bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
bpp::AbstractWrappedModel Class Referenceabstract

Abstract class of Wrapping model class, where all methods are redirected from model(). More...

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

+ Inheritance diagram for bpp::AbstractWrappedModel:
+ Collaboration diagram for bpp::AbstractWrappedModel:

Public Member Functions

 AbstractWrappedModel (const std::string &prefix)
 
virtual ~AbstractWrappedModel ()
 
virtual std::string getName () const override
 Get the name of the model. More...
 
void setNamespace (const std::string &prefix)
 
bool hasIndependentParameter (const std::string &name) const
 
const ParameterList & getIndependentParameters () const
 
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)
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const
 
std::string getFrom (const std::string &name) const
 
bool hasParameter (const std::string &name) const override
 
const ParameterList & getParameters () const override
 
const Parameter & parameter (const std::string &name) const override
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const override
 
void setAllParametersValues (const ParameterList &parameters) override
 
void setParameterValue (const std::string &name, double value) override
 
void setParametersValues (const ParameterList &parameters) override
 
bool matchParametersValues (const ParameterList &parameters) override
 
void removeConstraint (const std::string &name) override
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
size_t getNumberOfParameters () const override
 
std::string getNamespace () const override
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
virtual void fireParameterChanged (const ParameterList &parameters)
 
virtual Clonable * clone () const=0
 
virtual const BranchModelInterface & model () const =0
 
BranchModelInterface * clone () const =0
 
virtual double getInitValue (size_t i, int state) const =0
 
virtual const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const =0
 
virtual const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const =0
 
virtual const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
const std::vector< int > & getAlphabetStates () const override
 
const StateMapInterface & stateMap () const override
 
std::shared_ptr< const StateMapInterface > getStateMap () const override
 
int getAlphabetStateAsInt (size_t i) const override
 
std::string getAlphabetStateAsChar (size_t i) const override
 
std::vector< size_t > getModelStates (int code) const override
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
std::vector< size_t > getModelStates (const std::string &code) const override
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
const Alphabet & alphabet () const override
 
std::shared_ptr< const Alphabet > getAlphabet () const override
 
size_t getNumberOfStates () const override
 Get the number of states. More...
 
const FrequencySetInterface & frequencySet () const override
 

Protected Member Functions

const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
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_ () override
 

Private Attributes

ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Abstract class of Wrapping model class, where all methods are redirected from model().

Definition at line 21 of file AbstractWrappedModel.h.

Constructor & Destructor Documentation

◆ AbstractWrappedModel()

bpp::AbstractWrappedModel::AbstractWrappedModel ( const std::string &  prefix)
inline

Definition at line 26 of file AbstractWrappedModel.h.

◆ ~AbstractWrappedModel()

virtual bpp::AbstractWrappedModel::~AbstractWrappedModel ( )
inlinevirtual

Definition at line 30 of file AbstractWrappedModel.h.

Member Function Documentation

◆ addRateParameter()

virtual void bpp::BranchModelInterface::addRateParameter ( )
pure virtualinherited

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::AbstractTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractBiblioTransitionModel.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::addRateParameter(), bpp::MultinomialFromTransitionModel::addRateParameter(), bpp::TransitionFromTransitionModel::addRateParameter(), and bpp::BppOSubstitutionModelFormat::updateParameters_().

◆ alphabet()

const Alphabet& bpp::AbstractWrappedModel::alphabet ( ) const
inlineoverridevirtual
Returns
A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 53 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::alphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::alphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ clone()

BranchModelInterface* bpp::BranchModelInterface::clone ( ) const
pure virtualinherited

Implements bpp::ParameterAliasable.

Implemented in bpp::ReversibleSubstitutionModelInterface, bpp::SubstitutionModelInterface, bpp::AbstractReversibleProteinSubstitutionModel, bpp::AbstractProteinSubstitutionModel, bpp::ProteinReversibleSubstitutionModelInterface, bpp::ProteinSubstitutionModelInterface, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::AbstractNucleotideSubstitutionModel, bpp::NucleotideReversibleSubstitutionModelInterface, bpp::NucleotideSubstitutionModelInterface, bpp::MixedTransitionModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::YNGP_M, bpp::CodonReversibleSubstitutionModelInterface, bpp::CodonSubstitutionModelInterface, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractReversibleSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::WordSubstitutionModel, bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LLG08_UL3, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EHO::EmbeddedModel, bpp::LGL08_CAT, bpp::LGL08_CAT::EmbeddedModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::POMO, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::YpR_Gen, bpp::YpR_Sym, bpp::TN93, bpp::T92, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::K80, bpp::JCnuc, bpp::GTR, bpp::gBGC, bpp::F81, bpp::MultinomialFromTransitionModel, bpp::MixtureOfTransitionModels, bpp::MixtureOfSubstitutionModels, bpp::MixtureOfATransitionModel, bpp::MixtureOfASubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YNGP_M9, bpp::YNGP_M8, bpp::YNGP_M7, bpp::YNGP_M3, bpp::YNGP_M2, bpp::YNGP_M10, bpp::YNGP_M1, bpp::YN98, bpp::TripletSubstitutionModel, bpp::SENCA, bpp::RELAX, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::GY94, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DFP07, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AnonymousSubstitutionModel, bpp::TransitionModelInterface, bpp::TwoParameterBinarySubstitutionModel, bpp::LG10_EX_EHO, bpp::LG10_EX_EHO::EmbeddedModel, bpp::HKY85, bpp::F84, bpp::CodonDistanceSubstitutionModel, and bpp::BinarySubstitutionModel.

