bpp::WrappedModelInterface Class Reference

Wrapping model interface. More...

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

Inheritance diagram for bpp::WrappedModelInterface:

Collaboration diagram for bpp::WrappedModelInterface:

Public Member Functions
	WrappedModelInterface ()
virtual	~WrappedModelInterface ()
virtual const BranchModelInterface &	model () const =0
BranchModelInterface *	clone () const =0
virtual std::string	getName () const =0
	Get the name of the model. More...
virtual const std::vector< int > &	getAlphabetStates () const =0
virtual const StateMapInterface &	stateMap () const =0
virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0
virtual std::vector< size_t >	getModelStates (int code) const =0
	Get the state in the model corresponding to a particular state in the alphabet. More...
virtual std::vector< size_t >	getModelStates (const std::string &code) const =0
	Get the state in the model corresponding to a particular state in the alphabet. More...
virtual int	getAlphabetStateAsInt (size_t index) const =0
virtual std::string	getAlphabetStateAsChar (size_t index) const =0
virtual const Alphabet &	alphabet () const =0
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
virtual const FrequencySetInterface &	frequencySet () const =0
virtual size_t	getNumberOfStates () const =0
	Get the number of states. More...
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
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 ParameterList &	getIndependentParameters () const=0
virtual std::vector< std::string >	getAlias (const std::string &name) const=0
virtual std::map< std::string, std::string >	getAliases () const=0
virtual bool	hasParameter (const std::string &name) const=0
virtual const ParameterList &	getParameters () const=0
virtual const Parameter &	parameter (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 void	removeConstraint (const std::string &name)=0
virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=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

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

Detailed Description

Wrapping model interface.

Definition at line 17 of file WrappedModel.h.

Constructor & Destructor Documentation

WrappedModelInterface()

bpp::WrappedModelInterface::WrappedModelInterface ( )

inline

Definition at line 21 of file WrappedModel.h.

~WrappedModelInterface()

virtual bpp::WrappedModelInterface::~WrappedModelInterface ( )

inlinevirtual

Definition at line 22 of file WrappedModel.h.

Member Function Documentation

addRateParameter()

virtual void bpp::BranchModelInterface::addRateParameter ( )

pure virtualinherited

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

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()

virtual const Alphabet & bpp::BranchModelInterface::alphabet ( ) const

pure virtualinherited

Returns

A reference to the alphabet associated to this model.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::alphabet(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), and bpp::SENCA::setFreq().

clone()

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

pure virtualinherited

Implements bpp::ParameterAliasable.

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

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

dLik_dt()

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

pure virtualinherited

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

frequencySet()

virtual const FrequencySetInterface & bpp::BranchModelInterface::frequencySet ( ) const

pure virtualinherited

Returns

Get the FrequencySet of equilibrium of this model.

Exceptions

Exception

if no FrequenceSet is associated to this model.

Implemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::AbstractWrappedTransitionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::YN98, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::UserProteinSubstitutionModel, bpp::WAG01, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::RE08Codon::codonFrequencySet(), bpp::AbstractWrappedModel::frequencySet(), bpp::AbstractWrappedTransitionModel::frequencySet(), bpp::OneChangeRegisterTransitionModel::frequencySet(), bpp::OneChangeTransitionModel::frequencySet(), and bpp::BppOSubstitutionModelFormat::write().

getAlphabet()

virtual std::shared_ptr< const Alphabet > bpp::BranchModelInterface::getAlphabet ( ) const

pure virtualinherited

Returns

A pointer toward the alphabet associated to this model.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::YpR::checkModel(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), bpp::AbstractWrappedModel::getAlphabet(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::SENCA::setFreq(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

getAlphabetStateAsChar()

virtual std::string bpp::BranchModelInterface::getAlphabetStateAsChar ( size_t  index ) const

pure virtualinherited

Parameters

index

The model state.

Returns

The corresponding alphabet state as character code.

Implemented in bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().

getAlphabetStateAsInt()

virtual int bpp::BranchModelInterface::getAlphabetStateAsInt ( size_t  index ) const

pure virtualinherited

Parameters

index

The model state.

Returns

The corresponding alphabet state as character code.

