bpp-phyl  2.4.0
bpp::TripletSubstitutionModel Class Referenceabstract

Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional). More...

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

+ Inheritance diagram for bpp::TripletSubstitutionModel:
+ Collaboration diagram for bpp::TripletSubstitutionModel:

Public Member Functions

 TripletSubstitutionModel (const CodonAlphabet *palph, NucleotideSubstitutionModel *pmod)
 Build a new TripletSubstitutionModel object from a pointer to a NucleotideSubstitutionModel. More...
 
 TripletSubstitutionModel (const CodonAlphabet *palph, NucleotideSubstitutionModel *pmod1, NucleotideSubstitutionModel *pmod2, NucleotideSubstitutionModel *pmod3)
 Build a new TripletSubstitutionModel object from three pointers to NucleotideSubstitutionModels. More...
 
 ~TripletSubstitutionModel ()
 
TripletSubstitutionModelclone () const
 
std::string getName () const
 Get the name of the model. More...
 
virtual const RowMatrix< double > & getPij_t (double d) const
 
virtual const RowMatrix< double > & getdPij_dt (double d) const
 
virtual const RowMatrix< double > & getd2Pij_dt2 (double d) const
 
void setNamespace (const std::string &prefix)
 
virtual size_t getNumberOfStates () const
 Get the number of states. More...
 
const SubstitutionModelgetNModel (size_t i) const
 returns the ith model, or Null if i is not a valid number. More...
 
size_t getNumberOfModels () const
 
virtual void setFreq (std::map< int, double > &freqs)
 Estimation of the parameters of the models so that the equilibrium frequencies match the given ones. More...
 
const AlphabetgetAlphabet () const
 
const StateMapgetStateMap () const
 
const std::vector< int > & getAlphabetStates () const
 
std::string getAlphabetStateAsChar (size_t index) const
 
int getAlphabetStateAsInt (size_t index) const
 
std::vector< size_t > getModelStates (int code) const
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
std::vector< size_t > getModelStates (const std::string &code) const
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
const VdoublegetFrequencies () const
 
bool computeFrequencies () const
 
void computeFrequencies (bool yn)
 
const Matrix< double > & getGenerator () const
 
const Matrix< double > & getExchangeabilityMatrix () const
 
double Sij (size_t i, size_t j) const
 
const VdoublegetEigenValues () const
 
const VdoublegetIEigenValues () 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
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed. More...
 
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed. More...
 
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. More...
 
void addRateParameter ()
 add a "rate" parameter to the model, that handles the overall rate of the process. More...
 
void setScalable (bool scalable)
 sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...
 
virtual bool isScalable () const
 returns if model is scalable More...
 
double getScale () const
 return scale More...
 
void setScale (double scale)
 Multiplies the current generator by the given scale. More...
 
void normalize ()
 normalize the generator More...
 
void setDiagonal ()
 set the diagonal of the generator such that sum on each line equals 0. More...
 
virtual double getRate () const
 The rate of the substitution process. More...
 
virtual void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
virtual const FrequenciesSetgetFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 
virtual size_t getNumberOfIndependentParameters () const =0
 
size_t getNumberOfIndependentParameters () const
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
virtual const ParameterListgetIndependentParameters () const =0
 
const ParameterListgetIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const =0
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const =0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const =0
 
bool hasParameter (const std::string &name) const
 
virtual const ParameterListgetParameters () const =0
 
const ParameterListgetParameters () const
 
virtual const ParametergetParameter (const std::string &name) const =0
 
const ParametergetParameter (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 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
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 

Protected Member Functions

virtual void updateMatrices ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
virtual void completeMatrices ()
 Called by updateMatrices to handle specific modifications for inheriting classes. More...
 
virtual void fillBasicGenerator ()
 First fill of the generator, from the position model. More...
 
