Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers. More...

#include <Bpp/Phyl/Mapping/SubstitutionRegister.h>

Inheritance diagram for bpp::VectorOfSubstitutionRegisters:

Collaboration diagram for bpp::VectorOfSubstitutionRegisters:

Public Member Functions
	VectorOfSubstitutionRegisters (std::shared_ptr< const StateMapInterface > stateMap)

	VectorOfSubstitutionRegisters (const VectorOfSubstitutionRegisters &vosr)

VectorOfSubstitutionRegisters *	clone () const override

virtual	~VectorOfSubstitutionRegisters ()

void	addRegister (std::shared_ptr< SubstitutionRegisterInterface > reg)

size_t	getType (size_t i, size_t j) const override
	Get the substitution type far a given pair of model states. More...

size_t	getNumberOfSubstitutionTypes () const override

std::string	getTypeName (size_t type) const override
	names of the types are the list of their types in the registers (separated with _). More...

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

const std::string &	getName () const override
	Get the name of the register. More...

Protected Attributes
std::shared_ptr< const StateMapInterface >	stateMap_

std::string	name_

Private Attributes
std::vector< std::shared_ptr< SubstitutionRegisterInterface > >	vSubReg_
	the vector of pointers to SubstitutionRegisters. More...

Detailed Description

Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers.

Author: Laurent Guéguen

Definition at line 280 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ VectorOfSubstitutionRegisters() [1/2]

bpp::VectorOfSubstitutionRegisters::VectorOfSubstitutionRegisters ( std::shared_ptr< const StateMapInterface > stateMap )

inline

Definition at line 290 of file SubstitutionRegister.h.

Referenced by clone().

◆ VectorOfSubstitutionRegisters() [2/2]

bpp::VectorOfSubstitutionRegisters::VectorOfSubstitutionRegisters ( const VectorOfSubstitutionRegisters & vosr )

inline

Definition at line 295 of file SubstitutionRegister.h.

◆ ~VectorOfSubstitutionRegisters()

virtual bpp::VectorOfSubstitutionRegisters::~VectorOfSubstitutionRegisters ( )

inlinevirtual

Definition at line 305 of file SubstitutionRegister.h.

Member Function Documentation

◆ addRegister()

void bpp::VectorOfSubstitutionRegisters::addRegister ( std::shared_ptr< SubstitutionRegisterInterface > reg )

inline

Definition at line 307 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap(), and vSubReg_.

◆ alphabet()

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

inlineoverridevirtualinherited

Returns: The alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 133 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

◆ clone()

VectorOfSubstitutionRegisters* bpp::VectorOfSubstitutionRegisters::clone ( ) const

inlineoverridevirtual

Implements bpp::SubstitutionRegisterInterface.

Definition at line 300 of file SubstitutionRegister.h.

References VectorOfSubstitutionRegisters().

◆ getAlphabet()

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

inlineoverridevirtualinherited

Returns: A shared_ptr toward the alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 135 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

◆ getName()

const std::string& bpp::AbstractSubstitutionRegister::getName ( ) const

inlineoverridevirtualinherited

Get the name of the register.

Returns: A string describing the register.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 137 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::name_.

◆ getNumberOfSubstitutionTypes()

size_t bpp::VectorOfSubstitutionRegisters::getNumberOfSubstitutionTypes ( ) const

inlineoverridevirtual

Returns: The number of substitution types supported by this class.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 337 of file SubstitutionRegister.h.

References vSubReg_.

Referenced by getTypeName().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractSubstitutionRegister::getStateMap ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr toward the state map associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 131 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

◆ getType()

size_t bpp::VectorOfSubstitutionRegisters::getType	(	size_t	fromState,
		size_t	toState
	)		const

inlineoverridevirtual

Get the substitution type far a given pair of model states.

Parameters

fromState	Initial state (should be a state supported by the specified alphabet).
toState	Final state (should be a state supported by the specified alphabet).

Returns: The index of the corresponding substitution type, ranging from 0 to 'getNumberOfSubstitutionTypes' + 1, as non-substitution (that is when fromState == toState) will always return 0.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 318 of file SubstitutionRegister.h.

References vSubReg_.