bpp::AbstractStateMap Class Reference

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 (const Alphabet *alphabet)
	AbstractStateMap (const AbstractStateMap &absm)
AbstractStateMap &	operator= (const AbstractStateMap &absm)
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
virtual StateMap *	clone () const =0

Protected Attributes
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 115 of file StateMap.h.

Constructor & Destructor Documentation

AbstractStateMap() [1/2]

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

inline

Definition at line 123 of file StateMap.h.

AbstractStateMap() [2/2]

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

inline

Definition at line 128 of file StateMap.h.

Member Function Documentation

clone()

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

pure virtualinherited

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

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

getAlphabet()

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

inlinevirtual

Returns

The associated alphabet.

Implements bpp::StateMap.

Definition at line 141 of file StateMap.h.

References alphabet_.

getAlphabetStateAsChar()

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

inlinevirtual

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 alphabet_, and states_.

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

getAlphabetStateAsInt()

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

inlinevirtual

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 states_.

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

getAlphabetStates()

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

inlinevirtual

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 states_.

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

getModelStates() [1/2]

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

inlinevirtual

Parameters

code	The int code of the alphabet state to check.

Returns

The corresponding model states, is any.

Implements bpp::StateMap.

Definition at line 146 of file StateMap.h.

References states_.

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

getModelStates() [2/2]

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

inlinevirtual

Parameters

code	The character code of the alphabet state to check.

Returns

The corresponding model states, is any.

Implements bpp::StateMap.

Definition at line 149 of file StateMap.h.

References alphabet_, and states_.

getNumberOfModelStates()

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

inlinevirtual

Returns

The number of states supported by the model.

Implements bpp::StateMap.

Definition at line 142 of file StateMap.h.

References states_.

operator=()

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

inline

Definition at line 133 of file StateMap.h.

References alphabet_, and states_.

Member Data Documentation

alphabet_

const Alphabet* bpp::AbstractStateMap::alphabet_

protected

Definition at line 119 of file StateMap.h.

Referenced by getAlphabet(), getAlphabetStateAsChar(), getModelStates(), and operator=().

states_

std::vector<int> bpp::AbstractStateMap::states_

protected

Definition at line 120 of file StateMap.h.

Referenced by bpp::CanonicalStateMap::CanonicalStateMap(), getAlphabetStateAsChar(), getAlphabetStateAsInt(), getAlphabetStates(), getModelStates(), getNumberOfModelStates(), bpp::MarkovModulatedStateMap::MarkovModulatedStateMap(), and operator=().

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

• Bpp/Phyl/Model/StateMap.h