VdoublegetFrequencies_ ()
 
const std::shared_ptr< Parameter > & getSharedParameter (size_t i) const
 
std::shared_ptr< Parameter > & getSharedParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
ParametergetParameter_ (const std::string &name)
 
ParametergetParameter_ (size_t index)
 
const ParametergetParameter_ (size_t index) const
 
ParametergetParameterWithNamespace_ (const std::string &name)
 
const ParametergetParameterWithNamespace_ (const std::string &name) const
 
ParameterListgetParameters_ ()
 

Protected Attributes

std::vector< SubstitutionModel * > VSubMod_
 
std::vector< std::string > VnestedPrefix_
 
std::vector< double > Vrate_
 
const Alphabetalphabet_
 The alphabet relevant to this model. More...
 
std::shared_ptr< const StateMapstateMap_
 The map of model states with alphabet states. More...
 
size_t size_
 The size of the generator, i.e. the number of states. More...
 
bool isScalable_
 If the model is scalable (ie generator can be normalized automatically). More...
 
double rate_
 The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...
 
RowMatrix< double > generator_
 The generator matrix $Q$ of the model. More...
 
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies. More...
 
bool computeFreq_
 if the Frequencies must be computed from the generator More...
 
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. More...
 
RowMatrix< double > pijt_
 These ones are for bookkeeping: More...
 
RowMatrix< double > dpijt_
 
RowMatrix< double > d2pijt_
 
bool eigenDecompose_
 Tell if the eigen decomposition should be performed. More...
 
Vdouble eigenValues_
 The vector of eigen values. More...
 
Vdouble iEigenValues_
 The vector of the imaginary part of the eigen values. More...
 
bool isDiagonalizable_
 boolean value for diagonalizability in R of the generator_ More...
 
RowMatrix< double > rightEigenVectors_
 The $U^-1$ matrix made of right eigen vectors (by column). More...
 
bool isNonSingular_
 boolean value for non-singularity of rightEigenVectors_ More...
 
RowMatrix< double > leftEigenVectors_
 The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More...
 
std::vector< RowMatrix< double > > vPowGen_
 vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More...
 
RowMatrix< double > tmpMat_
 For computational issues. More...
 

Detailed Description

Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional).

Author
Laurent Gu├ęguen

Objects of this class are built from three substitution models of NucleicAlphabets. No model is directly accessible.

Definition at line 63 of file TripletSubstitutionModel.h.

Constructor & Destructor Documentation

TripletSubstitutionModel::TripletSubstitutionModel ( const CodonAlphabet palph,
NucleotideSubstitutionModel pmod1,
NucleotideSubstitutionModel pmod2,
NucleotideSubstitutionModel pmod3 
)

Build a new TripletSubstitutionModel object from three pointers to NucleotideSubstitutionModels.

Parameters
palphpointer to a CodonAlphabet
pmod1,pmod2,pmod3pointers to the NucleotideSubstitutionModels to use in the three positions. All the models must be different objects to avoid parameters redundancy, otherwise only the first model is used. The used models are owned by the instance.

Definition at line 84 of file TripletSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::ParameterAliasable::getNamespace(), bpp::ParameterAliasable::getParameters(), bpp::Parameter::PROP_CONSTRAINT_EX, bpp::ParameterAliasable::setNamespace(), bpp::TextTools::toString(), bpp::WordSubstitutionModel::updateMatrices(), bpp::AbstractWordSubstitutionModel::VnestedPrefix_, bpp::AbstractWordSubstitutionModel::Vrate_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

bpp::TripletSubstitutionModel::~TripletSubstitutionModel ( )
inline

Definition at line 97 of file TripletSubstitutionModel.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited
TripletSubstitutionModel* bpp::TripletSubstitutionModel::clone ( ) const
inlinevirtual

Implements bpp::AbstractSubstitutionModel.

Definition at line 99 of file TripletSubstitutionModel.h.

References getName(), and TripletSubstitutionModel().

void WordSubstitutionModel::completeMatrices ( )
protectedvirtualinherited

Called by updateMatrices to handle specific modifications for inheriting classes.

Implements bpp::AbstractWordSubstitutionModel.

Definition at line 133 of file WordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::getAlphabet(), bpp::Alphabet::getSize(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::WordSubstitutionModel::clone().

void bpp::AbstractSubstitutionModel::computeFrequencies ( bool  yn)
inlinevirtualinherited
Returns
Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModel.

