bpp-phyl  2.1.0
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bpp::AbstractSubstitutionModel Class Reference

Partial implementation of the SubstitutionModel interface. More...

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

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

Public Member Functions

 AbstractSubstitutionModel (const Alphabet *alpha, const std::string &prefix)
 AbstractSubstitutionModel (const AbstractSubstitutionModel &model)
AbstractSubstitutionModel & operator= (const AbstractSubstitutionModel &model)
virtual ~AbstractSubstitutionModel ()
virtual AbstractSubstitutionModel * clone () 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
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
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.
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).
virtual std::string getName () const =0
 Get the name of the model.
virtual size_t getNumberOfStates () const =0
 Get the number of states.
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
void setNamespace (const std::string &prefix)
const ParameterList & getIndependentParameters () const
size_t getNumberOfIndependentParameters () const
void aliasParameters (const std::string &p1, const std::string &p2)
void unaliasParameters (const std::string &p1, const std::string &p2)
std::vector< std::string > getAlias (const std::string &name) const
std::string getFrom (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

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

Friends

class AbstractBiblioSubstitutionModel

Detailed Description

Partial implementation of the SubstitutionModel interface.

This abstract class provides some fields, namely:

  • alphabet_: a pointer toward the alphabet,
  • size_: the size of the alphabet, a parameter frequently called during various computations,
  • rate_: the rate of the model
  • generator_, leftEigenVectors_, rightEigenVectors_: useful matrices,
  • eigenValues_, iEigenValues_, freq_: useful vectors.
  • isDiagonalizable_ : boolean value useful for computation of the exponential

Access methods for these fields are implemented.

This class also provides the updateMatrices() method, which computes eigen values and vectors and fills the corresponding vector (eigenValues_) and matrices (leftEigenVectors_ and rightEigenVectors_) from the generator.

The freq_ vector and generator_ matrices are hence the only things to provide to create a substitution model. It is also possible to redefine one of these methods for better efficiency. The Pij_t, dPij_dt and d2Pij_dt2 are particularly inefficient since the matrix formula is used to compute all probabilities, and then the result for the initial and final state of interest is retrieved.

Note:
This class is dedicated to "simple" substitution models, for which the number of states is equivalent to the number of characters in the alphabet. Consider using the MarkovModulatedSubstitutionModel for more complexe cases.

Definition at line 76 of file AbstractSubstitutionModel.h.

Constructor & Destructor Documentation

AbstractSubstitutionModel::AbstractSubstitutionModel ( const Alphabet *  alpha,
const std::string &  prefix 
)

Definition at line 56 of file AbstractSubstitutionModel.cpp.

References chars_, freq_, and size_.

bpp::AbstractSubstitutionModel::AbstractSubstitutionModel ( const AbstractSubstitutionModel &  model) [inline]

Definition at line 187 of file AbstractSubstitutionModel.h.

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

Definition at line 235 of file AbstractSubstitutionModel.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( ) [virtual]

Implements bpp::SubstitutionModel.

Definition at line 434 of file AbstractSubstitutionModel.cpp.

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

virtual AbstractSubstitutionModel* bpp::AbstractSubstitutionModel::clone ( ) const [pure virtual]

Implements bpp::AbstractParameterAliasable.

Implemented in bpp::AbstractReversibleSubstitutionModel, bpp::YpR_Gen, bpp::YpR_Sym, bpp::HKY85, bpp::F84, bpp::JCprot, bpp::T92, bpp::K80, bpp::GTR, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::RN95, bpp::MixtureOfSubstitutionModels, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::AbstractCodonSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::WAG01, bpp::SSR, bpp::L95, bpp::AbstractMixedSubstitutionModel, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::CodonRateFrequenciesSubstitutionModel, bpp::gBGC, bpp::WordSubstitutionModel, bpp::TripletSubstitutionModel, bpp::CodonRateSubstitutionModel, bpp::Coala, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, and bpp::LLG08_UL2::EmbeddedModel.

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

Implements bpp::SubstitutionModel.

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

Definition at line 280 of file AbstractSubstitutionModel.h.

References getd2Pij_dt2().

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

Implements bpp::SubstitutionModel.

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

Definition at line 279 of file AbstractSubstitutionModel.h.

References getdPij_dt().

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 288 of file AbstractSubstitutionModel.h.

References eigenDecompose_.

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

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 290 of file AbstractSubstitutionModel.h.

References eigenDecompose_.

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

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

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 updateMatrices().

virtual double bpp::AbstractSubstitutionModel::freq ( size_t  i) const [inline, virtual]
Returns:
Equilibrium frequency associated to character i.
See also:
getFrequencies(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 274 of file AbstractSubstitutionModel.h.

References freq_.

const Alphabet* bpp::AbstractSubstitutionModel::getAlphabet ( ) const [inline, virtual]
Returns:
Get the alphabet associated to this model.

Implements bpp::SubstitutionModel.

