Friends And Related Function Documentation

friend class AbstractBiblioSubstitutionModel [friend, inherited]

Definition at line 335 of file AbstractSubstitutionModel.h.

Member Data Documentation

const Alphabet* bpp::AbstractSubstitutionModel::alphabet_ [protected, inherited]

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=(), and bpp::AbstractWordSubstitutionModel::~AbstractWordSubstitutionModel().

std::vector<int> bpp::AbstractSubstitutionModel::chars_ [protected, inherited]

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=(), and bpp::RE08::RE08().

RowMatrix<double> bpp::AbstractSubstitutionModel::d2pijt_ [mutable, protected, inherited]

Definition at line 129 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), and bpp::AbstractSubstitutionModel::operator=().

std::map<std::string, DiscreteDistribution*> bpp::MixtureOfASubstitutionModel::distributionMap_ [private]

Definition at line 107 of file MixtureOfASubstitutionModel.h.

Referenced by getDistribution(), getSubmodelNumbers(), MixtureOfASubstitutionModel(), operator=(), updateMatrices(), and ~MixtureOfASubstitutionModel().

RowMatrix<double> bpp::AbstractSubstitutionModel::dpijt_ [mutable, protected, inherited]

Definition at line 128 of file AbstractSubstitutionModel.h.

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

bool bpp::AbstractSubstitutionModel::eigenDecompose_ [protected, inherited]

Tell if the eigen decomposition should be performed.

Definition at line 134 of file AbstractSubstitutionModel.h.

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

Vdouble bpp::AbstractSubstitutionModel::eigenValues_ [protected, inherited]

The vector of eigen values.

Definition at line 139 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_ [protected, inherited]

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.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::AbstractSubstitutionModel::getExchangeabilityMatrix(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::Coala::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::Sij(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::freq_ [protected, inherited]

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::Coala::computeEquilibriumFrequencies(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::AbstractSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::RN95s::getPij_t(), bpp::RE08::getPij_t(), bpp::RN95::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::RE08::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::L95::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

int bpp::MixtureOfASubstitutionModel::from_ [private]

Definition at line 108 of file MixtureOfASubstitutionModel.h.

Referenced by from(), operator=(), and updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_ [protected, inherited]

The generator matrix $Q$ of the model.

Definition at line 107 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractSubstitutionModel::getGenerator(), bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::Qij(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::L95::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_ [protected, inherited]

The vector of the imaginary part of the eigen values.

Definition at line 144 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getIEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

bool bpp::AbstractSubstitutionModel::isDiagonalizable_ [protected, inherited]

boolean value for diagonalizability in R of the generator_

Definition at line 150 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isDiagonalizable(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

bool bpp::AbstractSubstitutionModel::isNonSingular_ [protected, inherited]

boolean value for non-singularity of rightEigenVectors_

Definition at line 161 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isNonSingular(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_ [protected, inherited]

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

Definition at line 168 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRowLeftEigenVectors(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

std::vector<SubstitutionModel*> bpp::AbstractMixedSubstitutionModel::modelsContainer_ [protected, inherited]

Definition at line 81 of file AbstractMixedSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getNModel(), bpp::AbstractMixedSubstitutionModel::getNumberOfModels(), bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::getPij_t(), getSubmodelNumbers(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractMixedSubstitutionModel::operator=(), setFreq(), bpp::MixtureOfSubstitutionModels::setFreq(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractMixedSubstitutionModel::setVRates(), bpp::MixtureOfSubstitutionModels::setVRates(), updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), and bpp::AbstractMixedSubstitutionModel::~AbstractMixedSubstitutionModel().

RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_ [mutable, protected, inherited]

These ones are for bookkeeping:

Definition at line 127 of file AbstractSubstitutionModel.h.

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

double bpp::AbstractSubstitutionModel::rate_ [protected, inherited]

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.

Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::RN95s::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::RN95s::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::TN93::dPij_dt(), bpp::RN95::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::RN95s::getPij_t(), bpp::JCnuc::getPij_t(), bpp::TN93::getPij_t(), bpp::RN95::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::JCprot::getPij_t(), bpp::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::JCnuc::Pij_t(), bpp::TN93::Pij_t(), bpp::RN95::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::JCprot::Pij_t(), bpp::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), and bpp::BinarySubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_ [protected, inherited]

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

Definition at line 155 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getColumnRightEigenVectors(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

size_t bpp::AbstractSubstitutionModel::size_ [protected, inherited]

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

Definition at line 89 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::JCnuc::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::RE08::getNumberOfStates(), bpp::JCnuc::getPij_t(), bpp::RE08::getPij_t(), bpp::JCprot::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractSubstitutionModel::setFreqFromData(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RE08::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_ [mutable, protected, inherited]

For computational issues.

Definition at line 182 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), and bpp::YpR::updateMatrices().

int bpp::MixtureOfASubstitutionModel::to_ [private]

Definition at line 108 of file MixtureOfASubstitutionModel.h.

Referenced by operator=(), to(), and updateMatrices().

std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_ [protected, inherited]

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

Definition at line 175 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

std::vector<double> bpp::AbstractMixedSubstitutionModel::vProbas_ [protected, inherited]

Definition at line 88 of file AbstractMixedSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getNProbability(), bpp::AbstractMixedSubstitutionModel::getPij_t(), bpp::AbstractMixedSubstitutionModel::getProbabilities(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractMixedSubstitutionModel::operator=(), bpp::AbstractMixedSubstitutionModel::setNProbability(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::MixtureOfSubstitutionModels::setVRates(), updateMatrices(), and bpp::MixtureOfSubstitutionModels::updateMatrices().

std::vector<double> bpp::AbstractMixedSubstitutionModel::vRates_ [protected, inherited]

Definition at line 103 of file AbstractMixedSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::getNRate(), bpp::AbstractMixedSubstitutionModel::getVRates(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractMixedSubstitutionModel::operator=(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractMixedSubstitutionModel::setVRates(), bpp::MixtureOfSubstitutionModels::setVRates(), and bpp::MixtureOfSubstitutionModels::updateMatrices().

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