Definition at line 269 of file AbstractSubstitutionModel.h.

virtual double bpp::AbstractSubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
Returns
The second order derivative of the probability of change from state i to state j with respect to time t, at time t.
See also
getd2Pij_dt2(), getStates()

Implements bpp::TransitionModel.

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

Definition at line 299 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getInitValue(), bpp::AbstractSubstitutionModel::setFreq(), and bpp::AbstractSubstitutionModel::setFreqFromData().

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

virtual double bpp::AbstractSubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
Returns
The first order derivative of the probability of change from state i to state j with respect to time t, at time t.
See also
getdPij_dt(), getStates()

Implements bpp::TransitionModel.

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

Definition at line 298 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

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

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 307 of file AbstractSubstitutionModel.h.

virtual void bpp::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList parameters)
inlinevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::JCprot, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::YpR, bpp::RE08, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::JTT92, bpp::WAG01, bpp::DSO78, bpp::CodonDistanceSubstitutionModel, bpp::LG08, bpp::gBGC, and bpp::SENCA.

Definition at line 316 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::addRateParameter(), bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::ParameterList::size(), and bpp::AbstractSubstitutionModel::updateMatrices().

Referenced by bpp::SENCA::fireParameterChanged(), bpp::gBGC::fireParameterChanged(), bpp::LG08::fireParameterChanged(), bpp::CodonDistanceSubstitutionModel::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonAdHocSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), and bpp::JCprot::fireParameterChanged().

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

Implements bpp::TransitionModel.

Definition at line 293 of file AbstractSubstitutionModel.h.

std::string bpp::AbstractSubstitutionModel::getAlphabetStateAsChar ( size_t  index) const
inlinevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 257 of file AbstractSubstitutionModel.h.

int bpp::AbstractSubstitutionModel::getAlphabetStateAsInt ( size_t  index) const
inlinevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 259 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices(), and bpp::AbstractSubstitutionModel::getInitValue().

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetStates ( ) const
inlinevirtualinherited
Returns
The alphabet states of each state of the model, as a vector of int codes.
See also
Alphabet

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 255 of file AbstractSubstitutionModel.h.

const Matrix<double>& bpp::AbstractSubstitutionModel::getColumnRightEigenVectors ( ) const
inlinevirtualinherited
Returns
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 291 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

const RowMatrix< double > & WordSubstitutionModel::getd2Pij_dt2 ( double  t) const
virtualinherited
const RowMatrix< double > & WordSubstitutionModel::getdPij_dt ( double  t) const
virtualinherited
const Vdouble& bpp::AbstractSubstitutionModel::getEigenValues ( ) const
inlinevirtualinherited
Returns
A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 281 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getExchangeabilityMatrix ( ) const
inlinevirtualinherited
Returns
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

Implements bpp::SubstitutionModel.

Definition at line 273 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

const Vdouble& bpp::AbstractSubstitutionModel::getFrequencies ( ) const
inlinevirtualinherited
Returns
A vector of all equilibrium frequencies.
See also
freq()

Implements bpp::TransitionModel.

Definition at line 265 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

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

const Matrix<double>& bpp::AbstractSubstitutionModel::getGenerator ( ) const
inlinevirtualinherited
Returns
The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $ \forall i; \sum_j Q_{i,j} = 0 $, meaning that $ $ \forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$, and (ii) $ \sum_i Q_{i,i} \times \pi_i = -1$. This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time $t$ 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 271 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator().

const Vdouble& bpp::AbstractSubstitutionModel::getIEigenValues ( ) const
inlinevirtualinherited
Returns
A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 283 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

double AbstractSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const
virtualinherited

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

Parameters
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::TransitionModel.

Reimplemented in bpp::RE08.

Definition at line 541 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::alphabet_, bpp::Alphabet::getAlias(), bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(), bpp::Alphabet::intToChar(), and bpp::AbstractSubstitutionModel::size_.

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

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

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 261 of file AbstractSubstitutionModel.h.

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( const std::string &  code) const
inlinevirtualinherited

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 263 of file AbstractSubstitutionModel.h.

string TripletSubstitutionModel::getName ( ) const
virtual

Get the name of the model.

Returns
The name of this model.

Reimplemented from bpp::WordSubstitutionModel.

