Distinguishes all types of substitutions. More...

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

Inheritance diagram for bpp::ComprehensiveSubstitutionRegister:

Collaboration diagram for bpp::ComprehensiveSubstitutionRegister:

Public Member Functions
	ComprehensiveSubstitutionRegister (const SubstitutionModel *model, bool within=false)

ComprehensiveSubstitutionRegister *	clone () const

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

size_t	getNumberOfSubstitutionTypes () const

virtual 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...

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_

Detailed Description

Distinguishes all types of substitutions.

This register has all n * (n-1) substitution type, where n is the size of the alphabet, mapped as:

0 not a substitution
x in [1, n(n-1)] a substitution

Definition at line 448 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ ComprehensiveSubstitutionRegister()

bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister	(	const SubstitutionModel *	model,
		bool	within = `false`
	)

inline

Definition at line 452 of file SubstitutionRegister.h.

References bpp::SubstitutionModel::getAlphabet().

Referenced by clone().

Member Function Documentation

◆ allowWithin()

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

inlinevirtualinherited

Definition at line 289 of file SubstitutionRegister.h.

References bpp::CategorySubstitutionRegister::within_.

◆ clone()

ComprehensiveSubstitutionRegister* bpp::ComprehensiveSubstitutionRegister::clone ( ) const

inlinevirtual

Implements bpp::SubstitutionRegister.

Definition at line 463 of file SubstitutionRegister.h.

References ComprehensiveSubstitutionRegister().

◆ 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::CategorySubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtualinherited

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

Implements bpp::SubstitutionRegister.

Reimplemented in bpp::GCSynonymousSubstitutionRegister.

Definition at line 293 of file SubstitutionRegister.h.

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

◆ 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()

virtual size_t bpp::CategorySubstitutionRegister::getType	(	size_t	fromState,
		size_t	toState
	)		const

inlinevirtualinherited

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::SubstitutionRegister.

Reimplemented in bpp::GCSynonymousSubstitutionRegister.

Definition at line 295 of file SubstitutionRegister.h.

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