bpp-phyl  2.1.0
bpp::JTT92 Class Reference

The Jones, Taylor and Thornton substitution model for proteins. More...

#include <Bpp/Phyl/Model/Protein/JTT92.h>

+ Inheritance diagram for bpp::JTT92:
+ Collaboration diagram for bpp::JTT92:

List of all members.

Public Member Functions

 JTT92 (const ProteicAlphabet *alpha)
 Build a simple JTT92 model, with original equilibrium frequencies.
 JTT92 (const ProteicAlphabet *alpha, ProteinFrequenciesSet *freqSet, bool initFreqs=false)
 Build a JTT92 model with special equilibrium frequencies.
 JTT92 (const JTT92 &model)
JTT92operator= (const JTT92 &model)
virtual ~JTT92 ()
JTT92clone () const
std::string getName () const
 Get the name of the model.
void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed.
void setFrequenciesSet (const ProteinFrequenciesSet &freqSet)
const FrequenciesSetgetFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
void setFreqFromData (const SequenceContainer &data)
size_t getNumberOfStates () const
 Get the number of states.
virtual const std::vector< int > & getAlphabetChars () const =0
virtual int getAlphabetChar (size_t i) const =0
 Get the char in the alphabet corresponding to a given state in the model.
virtual std::vector< size_t > getModelStates (int i) const =0
 Get the state in the model corresponding to a particular char in the alphabet.
virtual double freq (size_t i) const =0
virtual double Qij (size_t i, size_t j) const =0
virtual double Pij_t (size_t i, size_t j, double t) const =0
virtual double dPij_dt (size_t i, size_t j, double t) const =0
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const =0
virtual const VdoublegetFrequencies () const =0
virtual const Matrix< double > & getGenerator () const =0
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
virtual double Sij (size_t i, size_t j) const =0
virtual const Matrix< double > & getPij_t (double t) const =0
virtual const Matrix< double > & getdPij_dt (double t) const =0
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed.
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed.
virtual const VdoublegetEigenValues () const =0
virtual const VdoublegetIEigenValues () const =0
virtual bool isDiagonalizable () const =0
virtual bool isNonSingular () const =0
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
virtual const AlphabetgetAlphabet () const =0
virtual double getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale.
virtual double getRate () const =0
 Get the rate.
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive).
virtual void addRateParameter ()=0
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual void setFreq (std::map< int, double > &frequencies)
 Set equilibrium frequencies.
virtual size_t getNumberOfIndependentParameters () const =0
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
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
virtual const ParameterListgetIndependentParameters () 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 ParameterListgetParameters () const =0
virtual const ParametergetParameter (const std::string &name) const =0
virtual double getParameterValue (const std::string &name) const =0
virtual void setAllParametersValues (const ParameterList &parameters)=0
virtual void setParameterValue (const std::string &name, double value)=0
virtual void setParametersValues (const ParameterList &parameters)=0
virtual bool matchParametersValues (const ParameterList &parameters)=0
virtual size_t getNumberOfParameters () const =0
virtual void setNamespace (const std::string &prefix)=0
virtual std::string getNamespace () const =0
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
const AlphabetgetAlphabet () 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 VdoublegetFrequencies () 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 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 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.
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)
 Multiplies the current generator by the given scale.
virtual double getRate () const
 Get the rate.
virtual void setRate (double rate)
 Set the rate of the model (must be positive).
size_t getNumberOfIndependentParameters () const
void aliasParameters (const std::string &p1, const std::string &p2)
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
void unaliasParameters (const std::string &p1, const std::string &p2)
const ParameterListgetIndependentParameters () const
std::vector< std::string > getAlias (const std::string &name) const
bool hasParameter (const std::string &name) const
const ParameterListgetParameters () const
const ParametergetParameter (const std::string &name) const
double getParameterValue (const std::string &name) const
void setAllParametersValues (const ParameterList &parameters)
void setParameterValue (const std::string &name, double value)
void setParametersValues (const ParameterList &parameters)
bool matchParametersValues (const ParameterList &parameters)
size_t getNumberOfParameters () const
void setNamespace (const std::string &prefix)
std::string getNamespace () const
std::string getParameterNameWithoutNamespace (const std::string &name) const
ParameterList getAliasedParameters (const ParameterList &pl) const
std::string getFrom (const std::string &name) const

Protected Member Functions

virtual void updateMatrices ()
 Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.
void addParameter_ (Parameter *parameter)
void addParameters_ (const ParameterList &parameters)
void deleteParameter_ (size_t index)
void deleteParameter_ (std::string &name)
void deleteParameters_ (const std::vector< std::string > &names)
void resetParameters_ ()
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

const Alphabetalphabet_
 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

ProteinFrequenciesSetfreqSet_

Friends

class AbstractBiblioSubstitutionModel

Detailed Description

The Jones, Taylor and Thornton substitution model for proteins.

Exchangeabilities have been computed using the DCMut method of Kosiol and Goldman. The exchangability matrix is normalized so that $Q = S . \pi$ and $\sum_i Q_{i,i}\pi_i = -1$. The original frequencies can be used, or alternatively a parametrized version, corresponding to the so-called JTT92+F model. Eigen values and vectors are obtained numerically.

References:

  • Jones DT, Taylor WR and Thornton JM (1992), _Computer Applications In The Biosciences_, 8(3) 275-82.
  • Kosiol C and Goldman N (2005), _Molecular Biology And Evolution_ 22(2) 193-9.

Definition at line 66 of file JTT92.h.


Constructor & Destructor Documentation

JTT92::JTT92 ( const ProteicAlphabet alpha)

Build a simple JTT92 model, with original equilibrium frequencies.

