bpp::AbstractSubstitutionRegister Class Reference

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

Inheritance diagram for bpp::AbstractSubstitutionRegister:

Collaboration diagram for bpp::AbstractSubstitutionRegister:

Public Member Functions
	AbstractSubstitutionRegister (std::shared_ptr< const StateMapInterface > stateMap, const std::string &name)
	AbstractSubstitutionRegister (const AbstractSubstitutionRegister &asr)
AbstractSubstitutionRegister &	operator= (const AbstractSubstitutionRegister &asr)
virtual	~AbstractSubstitutionRegister ()
const StateMapInterface &	stateMap () const override
std::shared_ptr< const StateMapInterface >	getStateMap () const override
const Alphabet &	alphabet () const override
std::shared_ptr< const Alphabet >	getAlphabet () const override
const std::string &	getName () const override
	Get the name of the register. More...
virtual SubstitutionRegisterInterface *	clone () 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...

Protected Attributes
std::shared_ptr< const StateMapInterface >	stateMap_
std::string	name_

Detailed Description

Definition at line 103 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

AbstractSubstitutionRegister() [1/2]

bpp::AbstractSubstitutionRegister::AbstractSubstitutionRegister ( std::shared_ptr< const StateMapInterface >  stateMap, const std::string &  name  )

inline

Definition at line 111 of file SubstitutionRegister.h.

AbstractSubstitutionRegister() [2/2]

bpp::AbstractSubstitutionRegister::AbstractSubstitutionRegister ( const AbstractSubstitutionRegister &  asr )

inline

Definition at line 115 of file SubstitutionRegister.h.

~AbstractSubstitutionRegister()

virtual bpp::AbstractSubstitutionRegister::~AbstractSubstitutionRegister ( )

inlinevirtual

Definition at line 126 of file SubstitutionRegister.h.

Member Function Documentation

alphabet()

const Alphabet& bpp::AbstractSubstitutionRegister::alphabet ( ) const

inlineoverridevirtual

Returns

The alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 133 of file SubstitutionRegister.h.

References stateMap_.

clone()

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

pure virtualinherited

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()

std::shared_ptr<const Alphabet> bpp::AbstractSubstitutionRegister::getAlphabet ( ) const

inlineoverridevirtual

Returns

A shared_ptr toward the alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 135 of file SubstitutionRegister.h.

References stateMap_.

getName()

const std::string& bpp::AbstractSubstitutionRegister::getName ( ) const

inlineoverridevirtual

Get the name of the register.

Returns

A string describing the register.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 137 of file SubstitutionRegister.h.

References name_.

getNumberOfSubstitutionTypes()

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

pure virtualinherited

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()

std::shared_ptr<const StateMapInterface> bpp::AbstractSubstitutionRegister::getStateMap ( ) const

inlineoverridevirtual

Returns

A shared_ptr toward the state map associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 131 of file SubstitutionRegister.h.

References stateMap_.

getType()

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

pure virtualinherited

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 virtualinherited

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().

operator=()

AbstractSubstitutionRegister& bpp::AbstractSubstitutionRegister::operator= ( const AbstractSubstitutionRegister &  asr )

inline

Definition at line 119 of file SubstitutionRegister.h.

References name_, and stateMap_.

Referenced by bpp::CompleteSubstitutionRegister::operator=(), bpp::DnDsSubstitutionRegister::operator=(), bpp::GCPositionSubstitutionRegister::operator=(), bpp::GCSynonymousSubstitutionRegister::operator=(), bpp::GeneralSubstitutionRegister::operator=(), bpp::KrKcSubstitutionRegister::operator=(), bpp::SWSubstitutionRegister::operator=(), and bpp::TsTvSubstitutionRegister::operator=().

stateMap()

const StateMapInterface& bpp::AbstractSubstitutionRegister::stateMap ( ) const

inlineoverridevirtual

Returns

The state map associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 129 of file SubstitutionRegister.h.

References stateMap_.

Referenced by bpp::VectorOfSubstitutionRegisters::addRegister(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::GCSynonymousSubstitutionRegister::getType(), bpp::GCPositionSubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::SWSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::KrKcSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setAlphabetCategories(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::AAInteriorSubstitutionRegister::updateMatrix_(), and bpp::AAExteriorSubstitutionRegister::updateMatrix_().

Member Data Documentation

name_

std::string bpp::AbstractSubstitutionRegister::name_

protected

Definition at line 108 of file SubstitutionRegister.h.

Referenced by getName(), and operator=().

stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractSubstitutionRegister::stateMap_

protected

Definition at line 107 of file SubstitutionRegister.h.

Referenced by alphabet(), getAlphabet(), getStateMap(), operator=(), and stateMap().

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

• Bpp/Phyl/Mapping/SubstitutionRegister.h