bpp-phyl  2.1.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes
bpp::YNGKP_M7 Class Reference

The Yang et al (2000) M7 substitution model for codons. More...

#include <Bpp/Phyl/Model/Codon/YNGKP_M7.h>

+ Inheritance diagram for bpp::YNGKP_M7:
+ Collaboration diagram for bpp::YNGKP_M7:

List of all members.

Public Member Functions

 YNGKP_M7 (const GeneticCode *gc, FrequenciesSet *codonFreqs, unsigned int nclass)
 ~YNGKP_M7 ()
YNGKP_M7 * clone () const
 YNGKP_M7 (const YNGKP_M7 &)
YNGKP_M7 & operator= (const YNGKP_M7 &)
const SubstitutionModel & getModel () const
const MixedSubstitutionModel & getMixedModel () const
std::string getName () const
 Get the name of the model.
const SubstitutionModel * getNModel (size_t i) const
 Returns a specific model from the mixture.
SubstitutionModel * getNModel (size_t i)
double getNProbability (size_t i) const
 Returns the probability of a specific model from the mixture.
const std::vector< double > & getProbabilities () const
 Returns the vector of the probabilities of the submodels of the mixture.
void setNProbability (size_t i, double prob)
 Sets the probabilities of the submodels of the mixture.
size_t getNumberOfModels () const
 Returns the number of submodels.
void setVRates (const Vdouble &vd)
 sets the rates of the submodels.
void normalizeVRates ()
 normalizes the rates of the submodels.
const std::vector< double > & getVRates () const
 Returns the vector of all the rates of the mixture.
double getNRate (size_t i) const
 Returns the rate of a specific model from the mixture.
Vint getSubmodelNumbers (std::string &desc) const
virtual const std::vector< int > & getAlphabetChars () const =0
const std::vector< int > & getAlphabetChars () const
virtual int getAlphabetChar (size_t i) const =0
 Get the char in the alphabet corresponding to a given state in the model.
int getAlphabetChar (size_t i) const
 Get the char in the alphabet corresponding to a given state in the model.
virtual std::vector< size_t > getModelStates (int i) const =0
 Get the state in the model corresponding to a particular char in the alphabet.
std::vector< size_t > getModelStates (int i) const
 Get the state in the model corresponding to a particular char in the alphabet.
virtual double freq (size_t i) const =0
virtual double freq (size_t i) const
virtual double Qij (size_t i, size_t j) const =0
virtual double Qij (size_t i, size_t j) const
virtual double Pij_t (size_t i, size_t j, double t) const =0
virtual double Pij_t (size_t i, size_t j, double t) const
virtual double dPij_dt (size_t i, size_t j, double t) const =0
virtual double dPij_dt (size_t i, size_t j, double t) const
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const =0
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const
virtual const Vdouble & getFrequencies () const =0
virtual const Vdouble & getFrequencies () const
virtual const Matrix< double > & getGenerator () const =0
const Matrix< double > & getGenerator () const
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
const Matrix< double > & getExchangeabilityMatrix () const
virtual double Sij (size_t i, size_t j) const =0
double Sij (size_t i, size_t j) const
virtual const Matrix< double > & getPij_t (double t) const =0
const Matrix< double > & getPij_t (double t) const
virtual const Matrix< double > & getdPij_dt (double t) const =0
const Matrix< double > & getdPij_dt (double t) const
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
const Matrix< double > & getd2Pij_dt2 (double t) const
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed.
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed.
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed.
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed.
virtual const Vdouble & getEigenValues () const =0
const Vdouble & getEigenValues () const
virtual const Vdouble & getIEigenValues () const =0
const Vdouble & getIEigenValues () const
virtual bool isDiagonalizable () const =0
bool isDiagonalizable () const
virtual bool isNonSingular () const =0
bool isNonSingular () const
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
const Matrix< double > & getRowLeftEigenVectors () const
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
const Matrix< double > & getColumnRightEigenVectors () const
virtual const Alphabet * getAlphabet () const =0
const Alphabet * getAlphabet () const
virtual size_t getNumberOfStates () const =0
 Get the number of states.
size_t getNumberOfStates () const
 Get the number of states.
virtual double getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
double getInitValue (size_t i, int state) const throw (BadIntException)
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
double getScale () const
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
virtual void setScale (double scale)=0
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.
void setScale (double scale)
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.
virtual double getRate () const =0
 Get the rate.
double getRate () const
 Get the rate.
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive).
void setRate (double rate)
 Set the rate of the model (must be positive).
virtual void addRateParameter ()=0
void addRateParameter ()
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data.
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual void setFreq (std::map< int, double > &frequencies)
 Set equilibrium frequencies.
void setFreq (std::map< int, double > &frequ)
 Set equilibrium frequencies.
virtual const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
virtual size_t getNumberOfIndependentParameters () const =0
size_t getNumberOfIndependentParameters () const
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
void aliasParameters (const std::string &p1, const std::string &p2)
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
void unaliasParameters (const std::string &p1, const std::string &p2)
virtual const ParameterList & getIndependentParameters () const =0
const ParameterList & getIndependentParameters () const
virtual std::vector< std::string > getAlias (const std::string &name) const =0
std::vector< std::string > getAlias (const std::string &name) const
virtual bool hasParameter (const std::string &name) const =0
bool hasParameter (const std::string &name) const
virtual const ParameterList & getParameters () const =0
const ParameterList & getParameters () const
virtual const Parameter & getParameter (const std::string &name) const =0
const Parameter & getParameter (const std::string &name) const
virtual double getParameterValue (const std::string &name) const =0
double getParameterValue (const std::string &name) const
virtual void setAllParametersValues (const ParameterList &parameters)=0
void setAllParametersValues (const ParameterList &parameters)
virtual void setParameterValue (const std::string &name, double value)=0
void setParameterValue (const std::string &name, double value)
virtual void setParametersValues (const ParameterList &parameters)=0
void setParametersValues (const ParameterList &parameters)
virtual bool matchParametersValues (const ParameterList &parameters)=0
bool matchParametersValues (const ParameterList &parameters)
virtual size_t getNumberOfParameters () const =0
size_t getNumberOfParameters () const
virtual void setNamespace (const std::string &prefix)=0
void setNamespace (const std::string &prefix)
virtual std::string getNamespace () const =0
std::string getNamespace () const
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
std::string getParameterNameWithoutNamespace (const std::string &name) const
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed.
std::string getFrom (const std::string &name) const

