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

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

Inheritance diagram for bpp::GCSynonymousSubstitutionRegister:

Collaboration diagram for bpp::GCSynonymousSubstitutionRegister:

Public Member Functions
	GCSynonymousSubstitutionRegister (const CodonSubstitutionModel *model, bool within=false)

	GCSynonymousSubstitutionRegister (const GCSynonymousSubstitutionRegister &reg)

GCSynonymousSubstitutionRegister &	operator= (const GCSynonymousSubstitutionRegister &reg)

GCSynonymousSubstitutionRegister *	clone () const

size_t	getNumberOfSubstitutionTypes () 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

size_t	getNumberOfCategories () const

const SubstitutionModel *	getSubstitutionModel () const

const Alphabet *	getAlphabet () const

Protected Member Functions
template<class T >
void	setCategories (const std::map< int, T > &categories)

Protected Attributes
bool	within_

size_t	nbCategories_

std::map< int, size_t >	categories_

std::vector< std::string >	categoryNames_

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

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

const SubstitutionModel *	model_

Private Attributes
const GeneticCode *	code_

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 953 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ GCSynonymousSubstitutionRegister() [1/2]

bpp::GCSynonymousSubstitutionRegister::GCSynonymousSubstitutionRegister	(	const CodonSubstitutionModel *	model,
		bool	within = `false`
	)

inline

Definition at line 960 of file SubstitutionRegister.h.

References code_.

Referenced by clone().

◆ GCSynonymousSubstitutionRegister() [2/2]

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

inline

Definition at line 985 of file SubstitutionRegister.h.

Member Function Documentation

◆ allowWithin()

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

inlinevirtualinherited

Definition at line 289 of file SubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::within_.

◆ clone()

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

inlinevirtual

Implements bpp::SubstitutionRegister.

Definition at line 997 of file SubstitutionRegister.h.

References GCSynonymousSubstitutionRegister().

◆ getAlphabet()

const Alphabet* bpp::AbstractSubstitutionRegister::getAlphabet ( ) const

inlinevirtualinherited

Returns: The alphabet associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 147 of file SubstitutionRegister.h.

References bpp::SubstitutionModel::getAlphabet(), and bpp::AbstractSubstitutionRegister::model_.

◆ getCategory()

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

inlinevirtualinherited

Definition at line 248 of file SubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categories_, bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::AbstractSubstitutionRegister::model_.

Referenced by bpp::SubstitutionMappingTools::getRelativeCountsPerBranch().

◆ getCategoryFrom()

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

inlinevirtualinherited

Definition at line 254 of file SubstitutionRegister.h.

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

Referenced by bpp::SubstitutionMappingTools::getRelativeCountsPerBranch(), and bpp::CategorySubstitutionRegister::getTypeName().

◆ getCategoryName()

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

inlinevirtualinherited

Definition at line 284 of file SubstitutionRegister.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 269 of file SubstitutionRegister.h.

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

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

◆ getNumberOfCategories()

size_t bpp::CategorySubstitutionRegister::getNumberOfCategories ( ) const

inlineinherited

Definition at line 291 of file SubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::nbCategories_.

Referenced by bpp::SubstitutionMappingTools::getRelativeCountsPerBranch().

◆ getNumberOfSubstitutionTypes()

size_t bpp::GCSynonymousSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

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

Reimplemented from bpp::CategorySubstitutionRegister.

Definition at line 1000 of file SubstitutionRegister.h.

◆ getSubstitutionModel()

const SubstitutionModel* bpp::AbstractSubstitutionRegister::getSubstitutionModel ( ) const

inlinevirtualinherited

Returns: The substitution model associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 145 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::model_.

◆ 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 1002 of file SubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categories_, code_, bpp::SubstitutionModel::getAlphabetStateAsInt(), bpp::CategorySubstitutionRegister::index_, and bpp::AbstractSubstitutionRegister::model_.

◆ getTypeName()

std::string bpp::GCSynonymousSubstitutionRegister::getTypeName ( size_t type ) const

inlinevirtual

Get the name of a given substitution type.

This method is only used for user-friendlyness purposes, not computational goal. I can therefore be left unimplemented in some cases.

Parameters

type	Index of the substitution (should be an size_t contained in the register).

Returns: A string describing the substitution type.

Reimplemented from bpp::CategorySubstitutionRegister.

Definition at line 1025 of file SubstitutionRegister.h.

