bpp::MarkovModulatedStateMap Class Reference

This class implements a state map for Markov modulated models. More...

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

Inheritance diagram for bpp::MarkovModulatedStateMap:

Collaboration diagram for bpp::MarkovModulatedStateMap:

Public Member Functions
	MarkovModulatedStateMap (const StateMap &unitMap, unsigned int nbClasses)
virtual MarkovModulatedStateMap *	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 for Markov modulated models.

For nucleotides with two classes, the underlying states are for instance: A (0), C (1), G (2), T/U (3), A (4), C (5), G (6), T/U (7).

Definition at line 185 of file StateMap.h.

Constructor & Destructor Documentation

MarkovModulatedStateMap()

MarkovModulatedStateMap::MarkovModulatedStateMap	(	const StateMap &	unitMap,
		unsigned int	nbClasses
	)

Definition at line 64 of file StateMap.cpp.

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

Referenced by clone().

Member Function Documentation

clone()

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

inlinevirtual

Implements bpp::StateMap.

Definition at line 190 of file StateMap.h.

References MarkovModulatedStateMap().

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().

getModelStates() [1/2]

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

inlinevirtualinherited

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 bpp::AbstractStateMap::states_.

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

getModelStates() [2/2]

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

inlinevirtualinherited

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

getNumberOfModelStates()

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

inlinevirtualinherited

Returns

The number of states supported by the model.

Implements bpp::StateMap.

Definition at line 142 of file StateMap.h.

References bpp::AbstractStateMap::states_.

Member Data Documentation

alphabet_

const Alphabet* bpp::AbstractStateMap::alphabet_

protectedinherited

Definition at line 119 of file StateMap.h.

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

states_

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

protectedinherited

Definition at line 120 of file StateMap.h.

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

---

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

• Bpp/Phyl/Model/StateMap.h
• Bpp/Phyl/Model/StateMap.cpp