Protected Member Functions

void updateMatrices ()
void addParameter_ (Parameter *parameter)
void addParameters_ (const ParameterList &parameters)
void deleteParameter_ (size_t index)
void resetParameters_ ()
Parameter & getParameter_ (const std::string &name)
Parameter & getParameter_ (size_t index)
const Parameter & getParameter_ (size_t index) const
Parameter & getParameterWithNamespace_ (const std::string &name)
const Parameter & getParameterWithNamespace_ (const std::string &name) const
ParameterList & getParameters_ ()

Protected Attributes

std::map< std::string,
std::string > 		mapParNamesFromPmodel_
 Tools to make the link between the Parameters of the object and those of pmixmodel_.
ParameterList lParPmodel_

Private Member Functions

SubstitutionModel & getModel ()
MixedSubstitutionModel & getMixedModel ()

Private Attributes

std::auto_ptr
< MixtureOfASubstitutionModel > 		pmixmodel_
int synfrom_
int synto_

Detailed Description

The Yang et al (2000) M7 substitution model for codons.

Author:
Laurent Guéguen

This model is a mixture of models as described in YN98 class, the mixture being defined on the selection parameter to allow it to vary among sites, following a Beta distribution.

This model includes 3 parameters ( $\kappa$, $ p $ and $q$) of the Beta distribution. The codon frequencies $\pi_j$ are either observed or infered.

References:

Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000) Genetics 155:431-449.

Definition at line 70 of file YNGKP_M7.h.

