bpp::StateMap 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::StateMap:

Collaboration diagram for bpp::StateMap:

Public Member Functions
virtual	~StateMap ()
virtual StateMap *	clone () const =0
virtual const Alphabet *	getAlphabet () const =0
virtual size_t	getNumberOfModelStates () 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

Detailed Description

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

Definition at line 58 of file StateMap.h.

Constructor & Destructor Documentation

~StateMap()

virtual bpp::StateMap::~StateMap ( )

inlinevirtual

Definition at line 62 of file StateMap.h.

Member Function Documentation

clone()

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

pure virtual

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

Referenced by bpp::AbstractTreeParsimonyScore::AbstractTreeParsimonyScore(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::AbstractTreeParsimonyScore::operator=().

getAlphabet()

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

pure virtual

Returns

The associated alphabet.

Implemented in bpp::AbstractStateMap.

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

getAlphabetStateAsChar()

virtual std::string bpp::StateMap::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::StateMap::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::FullPerAACodonFrequenciesSet::FullPerAACodonFrequenciesSet(), bpp::MarkovModulatedStateMap::MarkovModulatedStateMap(), bpp::FullPerAACodonFrequenciesSet::setFrequencies(), and bpp::FullPerAACodonFrequenciesSet::updateFrequencies().

getAlphabetStates()

virtual const std::vector<int>& bpp::StateMap::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.

getModelStates() [1/2]

virtual std::vector<size_t> bpp::StateMap::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.

getModelStates() [2/2]

virtual std::vector<size_t> bpp::StateMap::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::StateMap::getNumberOfModelStates ( ) const

pure virtual

Returns

The number of states supported by the model.

Implemented in bpp::AbstractStateMap.

Referenced by bpp::CanonicalStateMap::CanonicalStateMap(), bpp::FixedFrequenciesSet::FixedFrequenciesSet(), bpp::FullFrequenciesSet::FullFrequenciesSet(), bpp::FullPerAACodonFrequenciesSet::FullPerAACodonFrequenciesSet(), bpp::MarkovModulatedStateMap::MarkovModulatedStateMap(), bpp::FullPerAACodonFrequenciesSet::setFrequencies(), and bpp::FullPerAACodonFrequenciesSet::updateFrequencies().

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

• Bpp/Phyl/Model/StateMap.h