Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position. More...

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

Inheritance diagram for bpp::GCSynonymousSubstitutionRegister:

Collaboration diagram for bpp::GCSynonymousSubstitutionRegister:

Public Member Functions
	GCSynonymousSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const GeneticCode > genCode, bool within=false)

	GCSynonymousSubstitutionRegister (const GCSynonymousSubstitutionRegister &reg)

GCSynonymousSubstitutionRegister &	operator= (const GCSynonymousSubstitutionRegister &reg)

GCSynonymousSubstitutionRegister *	clone () const

size_t	getType (size_t fromState, size_t toState) const
	Get the substitution type far a given pair of model states. More...

std::string	getTypeName (size_t type) const
	Get the name of a given substitution type. More...

virtual size_t	getCategory (size_t state) const

virtual size_t	getCategoryFrom (size_t type) const

virtual size_t	getCategoryTo (size_t type) const

virtual std::string	getCategoryName (size_t category) const

virtual bool	allowWithin () const

bool	isStationary () const

void	setStationarity (bool stat)

size_t	getNumberOfCategories () const

size_t	getNumberOfSubstitutionTypes () const

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
template<class T >
void	setAlphabetCategories (const std::map< int, T > &categories)

template<class T >
void	setModelCategories (const std::map< size_t, T > &categories)

Protected Attributes
bool	within_

size_t	nbCategories_

std::map< size_t, size_t >	categories_

std::vector< std::string >	categoryNames_

std::vector< std::vector< size_t > >	index_

std::vector< std::vector< size_t > >	revIndex_

bool	stationarity_

std::shared_ptr< const StateMapInterface >	stateMap_

std::string	name_

Private Attributes
std::shared_ptr< const GeneticCode >	genCode_

Detailed Description

Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position.

This register has two substitution types, mapped as:

0 not a counted substitution
1 a AT->GC synonymous substitution
2 a GC->AT synonymous substitution

Multiple substitutions are forbidden.

Definition at line 275 of file CategorySubstitutionRegister.h.

Constructor & Destructor Documentation

◆ GCSynonymousSubstitutionRegister() [1/2]

bpp::GCSynonymousSubstitutionRegister::GCSynonymousSubstitutionRegister	(	std::shared_ptr< const StateMapInterface >	stateMap,
		std::shared_ptr< const GeneticCode >	genCode,
		bool	within = `false`
	)

inline

Definition at line 282 of file CategorySubstitutionRegister.h.

References genCode_.

Referenced by clone().

◆ GCSynonymousSubstitutionRegister() [2/2]

bpp::GCSynonymousSubstitutionRegister::GCSynonymousSubstitutionRegister ( const GCSynonymousSubstitutionRegister & reg )

inline

Definition at line 307 of file CategorySubstitutionRegister.h.

Member Function Documentation

◆ allowWithin()

virtual bool bpp::CategorySubstitutionRegister::allowWithin ( ) const

inlinevirtualinherited

Definition at line 177 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::within_.

◆ 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()

GCSynonymousSubstitutionRegister* bpp::GCSynonymousSubstitutionRegister::clone ( ) const

inlinevirtual

Implements bpp::SubstitutionRegisterInterface.

Definition at line 319 of file CategorySubstitutionRegister.h.

References GCSynonymousSubstitutionRegister().

◆ 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_.

◆ getCategory()

virtual size_t bpp::CategorySubstitutionRegister::getCategory ( size_t state ) const

inlinevirtualinherited

Definition at line 137 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categories_.

◆ getCategoryFrom()

virtual size_t bpp::CategorySubstitutionRegister::getCategoryFrom ( size_t type ) const

inlinevirtualinherited

Definition at line 142 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_, bpp::CategorySubstitutionRegister::revIndex_, and bpp::CategorySubstitutionRegister::within_.

Referenced by bpp::CategorySubstitutionRegister::getTypeName().

◆ getCategoryName()

virtual std::string bpp::CategorySubstitutionRegister::getCategoryName ( size_t category ) const

inlinevirtualinherited

Definition at line 172 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categoryNames_.

Referenced by bpp::CategorySubstitutionRegister::getTypeName().

◆ getCategoryTo()

virtual size_t bpp::CategorySubstitutionRegister::getCategoryTo ( size_t type ) const

inlinevirtualinherited

Definition at line 157 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_, bpp::CategorySubstitutionRegister::revIndex_, and bpp::CategorySubstitutionRegister::within_.

Referenced by bpp::CategorySubstitutionRegister::getTypeName().

◆ 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_.

◆ getNumberOfCategories()

size_t bpp::CategorySubstitutionRegister::getNumberOfCategories ( ) const

inlineinherited

Definition at line 189 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_.

◆ getNumberOfSubstitutionTypes()

size_t bpp::CategorySubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtualinherited

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

Implements bpp::SubstitutionRegisterInterface.

Definition at line 191 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_, and bpp::CategorySubstitutionRegister::within_.

◆ 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::GCSynonymousSubstitutionRegister::getType	(	size_t	fromState,
		size_t	toState
	)		const

inlinevirtual

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.

Reimplemented from bpp::CategorySubstitutionRegister.

Definition at line 322 of file CategorySubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categories_, genCode_, bpp::StateMapInterface::getAlphabetStateAsInt(), bpp::CategorySubstitutionRegister::index_, and bpp::AbstractSubstitutionRegister::stateMap().