Constructor & Destructor Documentation

YNGKP_M7::YNGKP_M7 ( const GeneticCode *  gc,
FrequenciesSet *  codonFreqs,
unsigned int  nclass 
)

Definition at line 53 of file YNGKP_M7.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::addParameter_(), bpp::GeneticCode::areSynonymous(), bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), bpp::ParameterList::getParameterNames(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::Parametrizable::getParameters(), bpp::Alphabet::getSize(), bpp::GeneticCode::getSourceAlphabet(), bpp::AbstractBiblioSubstitutionModel::lParPmodel_, bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, pmixmodel_, bpp::ParameterList::size(), synfrom_, synto_, bpp::TextTools::toString(), and updateMatrices().

Referenced by clone().

YNGKP_M7::~YNGKP_M7 ( )

Definition at line 140 of file YNGKP_M7.cpp.

YNGKP_M7::YNGKP_M7 ( const YNGKP_M7 &  mod2)

Definition at line 123 of file YNGKP_M7.cpp.

Member Function Documentation

void AbstractBiblioSubstitutionModel::addRateParameter ( ) [virtual, inherited]

Implements bpp::SubstitutionModel.

Definition at line 84 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::addParameters(), bpp::SubstitutionModel::addRateParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractBiblioSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::lParPmodel_, bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, bpp::Parameter::R_PLUS_STAR, and bpp::ParameterList::reset().

virtual void bpp::SubstitutionModel::addRateParameter ( ) [pure virtual, inherited]

Implemented in bpp::AbstractSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

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

YNGKP_M7* bpp::YNGKP_M7::clone ( ) const [inline, virtual]

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 96 of file YNGKP_M7.h.

References YNGKP_M7().

virtual double bpp::AbstractBiblioSubstitutionModel::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.

Definition at line 106 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::d2Pij_dt2(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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::AbstractBiblioSubstitutionModel::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.

Definition at line 105 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::dPij_dt(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 122 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::enableEigenDecomposition(), and bpp::AbstractBiblioSubstitutionModel::getModel().

bool bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition ( ) [inline, virtual, inherited]

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 124 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::enableEigenDecomposition(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool  yn) [pure virtual, inherited]

Set if eigenValues and Vectors must be computed.

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

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), bpp::gBGC::gBGC(), and bpp::YpR::YpR().

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( ) [pure virtual, inherited]

Tell if eigenValues and Vectors must be computed.

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

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

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 171 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::size(), and bpp::AbstractBiblioSubstitutionModel::updateMatrices().

virtual double bpp::AbstractBiblioSubstitutionModel::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 100 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::freq(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::AbstractBiblioSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getPij_t(), bpp::RE08::Pij_t(), and bpp::RE08::updateMatrices().

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

Implements bpp::SubstitutionModel.

Definition at line 147 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabet(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

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

int bpp::AbstractBiblioSubstitutionModel::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 96 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetChar(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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().

const std::vector<int>& bpp::AbstractBiblioSubstitutionModel::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 94 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetChars(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetChars ( ) const [pure virtual, inherited]
Returns:
The supported states of the model, as a vector of int codes.
See also:
Alphabet

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

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChars(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::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 135 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getColumnRightEigenVectors(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const [pure virtual, inherited]
Returns:
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

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

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2 ( double  t) const [inline, virtual, inherited]
Returns:
All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also:
d2Pij_dt2()

Implements bpp::SubstitutionModel.

Definition at line 120 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getd2Pij_dt2(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual const Matrix<double>& bpp::SubstitutionModel::getd2Pij_dt2 ( double  t) const [pure virtual, inherited]
Returns:
All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also:
d2Pij_dt2()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(), and bpp::RE08::getd2Pij_dt2().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getdPij_dt ( double  t) const [inline, virtual, inherited]
Returns:
Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also:
dPij_dt()

Implements bpp::SubstitutionModel.

Definition at line 118 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getdPij_dt(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual const Matrix<double>& bpp::SubstitutionModel::getdPij_dt ( double  t) const [pure virtual, inherited]
Returns:
Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also:
dPij_dt()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::getdPij_dt(), and bpp::RE08::getdPij_dt().

const Vdouble& bpp::AbstractBiblioSubstitutionModel::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 130 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getEigenValues(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const [pure virtual, inherited]
Returns:
A vector with all real parts of the eigen values of the generator of this model;

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

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::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 112 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getExchangeabilityMatrix(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

Referenced by bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

Implements bpp::SubstitutionModel.