Parameters:
alphaA proteic alphabet.

Definition at line 50 of file JTT92.cpp.

References bpp::AbstractSubstitutionModel::freq_, freqSet_, and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Referenced by clone().

JTT92::JTT92 ( const ProteicAlphabet alpha,
ProteinFrequenciesSet freqSet,
bool  initFreqs = false 
)

Build a JTT92 model with special equilibrium frequencies.

Parameters:
alphaA proteic alphabet.
freqSetA pointer toward a protein frequencies set, which will be owned by this instance.
initFreqsTell if the frequency set should be initialized with the original JTT92 values. Otherwise, the values of the set will be used.

Definition at line 62 of file JTT92.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractSubstitutionModel::freq_, freqSet_, bpp::FrequenciesSet::getFrequencies(), bpp::Parametrizable::getNamespace(), bpp::Parametrizable::getParameters(), bpp::FrequenciesSet::setFrequencies(), bpp::Parametrizable::setNamespace(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

bpp::JTT92::JTT92 ( const JTT92 model) [inline]

Definition at line 91 of file JTT92.h.

virtual bpp::JTT92::~JTT92 ( ) [inline, virtual]

Definition at line 108 of file JTT92.h.

References freqSet_.


Member Function Documentation

JTT92* bpp::JTT92::clone ( ) const [inline, virtual]

Implements bpp::AbstractReversibleSubstitutionModel.

Definition at line 115 of file JTT92.h.

References JTT92().

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_.

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.

void bpp::JTT92::fireParameterChanged ( const ParameterList parameters) [inline, virtual]

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 126 of file JTT92.h.

References bpp::AbstractSubstitutionModel::freq_, freqSet_, bpp::FrequenciesSet::getFrequencies(), and bpp::Parametrizable::matchParametersValues().

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_.

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]
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_.

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_.

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().

const FrequenciesSet* bpp::JTT92::getFrequenciesSet ( ) const [inline, virtual]

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented from bpp::SubstitutionModel.

Definition at line 141 of file JTT92.h.

References freqSet_.

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::JTT92::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 118 of file JTT92.h.

References freqSet_, and bpp::Parametrizable::getNamespace().

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

Get the number of states.

For most models, this equals the size of the alphabet.

Returns:
The number of different states in the model.

Implements bpp::SubstitutionModel.

Definition at line 68 of file ProteinSubstitutionModel.h.

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

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 416 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

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_.

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

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns:
Minus the scalar product of diagonal elements and the frequencies vector.

Implements bpp::SubstitutionModel.

Definition at line 401 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::diag(), bpp::AbstractSubstitutionModel::freq_, and bpp::AbstractSubstitutionModel::generator_.

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

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

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns:
Minus the scalar product of diagonal elements and the frequencies vector.

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 266 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const [pure virtual, inherited]
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]
JTT92& bpp::JTT92::operator= ( const JTT92 model) [inline]

Definition at line 98 of file JTT92.h.

References bpp::ProteinFrequenciesSet::clone(), and freqSet_.

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().

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

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 276 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void AbstractSubstitutionModel::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().

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

Multiplies the current generator by the given scale.

Parameters:
scalethe scale by which the generator is multiplied.

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]

Multiplies the current generator by the given scale.

Parameters:
scalethe scale by which the generator is multiplied.

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

Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().

double bpp::AbstractSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const [inline, virtual, inherited]
Returns:
The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModel.

Definition at line 256 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual double bpp::SubstitutionModel::Sij ( size_t  i,
size_t  j 
) const [pure virtual, inherited]
Returns:
The exchangeability between state i and state j.

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

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

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

void AbstractReversibleSubstitutionModel::updateMatrices ( ) [protected, virtual, inherited]

Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The exchangeability_ matrix and freq_ vector must be initialized. This function computes the generator_ matrix with the formula

\[ Q = S \times \pi \]

where $Q$ is the generator matrix, $S$ is the exchangeability matrix and $Pi$ the diagonal matrix with frequencies.

The generator is then scaled so that

\[ \sum_i Q_{i,i} \times \pi_i = -1 \]

( $\pi_i$ are the equilibrium frequencies).

Eigen values and vectors are computed from the scaled generator and assigned to the eigenValues_, rightEigenVectors_ and leftEigenVectors_ variables.

Reimplemented from bpp::AbstractSubstitutionModel.

Reimplemented in bpp::JCprot, bpp::F84, bpp::HKY85, bpp::T92, bpp::RE08, bpp::K80, bpp::JCnuc, bpp::TN93, bpp::GTR, bpp::BinarySubstitutionModel, bpp::SSR, and bpp::Coala.

Definition at line 441 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::diag(), bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::getScale(), bpp::MatrixTools::mult(), bpp::MatrixTools::scale(), and bpp::AbstractSubstitutionModel::size_.

Referenced by bpp::DSO78::DSO78(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::LLG08_UL2::EmbeddedModel::EmbeddedModel(), bpp::LLG08_EX2::EmbeddedModel::EmbeddedModel(), bpp::LG10_EX_EHO::EmbeddedModel::EmbeddedModel(), bpp::LLG08_UL3::EmbeddedModel::EmbeddedModel(), bpp::LLG08_EHO::EmbeddedModel::EmbeddedModel(), bpp::LLG08_EX3::EmbeddedModel::EmbeddedModel(), JTT92(), bpp::LG08::LG08(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().


Friends And Related Function Documentation

friend class AbstractBiblioSubstitutionModel [friend, inherited]

Definition at line 342 of file AbstractSubstitutionModel.h.


Member Data Documentation

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(), 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(), 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(), setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::L95::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(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

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().


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