Sets a Register based on a matrix of integers. If M is the matrix, M[i,j] is the number of the substitution type from i to j, or 0 if there is no substitution type from i to j. More...

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

Inheritance diagram for bpp::GeneralSubstitutionRegister:

Collaboration diagram for bpp::GeneralSubstitutionRegister:

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

	GeneralSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, const RowMatrix< size_t > &matrix)

	GeneralSubstitutionRegister (const GeneralSubstitutionRegister &gsr)

GeneralSubstitutionRegister &	operator= (const GeneralSubstitutionRegister &gsr)

GeneralSubstitutionRegister *	clone () const override

virtual	~GeneralSubstitutionRegister ()

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 their number. 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 Member Functions
void	updateTypes_ ()

Protected Attributes
size_t	size_
	The size of the matrix, i.e. the number of states. More...

RowMatrix< size_t >	matrix_
	The matrix of the substitution register. More...

std::map< size_t, std::map< size_t, std::vector< size_t > > >	types_
	The map from substitution types to the map of from states to the vector of target states. More...

std::shared_ptr< const StateMapInterface >	stateMap_

std::string	name_

Detailed Description

Sets a Register based on a matrix of integers. If M is the matrix, M[i,j] is the number of the substitution type from i to j, or 0 if there is no substitution type from i to j.

Author: Laurent Guéguen

Definition at line 385 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ GeneralSubstitutionRegister() [1/3]

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

inline

Definition at line 408 of file SubstitutionRegister.h.

Referenced by clone().

◆ GeneralSubstitutionRegister() [2/3]

bpp::GeneralSubstitutionRegister::GeneralSubstitutionRegister	(	std::shared_ptr< const StateMapInterface >	stateMap,
		const RowMatrix< size_t > &	matrix
	)

inline

Definition at line 415 of file SubstitutionRegister.h.

References bpp::RowMatrix< class >::getNumberOfColumns(), bpp::RowMatrix< class >::getNumberOfRows(), matrix_, size_, and updateTypes_().

◆ GeneralSubstitutionRegister() [3/3]

bpp::GeneralSubstitutionRegister::GeneralSubstitutionRegister ( const GeneralSubstitutionRegister & gsr )

inline

Definition at line 428 of file SubstitutionRegister.h.

◆ ~GeneralSubstitutionRegister()

virtual bpp::GeneralSubstitutionRegister::~GeneralSubstitutionRegister ( )

inlinevirtual

Definition at line 449 of file SubstitutionRegister.h.

Member Function Documentation

◆ 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()

GeneralSubstitutionRegister* bpp::GeneralSubstitutionRegister::clone ( ) const

inlineoverridevirtual

Implements bpp::SubstitutionRegisterInterface.

Reimplemented in bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, and bpp::SelectedSubstitutionRegister.

Definition at line 444 of file SubstitutionRegister.h.

References GeneralSubstitutionRegister().

◆ 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::GeneralSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlineoverridevirtual

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

Implements bpp::SubstitutionRegisterInterface.

Definition at line 456 of file SubstitutionRegister.h.

References types_.

◆ 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::GeneralSubstitutionRegister::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 451 of file SubstitutionRegister.h.

References matrix_.