The SubstitutionRegister interface. More...

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

Inheritance diagram for bpp::SubstitutionRegister:

Collaboration diagram for bpp::SubstitutionRegister:

Public Member Functions
	SubstitutionRegister ()

virtual	~SubstitutionRegister ()

virtual SubstitutionRegister *	clone () const =0

virtual const Alphabet *	getAlphabet () const =0

virtual const SubstitutionModel *	getSubstitutionModel () const =0

virtual size_t	getNumberOfSubstitutionTypes () const =0

virtual size_t	getType (size_t fromState, size_t toState) const =0
	Get the substitution type far a given pair of model states. More...

virtual std::string	getTypeName (size_t type) const =0
	Get the name of a given substitution type. More...

Detailed Description

The SubstitutionRegister interface.

Substitution registers are simple classes that define categories of substitutions, and assign an index to them. Substitution registers are defined according to a given substitution model.

Author: Julien Dutheil

Definition at line 72 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ SubstitutionRegister()

bpp::SubstitutionRegister::SubstitutionRegister ( )

inline

Definition at line 76 of file SubstitutionRegister.h.

◆ ~SubstitutionRegister()

virtual bpp::SubstitutionRegister::~SubstitutionRegister ( )

inlinevirtual

Definition at line 77 of file SubstitutionRegister.h.

Member Function Documentation

◆ clone()

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

pure virtual

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()

virtual const Alphabet* bpp::SubstitutionRegister::getAlphabet ( ) const

pure virtual

Returns: The alphabet associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

Referenced by bpp::CompleteSubstitutionRegister::CompleteSubstitutionRegister(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::SubstitutionCount::getAlphabet(), bpp::SubstitutionCount::getNumberOfStates(), and bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount().

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::SubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

pure virtual

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

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::MutationPath::getEventCounts(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::SubstitutionCount::getNumberOfSubstitutionTypes(), bpp::CompleteSubstitutionRegister::getNumberOfSubstitutionTypes(), bpp::SiteSimulationResult::getSubstitutionVector(), and bpp::SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite().

◆ getSubstitutionModel()

virtual const SubstitutionModel* bpp::SubstitutionRegister::getSubstitutionModel ( ) const

pure virtual

Returns: The substitution model associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

◆ getType()

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

pure virtual

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.

Implemented in bpp::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::CompleteSubstitutionRegister::CompleteSubstitutionRegister(), bpp::MutationPath::getEventCounts(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), and bpp::CompleteSubstitutionRegister::getType().