bpp::StateMapInterface Class Reference

Map the states of a given alphabet which have a model state. More...

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

Inheritance diagram for bpp::StateMapInterface:

Collaboration diagram for bpp::StateMapInterface:

Public Member Functions
virtual	~StateMapInterface ()
virtual StateMapInterface *	clone () const override=0
virtual const Alphabet &	alphabet () const =0
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
virtual size_t	getNumberOfModelStates () const =0
virtual std::string	getStateDescription (size_t index) const =0
virtual const std::vector< int > &	getAlphabetStates () const =0
virtual std::string	getAlphabetStateAsChar (size_t index) const =0
virtual int	getAlphabetStateAsInt (size_t index) const =0
virtual std::vector< size_t >	getModelStates (const std::string &code) const =0
virtual std::vector< size_t >	getModelStates (int code) const =0
virtual bool	operator== (const StateMapInterface &sm) const =0
	Comparison operator==. More...
virtual bool	operator!= (const StateMapInterface &sm) const =0
	Comparison operator!=. More...

Detailed Description

Map the states of a given alphabet which have a model state.

Definition at line 23 of file StateMap.h.

Constructor & Destructor Documentation

~StateMapInterface()

virtual bpp::StateMapInterface::~StateMapInterface ( )

inlinevirtual

Definition at line 27 of file StateMap.h.

Member Function Documentation

alphabet()

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

pure virtual

Returns

The associated alphabet.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::AbstractStateMap::operator!=(), bpp::AbstractStateMap::operator==(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and bpp::AAExteriorSubstitutionRegister::updateMatrix_().

clone()

virtual StateMapInterface* bpp::StateMapInterface::clone ( ) const

overridepure virtual

Implements bpp::Clonable.

Implemented in bpp::MarkovModulatedStateMap, and bpp::CanonicalStateMap.

getAlphabet()

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

pure virtual

Returns

A shared_ptr towards the associated alphabet.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::CanonicalStateMap::CanonicalStateMap(), bpp::AbstractSubstitutionProcess::getAlphabet(), bpp::LikelihoodCalculationOnABranch::getAlphabet(), and bpp::SingleProcessPhyloLikelihood::getAlphabet().

getAlphabetStateAsChar()

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

pure virtual

Parameters

index

The model state.

Returns

The corresponding alphabet state as character code.

Implemented in bpp::AbstractStateMap.

getAlphabetStateAsInt()

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

pure virtual

Parameters

index

The model state.

Returns

The corresponding alphabet state as int code.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::CanonicalStateMap::CanonicalStateMap(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::SWSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::KrKcSubstitutionRegister::getType(), bpp::MarkovModulatedStateMap::MarkovModulatedStateMap(), and bpp::FromModelFrequencySet::setFrequencies().

getAlphabetStates()

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

pure virtual

Returns

A vector with the corresponding alphabet states for each model state. the size of the vector is the number of model states, not the number of supported alphabet states, as distinct model states can correspond to a single alphabet state.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::AbstractStateMap::operator!=(), and bpp::AbstractStateMap::operator==().

getModelStates() [1/2]

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

pure virtual

Parameters

code	The character code of the alphabet state to check.

Returns

The corresponding model states, is any.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::CategorySubstitutionRegister::setAlphabetCategories().

getModelStates() [2/2]

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

pure virtual

Parameters

code	The int code of the alphabet state to check.

Returns

The corresponding model states, is any.

Implemented in bpp::AbstractStateMap.

getNumberOfModelStates()

virtual size_t bpp::StateMapInterface::getNumberOfModelStates ( ) const

pure virtual

Returns

The number of states supported by the model.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::CanonicalStateMap::CanonicalStateMap(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::FixedFrequencySet::FixedFrequencySet(), bpp::FullFrequencySet::FullFrequencySet(), bpp::AbstractSubstitutionProcess::getNumberOfStates(), bpp::RegisterRatesSubstitutionModel::getNumberOfStates(), bpp::LikelihoodCalculationOnABranch::LikelihoodCalculationOnABranch(), bpp::LikelihoodCalculationSingleProcess::makeRootFreqs_(), bpp::MarkovModulatedStateMap::MarkovModulatedStateMap(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and bpp::AAExteriorSubstitutionRegister::updateMatrix_().

getStateDescription()

virtual std::string bpp::StateMapInterface::getStateDescription ( size_t  index ) const

pure virtual

Returns

A string describing the model state.

Parameters

index

The state index.

Implemented in bpp::MarkovModulatedStateMap, and bpp::CanonicalStateMap.

Referenced by bpp::CategorySubstitutionRegister::setModelCategories().

operator!=()

virtual bool bpp::StateMapInterface::operator!= ( const StateMapInterface &  sm ) const

pure virtual

Comparison operator!=.

Two StateMaps are not identical if they do not share the same alphabet or states.

Implemented in bpp::AbstractStateMap.

operator==()

virtual bool bpp::StateMapInterface::operator== ( const StateMapInterface &  sm ) const

pure virtual

Comparison operator==.

Two StateMaps are identical if they share the same alphabet and states.

Implemented in bpp::AbstractStateMap.

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

• Bpp/Phyl/Model/StateMap.h