A convenience partial implementation of the StateMap interface. More...

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

Inheritance diagram for bpp::AbstractStateMap:

Collaboration diagram for bpp::AbstractStateMap:

Public Member Functions
	AbstractStateMap (std::shared_ptr< const Alphabet > alphabet)

	AbstractStateMap (const AbstractStateMap &absm)

AbstractStateMap &	operator= (const AbstractStateMap &absm)

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

size_t	getNumberOfModelStates () const override

const std::vector< int > &	getAlphabetStates () const override

int	getAlphabetStateAsInt (size_t index) const override

std::string	getAlphabetStateAsChar (size_t index) const override

std::vector< size_t >	getModelStates (int code) const override

std::vector< size_t >	getModelStates (const std::string &code) const override

bool	operator== (const StateMapInterface &sm) const override
	Comparison operator==. More...

bool	operator!= (const StateMapInterface &sm) const override
	Comparison operator!=. More...

virtual StateMapInterface *	clone () const override=0

virtual std::string	getStateDescription (size_t index) const =0

Protected Attributes
std::shared_ptr< const Alphabet >	alphabet_

std::vector< int >	states_

Detailed Description

A convenience partial implementation of the StateMap interface.

Model states are stored as their corresponding int codes, stored in a vector 'states_'. This vector has to be initialized and filled by the derived class.

Definition at line 104 of file StateMap.h.

Constructor & Destructor Documentation

◆ AbstractStateMap() [1/2]

bpp::AbstractStateMap::AbstractStateMap ( std::shared_ptr< const Alphabet > alphabet )

inline

Definition at line 112 of file StateMap.h.

◆ AbstractStateMap() [2/2]

bpp::AbstractStateMap::AbstractStateMap ( const AbstractStateMap & absm )

inline

Definition at line 117 of file StateMap.h.

Member Function Documentation

◆ alphabet()

const Alphabet & bpp::AbstractStateMap::alphabet ( ) const

inlineoverridevirtual

Returns: The associated alphabet.

Implements bpp::StateMapInterface.

Definition at line 130 of file StateMap.h.

References alphabet_.

Referenced by bpp::CanonicalStateMap::CanonicalStateMap().

◆ clone()

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

overridepure virtualinherited

Implements bpp::Clonable.

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

◆ getAlphabet()

std::shared_ptr< const Alphabet > bpp::AbstractStateMap::getAlphabet ( ) const

inlineoverridevirtual

Returns: A shared_ptr towards the associated alphabet.

Implements bpp::StateMapInterface.

Definition at line 131 of file StateMap.h.

References alphabet_.

◆ getAlphabetStateAsChar()

std::string bpp::AbstractStateMap::getAlphabetStateAsChar ( size_t index ) const

inlineoverridevirtual

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::StateMapInterface.

Definition at line 135 of file StateMap.h.

References alphabet_, and states_.

Referenced by bpp::CanonicalStateMap::getStateDescription(), and bpp::MarkovModulatedStateMap::getStateDescription().

◆ getAlphabetStateAsInt()

int bpp::AbstractStateMap::getAlphabetStateAsInt ( size_t index ) const

inlineoverridevirtual

Parameters

index The model state.

Returns: The corresponding alphabet state as int code.

Implements bpp::StateMapInterface.

Definition at line 134 of file StateMap.h.

References states_.

◆ getAlphabetStates()

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

inlineoverridevirtual

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.

Implements bpp::StateMapInterface.

Definition at line 133 of file StateMap.h.

References states_.