Definition at line 140 of file TripletSubstitutionModel.cpp.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by clone().

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

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

Definition at line 234 of file AbstractWordSubstitutionModel.h.

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

size_t bpp::AbstractWordSubstitutionModel::getNumberOfModels ( ) const
inlineinherited
const RowMatrix< double > & WordSubstitutionModel::getPij_t ( double  t) const
virtualinherited
double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

The rate of the substitution process.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 643 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

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

const Matrix<double>& bpp::AbstractSubstitutionModel::getRowLeftEigenVectors ( ) const
inlinevirtualinherited
Returns
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 289 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

double AbstractSubstitutionModel::getScale ( ) const
virtualinherited
const StateMap& bpp::AbstractSubstitutionModel::getStateMap ( ) const
inlinevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 253 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const
inlinevirtualinherited
Returns
True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 285 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const
inlinevirtualinherited
Returns
True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 287 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

virtual double bpp::AbstractSubstitutionModel::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
Returns
The probability of change from state i to state j during time t.
See also
getPij_t(), getStates()

Implements bpp::TransitionModel.

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

Definition at line 297 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_t().

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

virtual double bpp::AbstractSubstitutionModel::Qij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited
Returns
The rate in the generator of change from state i to state j.
See also
getStates();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 295 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void AbstractWordSubstitutionModel::setFreq ( std::map< int, double > &  freqs)
virtualinherited

Estimation of the parameters of the models so that the equilibrium frequencies match the given ones.

Parameters
freqsmap of the frequencies

When there is one submodel for all the positions, the submodel parameters are fit on the means of the frequencies on each position. Otherwise, each model is fit on the frequencies on its corresponding position in the word.

Reimplemented from bpp::AbstractSubstitutionModel.

Reimplemented in bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, and bpp::SENCA.

Definition at line 401 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractWordSubstitutionModel::getNumberOfStates(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

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

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

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::TransitionModel.

Reimplemented in bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::JTT92, bpp::DSO78, bpp::LG08, and bpp::Coala.

Definition at line 559 of file AbstractSubstitutionModel.cpp.

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

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

void AbstractSubstitutionModel::setRate ( double  rate)
virtualinherited
void bpp::AbstractSubstitutionModel::setScalable ( bool  scalable)
inlinevirtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implements bpp::SubstitutionModel.

Definition at line 376 of file AbstractSubstitutionModel.h.

double bpp::AbstractSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited
Returns
The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModel.

Definition at line 275 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractSubstitutionModel::getPij_t().

void WordSubstitutionModel::updateMatrices ( )
protectedvirtualinherited

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.

!! Here there is no normalization of the generator.

Now check inversion and diagonalization

Reimplemented from bpp::AbstractWordSubstitutionModel.

Definition at line 116 of file WordSubstitutionModel.cpp.

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

Referenced by bpp::WordSubstitutionModel::clone(), TripletSubstitutionModel(), and bpp::WordSubstitutionModel::WordSubstitutionModel().

Member Data Documentation

bool bpp::AbstractSubstitutionModel::computeFreq_
protectedinherited
bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited
Vdouble bpp::AbstractSubstitutionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 121 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::WAG01::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::AbstractSubstitutionModel::getFrequencies_(), bpp::RN95s::getPij_t(), bpp::RN95::getPij_t(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::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::L95::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), bpp::MixtureOfASubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

bool bpp::AbstractSubstitutionModel::isScalable_
protectedinherited
RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_
mutableprotectedinherited
double bpp::AbstractSubstitutionModel::rate_
protectedinherited

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

Definition at line 111 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::BinarySubstitutionModel::d2Pij_dt2(), 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::F84::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::BinarySubstitutionModel::dPij_dt(), 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::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::BinarySubstitutionModel::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::BinarySubstitutionModel::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::BinarySubstitutionModel::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::BinarySubstitutionModel::Pij_t(), 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(), bpp::BinarySubstitutionModel::updateMatrices(), and bpp::MixtureOfSubstitutionModels::updateMatrices().

std::shared_ptr<const StateMap> bpp::AbstractSubstitutionModel::stateMap_
protectedinherited

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