◆ operator=()

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

inline

Definition at line 990 of file SubstitutionRegister.h.

References code_, and bpp::AbstractSubstitutionRegister::operator=().

◆ setCategories()

template<class T >

void bpp::CategorySubstitutionRegister::setCategories ( const std::map< int, T > & categories )

inlineprotectedinherited

Definition at line 185 of file SubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::categories_, bpp::CategorySubstitutionRegister::categoryNames_, bpp::SubstitutionModel::getAlphabet(), bpp::SubstitutionModel::getAlphabetStates(), bpp::CategorySubstitutionRegister::index_, bpp::AbstractSubstitutionRegister::model_, bpp::CategorySubstitutionRegister::nbCategories_, bpp::CategorySubstitutionRegister::revIndex_, and bpp::CategorySubstitutionRegister::within_.

Member Data Documentation

◆ categories_

std::map<int, size_t> bpp::CategorySubstitutionRegister::categories_

mutableprotectedinherited

Definition at line 161 of file SubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getCategory(), bpp::CategorySubstitutionRegister::getType(), getType(), and bpp::CategorySubstitutionRegister::setCategories().

◆ categoryNames_

std::vector<std::string> bpp::CategorySubstitutionRegister::categoryNames_

protectedinherited

Definition at line 162 of file SubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getCategoryName(), and bpp::CategorySubstitutionRegister::setCategories().

◆ code_

const GeneticCode* bpp::GCSynonymousSubstitutionRegister::code_

private

Definition at line 957 of file SubstitutionRegister.h.

Referenced by GCSynonymousSubstitutionRegister(), getType(), and operator=().

◆ index_

std::vector< std::vector<size_t> > bpp::CategorySubstitutionRegister::index_

protectedinherited

Definition at line 163 of file SubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getType(), getType(), and bpp::CategorySubstitutionRegister::setCategories().

◆ model_

const SubstitutionModel* bpp::AbstractSubstitutionRegister::model_

protectedinherited

Definition at line 125 of file SubstitutionRegister.h.

Referenced by bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::CategorySubstitutionRegister::getCategory(), bpp::AbstractSubstitutionRegister::getSubstitutionModel(), bpp::CategorySubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), getType(), bpp::AbstractSubstitutionRegister::operator=(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), and bpp::CategorySubstitutionRegister::setCategories().

◆ nbCategories_

size_t bpp::CategorySubstitutionRegister::nbCategories_

protectedinherited

Definition at line 160 of file SubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getCategoryFrom(), bpp::CategorySubstitutionRegister::getCategoryTo(), bpp::CategorySubstitutionRegister::getNumberOfCategories(), bpp::CategorySubstitutionRegister::getNumberOfSubstitutionTypes(), and bpp::CategorySubstitutionRegister::setCategories().

◆ revIndex_

std::vector< std::vector<size_t> > bpp::CategorySubstitutionRegister::revIndex_

protectedinherited

Definition at line 164 of file SubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::getCategoryFrom(), bpp::CategorySubstitutionRegister::getCategoryTo(), and bpp::CategorySubstitutionRegister::setCategories().

◆ within_

bool bpp::CategorySubstitutionRegister::within_

protectedinherited

Definition at line 159 of file SubstitutionRegister.h.

Referenced by bpp::CategorySubstitutionRegister::allowWithin(), bpp::CategorySubstitutionRegister::getCategoryFrom(), bpp::CategorySubstitutionRegister::getCategoryTo(), bpp::CategorySubstitutionRegister::getNumberOfSubstitutionTypes(), and bpp::CategorySubstitutionRegister::setCategories().

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

Bpp/Phyl/Mapping/SubstitutionRegister.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GCSynonymousSubstitutionRegister() [1/2]

◆ GCSynonymousSubstitutionRegister() [2/2]

Member Function Documentation

◆ allowWithin()

◆ clone()

◆ getAlphabet()

◆ getCategory()

◆ getCategoryFrom()

◆ getCategoryName()

◆ getCategoryTo()

◆ getNumberOfCategories()

◆ getNumberOfSubstitutionTypes()

◆ getSubstitutionModel()

◆ getType()

◆ getTypeName()

◆ operator=()

◆ setCategories()

Member Data Documentation

◆ categories_

◆ categoryNames_

◆ code_

◆ index_

◆ model_

◆ nbCategories_

◆ revIndex_

◆ within_