Definition at line 108 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getFrequencies(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

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

Reimplemented from bpp::SubstitutionModel.

Definition at line 153 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getFrequenciesSet(), and bpp::AbstractBiblioSubstitutionModel::getModel().

Referenced by bpp::YNGKP_M1::YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

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::AbstractBiblioSubstitutionModel::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 110 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getGenerator(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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::AbstractBiblioSubstitutionModel::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 132 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getIEigenValues(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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 bpp::AbstractBiblioSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const throw (BadIntException) [inline, 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.

Definition at line 151 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getInitValue(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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().

const MixedSubstitutionModel& bpp::YNGKP_M7::getMixedModel ( ) const [inline, virtual]

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 108 of file YNGKP_M7.h.

References pmixmodel_.

MixedSubstitutionModel& bpp::YNGKP_M7::getMixedModel ( ) [inline, private, virtual]

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 115 of file YNGKP_M7.h.

References pmixmodel_.

const SubstitutionModel& bpp::YNGKP_M7::getModel ( ) const [inline, virtual]

Implements bpp::AbstractBiblioSubstitutionModel.

Definition at line 106 of file YNGKP_M7.h.

References pmixmodel_.

SubstitutionModel& bpp::YNGKP_M7::getModel ( ) [inline, private, virtual]

Implements bpp::AbstractBiblioSubstitutionModel.

Definition at line 113 of file YNGKP_M7.h.

References pmixmodel_.

std::vector<size_t> bpp::AbstractBiblioSubstitutionModel::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 98 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getModelStates().

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::string bpp::YNGKP_M7::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 110 of file YNGKP_M7.h.

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

Returns a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 77 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNModel().

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

Implements bpp::MixedSubstitutionModel.

Definition at line 82 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNModel().

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

Returns the probability of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 90 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNProbability().

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

Returns the rate of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 154 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNRate().

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

Returns the number of submodels.

Implements bpp::MixedSubstitutionModel.

Definition at line 119 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNumberOfModels().

size_t bpp::AbstractBiblioSubstitutionModel::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 149 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getNumberOfStates().

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>& bpp::AbstractBiblioSubstitutionModel::getPij_t ( double  t) const [inline, virtual, inherited]
Returns:
All probabilities of change from state i to state j during time t.
See also:
Pij_t()

Implements bpp::SubstitutionModel.

Definition at line 116 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getPij_t().

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

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractBiblioSubstitutionModel::getPij_t(), and bpp::RE08::getPij_t().

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

Returns the vector of the probabilities of the submodels of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 101 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getProbabilities().

double bpp::AbstractBiblioSubstitutionModel::getRate ( ) const [inline, virtual, inherited]

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 137 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getRate().

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), and bpp::LLG08_UL3::LLG08_UL3().

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

Get the rate.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

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

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::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 134 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getRowLeftEigenVectors().

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const [pure virtual, inherited]
Returns:
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

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

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

double bpp::AbstractBiblioSubstitutionModel::getScale ( ) const [inline, 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 184 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getScale().

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

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

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

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

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

Vint AbstractBiblioMixedSubstitutionModel::getSubmodelNumbers ( std::string &  desc) const [virtual, inherited]

Implements bpp::MixedSubstitutionModel.

Definition at line 62 of file AbstractBiblioMixedSubstitutionModel.cpp.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::MixedSubstitutionModel::getSubmodelNumbers(), bpp::StringTokenizer::hasMoreToken(), and bpp::StringTokenizer::nextToken().

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

Returns the vector of all the rates of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 146 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getVRates().

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

Implements bpp::SubstitutionModel.

Definition at line 126 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::isDiagonalizable().

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

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 128 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::isNonSingular().

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

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

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

void bpp::AbstractBiblioMixedSubstitutionModel::normalizeVRates ( ) [inline, virtual, inherited]

normalizes the rates of the submodels.

Implements bpp::MixedSubstitutionModel.

