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 (const Alphabet *alphabet, bool includeGaps)

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

virtual CanonicalStateMap *	clone () const

virtual const Alphabet *	getAlphabet () const

virtual size_t	getNumberOfModelStates () const

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

virtual int	getAlphabetStateAsInt (size_t index) const

virtual std::string	getAlphabetStateAsChar (size_t index) const

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

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

Protected Attributes
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 161 of file StateMap.h.

Constructor & Destructor Documentation

◆ CanonicalStateMap() [1/2]

CanonicalStateMap::CanonicalStateMap	(	const Alphabet *	alphabet,
		bool	includeGaps
	)

Definition at line 44 of file StateMap.cpp.

References bpp::AbstractStateMap::states_.

Referenced by clone().

◆ CanonicalStateMap() [2/2]

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

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

Definition at line 54 of file StateMap.cpp.

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

Member Function Documentation

◆ clone()

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

inlinevirtual

Implements bpp::StateMap.

Definition at line 173 of file StateMap.h.

References CanonicalStateMap().

◆ getAlphabet()

virtual const Alphabet* bpp::AbstractStateMap::getAlphabet ( ) const

inlinevirtualinherited

Returns: The associated alphabet.

Implements bpp::StateMap.

Definition at line 141 of file StateMap.h.

References bpp::AbstractStateMap::alphabet_.

◆ getAlphabetStateAsChar()

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

inlinevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::StateMap.

Definition at line 145 of file StateMap.h.

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

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

◆ getAlphabetStateAsInt()

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

inlinevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as int code.

Implements bpp::StateMap.

Definition at line 144 of file StateMap.h.

References bpp::AbstractStateMap::states_.

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

◆ getAlphabetStates()

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

inlinevirtualinherited

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::StateMap.

Definition at line 143 of file StateMap.h.

References bpp::AbstractStateMap::states_.

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