Definition at line 242 of file AbstractSubstitutionModel.h.

References alphabet_.

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

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

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 chars_.

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetChars ( ) const [inline, virtual]
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 chars_.

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

const Matrix< double > & AbstractSubstitutionModel::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()

Implements bpp::SubstitutionModel.

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

Definition at line 275 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), d2pijt_, eigenValues_, bpp::VectorTools::exp(), bpp::MatrixTools::getId(), iEigenValues_, isDiagonalizable_, isNonSingular_, leftEigenVectors_, bpp::MatrixTools::mult(), rate_, rightEigenVectors_, bpp::MatrixTools::scale(), size_, bpp::NumTools::sqr(), tmpMat_, and vPowGen_.

Referenced by d2Pij_dt2().

const Matrix< double > & AbstractSubstitutionModel::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()

Implements bpp::SubstitutionModel.

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

Definition at line 206 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), dpijt_, eigenValues_, bpp::VectorTools::exp(), bpp::MatrixTools::getId(), iEigenValues_, isDiagonalizable_, isNonSingular_, leftEigenVectors_, bpp::MatrixTools::mult(), rate_, rightEigenVectors_, bpp::MatrixTools::scale(), size_, tmpMat_, and vPowGen_.

Referenced by dPij_dt().

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

const Matrix<double>& bpp::AbstractSubstitutionModel::getExchangeabilityMatrix ( ) const [inline, virtual]
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 exchangeability_.

virtual const Vdouble& bpp::AbstractSubstitutionModel::getFrequencies ( ) const [inline, virtual]
Returns:
A vector of all equilibrium frequencies.
See also:
freq()

Implements bpp::SubstitutionModel.

Definition at line 250 of file AbstractSubstitutionModel.h.

References freq_.

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

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]
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 generator_.

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

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

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.

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( int  i) const [inline, virtual]

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

virtual std::string bpp::SubstitutionModel::getName ( ) const [pure virtual, inherited]

Get the name of the model.

Returns:
The name of this model.

Implemented in bpp::YpR_Gen, bpp::YpR_Sym, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::GTR, bpp::TN93, bpp::RE08, bpp::MixtureOfSubstitutionModels, bpp::JCnuc, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::LLG08_EX3, bpp::WAG01, bpp::WordSubstitutionModel, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::SSR, bpp::L95, bpp::DSO78, bpp::JTT92, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::gBGC, bpp::LG08, bpp::CodonRateFrequenciesSubstitutionModel, bpp::G2001, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::TS98, bpp::YNGKP_M7, bpp::GY94, bpp::YNGKP_M2, bpp::YNGKP_M3, bpp::TripletSubstitutionModel, bpp::YN98, bpp::CodonRateSubstitutionModel, bpp::MG94, bpp::Coala, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, and bpp::LLG08_UL2::EmbeddedModel.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), fireParameterChanged(), bpp::gBGC::getName(), bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), bpp::BppOSubstitutionModelFormat::readMixed_(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().

virtual size_t bpp::SubstitutionModel::getNumberOfStates ( ) const [pure 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.

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

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

const Matrix< double > & AbstractSubstitutionModel::getPij_t ( double  t) const [virtual]
Returns:
All probabilities of change from state i to state j during time t.
See also:
Pij_t()

Implements bpp::SubstitutionModel.

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

Definition at line 135 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), eigenValues_, bpp::VectorTools::exp(), bpp::MatrixTools::getId(), iEigenValues_, isDiagonalizable_, isNonSingular_, leftEigenVectors_, bpp::MatrixTools::mult(), pijt_, rate_, rightEigenVectors_, size_, tmpMat_, and vPowGen_.

Referenced by Pij_t().

double AbstractSubstitutionModel::getRate ( ) const [virtual]

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 416 of file AbstractSubstitutionModel.cpp.

References rate_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getRowLeftEigenVectors ( ) const [inline, virtual]
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 leftEigenVectors_.

double AbstractSubstitutionModel::getScale ( ) const [virtual]

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(), freq_, and generator_.

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

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const [inline, virtual]
Returns:
True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 266 of file AbstractSubstitutionModel.h.

References isDiagonalizable_.

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const [inline, virtual]
Returns:
True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 268 of file AbstractSubstitutionModel.h.

References isNonSingular_.

AbstractSubstitutionModel& bpp::AbstractSubstitutionModel::operator= ( const AbstractSubstitutionModel &  model) [inline]

Definition at line 210 of file AbstractSubstitutionModel.h.

References alphabet_, chars_, d2pijt_, dpijt_, eigenDecompose_, eigenValues_, exchangeability_, freq_, generator_, iEigenValues_, isDiagonalizable_, isNonSingular_, leftEigenVectors_, pijt_, rate_, rightEigenVectors_, size_, tmpMat_, and vPowGen_.

virtual double bpp::AbstractSubstitutionModel::Pij_t ( size_t  i,
size_t  j,
double  t 
) const [inline, virtual]
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 getPij_t().