Referenced by bpp::SubstitutionProcessCollection::addOnePerBranchSubstitutionProcess(), and bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess().

◆ d2Lik_dt2()

virtual const Eigen::VectorXd& bpp::BranchModelInterface::d2Lik_dt2 ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ dLik_dt()

virtual const Eigen::VectorXd& bpp::BranchModelInterface::dLik_dt ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractWrappedModel::frequencySet ( ) const
inlineoverridevirtual
Returns
Get the FrequencySet of equilibrium of this model.
Exceptions
Exceptionif no FrequenceSet is associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::YN98, and bpp::AbstractWrappedTransitionModel.

Definition at line 59 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::frequencySet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::YN98::frequencySet().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractWrappedModel::getAlphabet ( ) const
inlineoverridevirtual
Returns
A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 55 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ getAlphabetStateAsChar()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 46 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 44 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsInt().

◆ getAlphabetStates()

const std::vector<int>& bpp::AbstractWrappedModel::getAlphabetStates ( ) const
inlineoverridevirtual

@ brief Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 38 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStates().

◆ getInitValue()

virtual double bpp::BranchModelInterface::getInitValue ( size_t  i,
int  state 
) const
pure virtualinherited

This method is used to initialize likelihoods in recursions. 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::TransitionFromTransitionModel, bpp::RE08, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getInitValue(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::MultinomialFromTransitionModel::getInitValue(), bpp::OneChangeRegisterTransitionModel::getInitValue(), bpp::OneChangeTransitionModel::getInitValue(), and bpp::TransitionFromTransitionModel::getInitValue().

◆ getModelStates() [1/2]

std::vector<size_t> bpp::AbstractWrappedModel::getModelStates ( const std::string &  code) const
inlineoverridevirtual

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

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 50 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

◆ getModelStates() [2/2]

std::vector<size_t> bpp::AbstractWrappedModel::getModelStates ( int  code) const
inlineoverridevirtual

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

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 48 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getModelStates().

◆ getName()

virtual std::string bpp::AbstractWrappedModel::getName ( ) const
inlineoverridevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::LLG08_UL3, bpp::LLG08_UL2, bpp::LLG08_EX3, bpp::LLG08_EX2, bpp::LLG08_EHO, bpp::LGL08_CAT, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::InMixedSubstitutionModel, bpp::FromMixtureSubstitutionModel, bpp::YNGP_M9, bpp::YNGP_M8, bpp::YNGP_M7, bpp::YNGP_M3, bpp::YNGP_M2, bpp::YNGP_M10, bpp::YNGP_M1, bpp::YN98, bpp::RELAX, bpp::MG94, bpp::KCM, bpp::GY94, bpp::DFP07, and bpp::LG10_EX_EHO.

Definition at line 67 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getName(), and bpp::WrappedModelInterface::model().

Referenced by bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ getNumberOfStates()

size_t bpp::AbstractWrappedModel::getNumberOfStates ( ) const
inlineoverridevirtual

Get the number of states.

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

See also
getAlphabetChars for the list of supported states.
Returns
The number of different states in the model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 57 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getNumberOfStates(), and bpp::WrappedModelInterface::model().

◆ getRate()

virtual double bpp::BranchModelInterface::getRate ( ) const
pure virtualinherited

Get the rate.

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::InMixedSubstitutionModel::getRate(), bpp::MultinomialFromTransitionModel::getRate(), bpp::OneChangeRegisterTransitionModel::getRate(), bpp::OneChangeTransitionModel::getRate(), bpp::RegisterRatesSubstitutionModel::getRate(), and bpp::TransitionFromTransitionModel::getRate().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractWrappedModel::getStateMap ( ) const
inlineoverridevirtual
Returns
A shared_ptr to the mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 42 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getStateMap(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getStateMap().

◆ Lik_t()

virtual const Eigen::VectorXd& bpp::BranchModelInterface::Lik_t ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters
valuesAn vector of states on the site.
ttime
Exceptions
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif states are not allowed in the associated alphabet.

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ model()

virtual const BranchModelInterface& bpp::WrappedModelInterface::model ( ) const
pure virtualinherited

Implemented in bpp::TransitionFromTransitionModel, bpp::MultinomialFromTransitionModel, bpp::AbstractWrappedTransitionModel, and bpp::AbstractFromSubstitutionModelTransitionModel.

Referenced by alphabet(), frequencySet(), getAlphabet(), getAlphabetStateAsChar(), getAlphabetStateAsInt(), getAlphabetStates(), getModelStates(), getName(), getNumberOfStates(), getStateMap(), and stateMap().

◆ setRate()

virtual void bpp::BranchModelInterface::setRate ( double  rate)
pure virtualinherited

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

Parameters
ratemust be positive.

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractMixedTransitionModel.

Referenced by bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::AbstractTotallyWrappedTransitionModel::setRate(), bpp::InMixedSubstitutionModel::setRate(), bpp::MultinomialFromTransitionModel::setRate(), bpp::OneChangeRegisterTransitionModel::setRate(), bpp::OneChangeTransitionModel::setRate(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::TransitionFromTransitionModel::setRate().

◆ stateMap()

const StateMapInterface& bpp::AbstractWrappedModel::stateMap ( ) const
inlineoverridevirtual
Returns
The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 40 of file AbstractWrappedModel.h.

References bpp::WrappedModelInterface::model(), and bpp::BranchModelInterface::stateMap().

Referenced by bpp::RegisterRatesSubstitutionModel::stateMap().

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