bpp::SubstitutionRegisterInterface Class Reference

The SubstitutionRegister interface. More...

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

Inheritance diagram for bpp::SubstitutionRegisterInterface:

Collaboration diagram for bpp::SubstitutionRegisterInterface:

Public Member Functions
	SubstitutionRegisterInterface ()
virtual	~SubstitutionRegisterInterface ()
virtual SubstitutionRegisterInterface *	clone () const =0
virtual const Alphabet &	alphabet () const =0
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
virtual const StateMapInterface &	stateMap () const =0
virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0
virtual size_t	getNumberOfSubstitutionTypes () const =0
virtual const std::string &	getName () const =0
	Get the name of the register. More...
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 state map.

Author

Julien Dutheil

Definition at line 38 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

SubstitutionRegisterInterface()

bpp::SubstitutionRegisterInterface::SubstitutionRegisterInterface ( )

inline

Definition at line 42 of file SubstitutionRegister.h.

~SubstitutionRegisterInterface()

virtual bpp::SubstitutionRegisterInterface::~SubstitutionRegisterInterface ( )

inlinevirtual

Definition at line 43 of file SubstitutionRegister.h.

Member Function Documentation

alphabet()

virtual const Alphabet& bpp::SubstitutionRegisterInterface::alphabet ( ) const

pure virtual

Returns

The alphabet associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

clone()

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

pure virtual

Implements bpp::Clonable.

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

getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::SubstitutionRegisterInterface::getAlphabet ( ) const

pure virtual

Returns

A shared_ptr toward the alphabet associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

getName()

virtual const std::string& bpp::SubstitutionRegisterInterface::getName ( ) const

pure virtual

Get the name of the register.

Returns

A string describing the register.

Implemented in bpp::AbstractSubstitutionRegister.

getNumberOfSubstitutionTypes()

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

pure virtual

Returns

The number of substitution types supported by this class.

Implemented in bpp::GeneralSubstitutionRegister, bpp::VectorOfSubstitutionRegisters, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::SWSubstitutionRegister, bpp::TsTvSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::MutationPath::getEventCounts(), bpp::LegacySubstitutionMappingTools::getNormalizationsPerBranch(), bpp::SiteSimulationResult::getSubstitutionVector(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

getStateMap()

virtual std::shared_ptr<const StateMapInterface> bpp::SubstitutionRegisterInterface::getStateMap ( ) const

pure virtual

Returns

A shared_ptr toward the state map associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

getType()

virtual size_t bpp::SubstitutionRegisterInterface::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::GeneralSubstitutionRegister, bpp::VectorOfSubstitutionRegisters, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::SWSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::GCPositionSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::MutationPath::getEventCounts(), bpp::LegacySubstitutionMappingTools::getNormalizationsPerBranch(), bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel(), and bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel().

getTypeName()

virtual std::string bpp::SubstitutionRegisterInterface::getTypeName ( size_t  type ) const

pure virtual

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.

Implemented in bpp::GeneralSubstitutionRegister, bpp::VectorOfSubstitutionRegisters, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::SWSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::SelectedSubstitutionRegister, bpp::GCPositionSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::LegacySubstitutionMappingTools::getNormalizationsPerBranch(), bpp::LegacySubstitutionMappingTools::outputPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::outputPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::outputPerSitePerType(), bpp::LegacySubstitutionMappingTools::outputPerSitePerType(), bpp::SubstitutionMappingTools::outputPerType(), and bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel().

stateMap()

virtual const StateMapInterface& bpp::SubstitutionRegisterInterface::stateMap ( ) const

pure virtual

Returns

The state map associated to this instance.

Implemented in bpp::AbstractSubstitutionRegister.

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

• Bpp/Phyl/Mapping/SubstitutionRegister.h