Gather states into defined categories, and count the changes between categories. More...

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

Inheritance diagram for bpp::CategorySubstitutionRegister:

Collaboration diagram for bpp::CategorySubstitutionRegister:

Public Member Functions
	CategorySubstitutionRegister (const SubstitutionModel *model, bool within=false)
	Build a new substitution register with categories. This class is meant to be inherited. 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

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

virtual SubstitutionRegister *	clone () const =0

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

Gather states into defined categories, and count the changes between categories.

Optionally allows for within categories substitutions.

Definition at line 155 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ CategorySubstitutionRegister()

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

inline

Build a new substitution register with categories. This class is meant to be inherited.

Parameters

model	The model defining the states.
within	Specifies if within categories substitutions should be counted as well.

Definition at line 173 of file SubstitutionRegister.h.

Member Function Documentation

◆ allowWithin()

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

inlinevirtual

Definition at line 289 of file SubstitutionRegister.h.

References within_.

◆ clone()

virtual SubstitutionRegister* bpp::SubstitutionRegister::clone ( ) const

pure virtualinherited

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::GCSubstitutionRegister, bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::SelectedSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::ComprehensiveSubstitutionRegister, bpp::CompleteSubstitutionRegister, and bpp::TotalSubstitutionRegister.

Referenced by bpp::SubstitutionMappingTools::getCountsPerBranch(), bpp::CompleteSubstitutionRegister::operator=(), bpp::SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite(), and bpp::SubstitutionMappingTools::outputTotalCountsPerBranchPerSite().

◆ 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

inlinevirtual

Definition at line 248 of file SubstitutionRegister.h.

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

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

◆ getCategoryFrom()

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

inlinevirtual

Definition at line 254 of file SubstitutionRegister.h.

References nbCategories_, revIndex_, and within_.

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

◆ getCategoryName()

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

inlinevirtual

Definition at line 284 of file SubstitutionRegister.h.

References categoryNames_.

Referenced by getTypeName().

◆ getCategoryTo()

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

inlinevirtual

Definition at line 269 of file SubstitutionRegister.h.

References nbCategories_, revIndex_, and within_.

Referenced by getTypeName().

◆ getNumberOfCategories()

size_t bpp::CategorySubstitutionRegister::getNumberOfCategories ( ) const

inline

Definition at line 291 of file SubstitutionRegister.h.

References nbCategories_.

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

◆ getNumberOfSubstitutionTypes()

size_t bpp::CategorySubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

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 nbCategories_, and 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

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.

Implements bpp::SubstitutionRegister.

Reimplemented in bpp::GCSynonymousSubstitutionRegister.

Definition at line 295 of file SubstitutionRegister.h.

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