Definition at line 137 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::normalizeVRates().

YNGKP_M7 & YNGKP_M7::operator= ( const YNGKP_M7 &  mod2)

Definition at line 129 of file YNGKP_M7.cpp.

References pmixmodel_, synfrom_, and synto_.

virtual double bpp::AbstractBiblioSubstitutionModel::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.

Definition at line 104 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Pij_t().

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::Pij_t(), and bpp::RE08::Pij_t().

virtual double bpp::AbstractBiblioSubstitutionModel::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.

Definition at line 102 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Qij().

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

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

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::gBGC::updateMatrices(), and bpp::YpR::updateMatrices().

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

Set equilibrium frequencies.

Parameters:
frequenciesThe map of the frequencies to use.

Reimplemented from bpp::SubstitutionModel.

Definition at line 95 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::SubstitutionModel::setFreq().

virtual void bpp::SubstitutionModel::setFreq ( std::map< int, double > &  frequencies) [inline, virtual, inherited]

Set equilibrium frequencies.

Parameters:
frequenciesThe map of the frequencies to use.

Reimplemented in bpp::AbstractSubstitutionModel, 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::AbstractBiblioSubstitutionModel, bpp::BinarySubstitutionModel, bpp::SSR, bpp::L95, bpp::CodonRateFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, and bpp::AbstractCodonFitnessSubstitutionModel.

Definition at line 455 of file SubstitutionModel.h.

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

void AbstractBiblioSubstitutionModel::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 110 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::SubstitutionModel::setFreqFromData().

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

Sets the probabilities of the submodels of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 110 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::setNProbability().

void bpp::AbstractBiblioSubstitutionModel::setRate ( double  rate) [inline, virtual, inherited]

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

Parameters:
ratemust be positive.

Implements bpp::SubstitutionModel.

Definition at line 139 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::setRate().

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

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

Parameters:
ratemust be positive.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

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

void bpp::AbstractBiblioSubstitutionModel::setScale ( double  scale) [inline, virtual, inherited]

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implements bpp::SubstitutionModel.

Definition at line 186 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::setScale().

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

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

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

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

void bpp::AbstractBiblioMixedSubstitutionModel::setVRates ( const Vdouble &  vd) [inline, virtual, inherited]

sets the rates of the submodels.

Implements bpp::MixedSubstitutionModel.

Definition at line 128 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::setVRates().

double bpp::AbstractBiblioSubstitutionModel::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 114 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Sij().

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 YNGKP_M7::updateMatrices ( ) [protected, virtual]

Reimplemented from bpp::AbstractBiblioSubstitutionModel.

Definition at line 142 of file YNGKP_M7.cpp.

References pmixmodel_, synfrom_, and synto_.

Referenced by YNGKP_M7().

Member Data Documentation

ParameterList bpp::AbstractBiblioSubstitutionModel::lParPmodel_ [protected, inherited]

Definition at line 70 of file AbstractBiblioSubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::GY94::GY94(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::YNGKP_M3::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), bpp::YN98::YN98(), bpp::YNGKP_M1::YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

std::map<std::string, std::string> bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_ [protected, inherited]

Tools to make the link between the Parameters of the object and those of pmixmodel_.

Definition at line 68 of file AbstractBiblioSubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::GY94::GY94(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioSubstitutionModel::setFreq(), bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), bpp::YNGKP_M3::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), bpp::YN98::YN98(), bpp::YNGKP_M1::YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

std::auto_ptr<MixtureOfASubstitutionModel> bpp::YNGKP_M7::pmixmodel_ [private]

Definition at line 75 of file YNGKP_M7.h.

Referenced by getMixedModel(), getModel(), operator=(), updateMatrices(), and YNGKP_M7().

int bpp::YNGKP_M7::synfrom_ [private]

Definition at line 83 of file YNGKP_M7.h.

Referenced by operator=(), updateMatrices(), and YNGKP_M7().

int bpp::YNGKP_M7::synto_ [private]

Definition at line 83 of file YNGKP_M7.h.

Referenced by operator=(), updateMatrices(), and YNGKP_M7().

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