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

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

Set equilibrium frequencies.

Parameters:
frequenciesThe 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 freq_, size_, and updateMatrices().

Referenced by setFreqFromData().

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

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(), setFreq(), and size_.

void AbstractSubstitutionModel::setRate ( double  rate) [virtual]

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

Parameters:
ratemust be positive.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 423 of file AbstractSubstitutionModel.cpp.

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

void AbstractSubstitutionModel::setScale ( double  scale) [virtual]

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

double bpp::AbstractSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const [inline, virtual]
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 exchangeability_.

void AbstractSubstitutionModel::updateMatrices ( ) [protected, 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 in bpp::AbstractReversibleSubstitutionModel, bpp::YpR_Gen, bpp::YpR_Sym, bpp::JCprot, bpp::F84, bpp::HKY85, bpp::T92, bpp::RE08, bpp::K80, bpp::YpR, bpp::JCnuc, bpp::RN95, bpp::TN93, bpp::GTR, bpp::MixtureOfSubstitutionModels, bpp::AbstractCodonSubstitutionModel, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::SSR, bpp::gBGC, bpp::L95, bpp::WordSubstitutionModel, bpp::Coala, and bpp::AbstractWordSubstitutionModel.

Definition at line 87 of file AbstractSubstitutionModel.cpp.

References bpp::ApplicationTools::displayMessage(), eigenValues_, enableEigenDecomposition(), exchangeability_, freq_, generator_, bpp::EigenValue< Real >::getImagEigenValues(), bpp::EigenValue< Real >::getRealEigenValues(), bpp::EigenValue< Real >::getV(), iEigenValues_, bpp::MatrixTools::inv(), isDiagonalizable_, isNonSingular_, leftEigenVectors_, rightEigenVectors_, size_, bpp::MatrixTools::Taylor(), bpp::NumConstants::TINY(), and vPowGen_.

Referenced by fireParameterChanged(), and setFreq().

Friends And Related Function Documentation

friend class AbstractBiblioSubstitutionModel [friend]

Definition at line 335 of file AbstractSubstitutionModel.h.

Member Data Documentation

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

The alphabet relevant to this model.

Definition at line 84 of file AbstractSubstitutionModel.h.

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

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

The list of supported chars.

Definition at line 102 of file AbstractSubstitutionModel.h.

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

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

Definition at line 129 of file AbstractSubstitutionModel.h.

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

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

Definition at line 128 of file AbstractSubstitutionModel.h.

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

bool bpp::AbstractSubstitutionModel::eigenDecompose_ [protected]

Tell if the eigen decomposition should be performed.

Definition at line 134 of file AbstractSubstitutionModel.h.

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

Vdouble bpp::AbstractSubstitutionModel::eigenValues_ [protected]

The vector of eigen values.

Definition at line 139 of file AbstractSubstitutionModel.h.

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

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

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(), getExchangeabilityMatrix(), operator=(), bpp::RE08::RE08(), bpp::Coala::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), 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(), updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::freq_ [protected]

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

Referenced by 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(), freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), getFrequencies(), bpp::RN95s::getPij_t(), bpp::RE08::getPij_t(), bpp::RN95::getPij_t(), getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), operator=(), bpp::RN95s::Pij_t(), bpp::RE08::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), 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(), bpp::MixtureOfASubstitutionModel::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(), updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

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

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(), getGenerator(), getScale(), operator=(), Qij(), bpp::RE08::RE08(), 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(), updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_ [protected]

The vector of the imaginary part of the eigen values.

Definition at line 144 of file AbstractSubstitutionModel.h.

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

bool bpp::AbstractSubstitutionModel::isDiagonalizable_ [protected]

boolean value for diagonalizability in R of the generator_

Definition at line 150 of file AbstractSubstitutionModel.h.

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

bool bpp::AbstractSubstitutionModel::isNonSingular_ [protected]

boolean value for non-singularity of rightEigenVectors_

Definition at line 161 of file AbstractSubstitutionModel.h.

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

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

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(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), getRowLeftEigenVectors(), 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 updateMatrices().

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

These ones are for bookkeeping:

Definition at line 127 of file AbstractSubstitutionModel.h.

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

double bpp::AbstractSubstitutionModel::rate_ [protected]

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 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(), 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(), 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(), getPij_t(), getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), 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(), setRate(), and bpp::BinarySubstitutionModel::updateMatrices().

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

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

Definition at line 155 of file AbstractSubstitutionModel.h.

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

size_t bpp::AbstractSubstitutionModel::size_ [protected]

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

Definition at line 89 of file AbstractSubstitutionModel.h.

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

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

For computational issues.

Definition at line 182 of file AbstractSubstitutionModel.h.

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

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

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

Definition at line 175 of file AbstractSubstitutionModel.h.

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

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