Implemented in bpp::AbstractWrappedModel, bpp::RegisterRatesSubstitutionModel, bpp::AbstractTransitionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

getAlphabetStates()

virtual const std::vector< int > & bpp::BranchModelInterface::getAlphabetStates ( ) const

pure virtualinherited

Returns

The alphabet states of each state of the model, as a vector of int codes.

See also

Alphabet

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractWrappedModel::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

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns

1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See also

getStates();

Implemented in bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, and bpp::TransitionFromTransitionModel.

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

getModelStates() [1/2]

virtual std::vector< size_t > bpp::BranchModelInterface::getModelStates ( const std::string &  code ) const

pure virtualinherited

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

Parameters

code	The alphabet state to check.

Returns

A vector of indices of model states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

getModelStates() [2/2]

virtual std::vector< size_t > bpp::BranchModelInterface::getModelStates ( int  code ) const

pure virtualinherited

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

Parameters

code	The alphabet state to check.

Returns

A vector of indices of model states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::getModelStates(), and bpp::AbstractWrappedModel::getModelStates().

getName()

virtual std::string bpp::BranchModelInterface::getName ( ) const

pure virtualinherited

Get the name of the model.

Returns

The name of this model.

Implemented in bpp::BinarySubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::F84, bpp::HKY85, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LG10_EX_EHO, bpp::TwoParameterBinarySubstitutionModel, bpp::AbstractWrappedModel, bpp::AnonymousSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::DFP07, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::GY94, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::MG94, bpp::RELAX, bpp::SENCA, bpp::TripletSubstitutionModel, bpp::YN98, bpp::YNGP_M1, bpp::YNGP_M10, bpp::YNGP_M2, bpp::YNGP_M3, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::FromMixtureSubstitutionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::MixtureOfATransitionModel, bpp::MixtureOfTransitionModels, bpp::MultinomialFromTransitionModel, bpp::F81, bpp::gBGC, bpp::GTR, bpp::JCnuc, bpp::K80, bpp::L95, bpp::RN95, bpp::RN95s, bpp::SSR, bpp::T92, bpp::TN93, bpp::YpR_Sym, bpp::YpR_Gen, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::POMO, bpp::Coala, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::LGL08_CAT::EmbeddedModel, bpp::LGL08_CAT, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL3, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::RE08, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, bpp::TS98, and bpp::WordSubstitutionModel.

Referenced by bpp::YpR::checkModel(), bpp::TransitionMatrixFromModel::compute(), bpp::AbstractWrappedModel::getName(), bpp::FromMixtureSubstitutionModel::getName(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::BppOSubstitutionModelFormat::initialize_(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::MixtureOfATransitionModel::model(), bpp::SubstitutionProcessCollectionMember::setModelScenario(), bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesWithAliases(), bpp::ModelPath::toString(), and bpp::BppOSubstitutionModelFormat::write().

getNumberOfStates()

virtual size_t bpp::BranchModelInterface::getNumberOfStates ( ) const

pure virtualinherited

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.

Implemented in bpp::BinarySubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::gBGC, bpp::YpR, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RE08Codon, bpp::RegisterRatesSubstitutionModel, and bpp::AbstractDFPSubstitutionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

getRate()

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

pure virtualinherited

Get the rate.

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

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

getStateMap()

virtual std::shared_ptr< const StateMapInterface > bpp::BranchModelInterface::getStateMap ( ) const

pure virtualinherited

Returns

A shared_ptr to the mapping of model states with alphabet states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::getStateMap(), bpp::SubstitutionProcessCollectionMember::getStateMap(), and bpp::AbstractWrappedModel::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

values	An vector of states on the site.
t	time

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

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

model()

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

pure virtual

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

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

setRate()

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

pure virtualinherited

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

Parameters

rate	must be positive.

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

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()

virtual const StateMapInterface & bpp::BranchModelInterface::stateMap ( ) const

pure virtualinherited

Returns

The mapping of model states with alphabet states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::stateMap(), bpp::SubstitutionProcessCollectionMember::stateMap(), and bpp::AbstractWrappedModel::stateMap().

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

• Bpp/Phyl/Model/WrappedModel.h