This class implements a state map where all resolved states are modeled. More...

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

Inheritance diagram for bpp::CanonicalStateMap:

Collaboration diagram for bpp::CanonicalStateMap:

Public Member Functions
	CanonicalStateMap (std::shared_ptr< const Alphabet > alphabet, bool includeGaps)

	CanonicalStateMap (const StateMapInterface &sm, bool includeGaps)
	this constructors takes an existing StateMap and adds one model states for gaps. If the original StateMap already had a state for gaps, a new one will be appended. More...

virtual CanonicalStateMap *	clone () const

virtual std::string	getStateDescription (size_t index) const

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...

Protected Attributes
std::shared_ptr< const Alphabet >	alphabet_

std::vector< int >	states_

Detailed Description

This class implements a state map where all resolved states are modeled.

For nucleotides, the underlying states are for instance: A (0), C (1), G (2), T/U (3). Optionally, gaps can be modeled.

Definition at line 166 of file StateMap.h.

Constructor & Destructor Documentation

◆ CanonicalStateMap() [1/2]

CanonicalStateMap::CanonicalStateMap	(	std::shared_ptr< const Alphabet >	alphabet,
		bool	includeGaps
	)

Definition at line 10 of file StateMap.cpp.

References bpp::AbstractStateMap::alphabet(), bpp::Alphabet::getGapCharacterCode(), bpp::Alphabet::getIntCodeAt(), bpp::Alphabet::getSize(), bpp::Alphabet::isGap(), and bpp::AbstractStateMap::states_.

Referenced by clone().

◆ CanonicalStateMap() [2/2]

CanonicalStateMap::CanonicalStateMap	(	const StateMapInterface &	sm,
		bool	includeGaps
	)

this constructors takes an existing StateMap and adds one model states for gaps. If the original StateMap already had a state for gaps, a new one will be appended.

Definition at line 25 of file StateMap.cpp.

References bpp::StateMapInterface::getAlphabet(), bpp::StateMapInterface::getAlphabetStateAsInt(), bpp::StateMapInterface::getNumberOfModelStates(), and bpp::AbstractStateMap::states_.

Member Function Documentation

◆ alphabet()

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

inlineoverridevirtualinherited

Returns: The associated alphabet.

Implements bpp::StateMapInterface.

Definition at line 130 of file StateMap.h.

References bpp::AbstractStateMap::alphabet_.

Referenced by CanonicalStateMap().

◆ clone()

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

inlinevirtual

Implements bpp::StateMapInterface.

Definition at line 178 of file StateMap.h.

References CanonicalStateMap().

◆ getAlphabet()

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

inlineoverridevirtualinherited

Returns: A shared_ptr towards the associated alphabet.

Implements bpp::StateMapInterface.

Definition at line 131 of file StateMap.h.

References bpp::AbstractStateMap::alphabet_.

◆ getAlphabetStateAsChar()

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

inlineoverridevirtualinherited

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 bpp::AbstractStateMap::alphabet_, and bpp::AbstractStateMap::states_.

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

◆ getAlphabetStateAsInt()

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

inlineoverridevirtualinherited

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 bpp::AbstractStateMap::states_.

◆ getAlphabetStates()

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

inlineoverridevirtualinherited

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 bpp::AbstractStateMap::states_.