bpp::AbstractSubstitutionRegister Class Reference

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

Inheritance diagram for bpp::AbstractSubstitutionRegister:

Collaboration diagram for bpp::AbstractSubstitutionRegister:

Public Member Functions
	AbstractSubstitutionRegister (const SubstitutionModel *model)
	AbstractSubstitutionRegister (const AbstractSubstitutionRegister &asr)
AbstractSubstitutionRegister &	operator= (const AbstractSubstitutionRegister &asr)
virtual	~AbstractSubstitutionRegister ()
const SubstitutionModel *	getSubstitutionModel () const
const Alphabet *	getAlphabet () const
virtual SubstitutionRegister *	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
const SubstitutionModel *	model_

Detailed Description

Definition at line 121 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

AbstractSubstitutionRegister() [1/2]

bpp::AbstractSubstitutionRegister::AbstractSubstitutionRegister ( const SubstitutionModel *  model )

inline

Definition at line 128 of file SubstitutionRegister.h.

AbstractSubstitutionRegister() [2/2]

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

inline

Definition at line 132 of file SubstitutionRegister.h.

~AbstractSubstitutionRegister()

virtual bpp::AbstractSubstitutionRegister::~AbstractSubstitutionRegister ( )

inlinevirtual

Definition at line 142 of file SubstitutionRegister.h.

Member Function Documentation

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

inlinevirtual

Returns

The alphabet associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 147 of file SubstitutionRegister.h.

References bpp::SubstitutionModel::getAlphabet(), and model_.

getNumberOfSubstitutionTypes()

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

pure virtualinherited

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()

const SubstitutionModel* bpp::AbstractSubstitutionRegister::getSubstitutionModel ( ) const

inlinevirtual

Returns

The substitution model associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 145 of file SubstitutionRegister.h.

References model_.

getType()

virtual size_t bpp::SubstitutionRegister::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::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().

getTypeName()

virtual std::string bpp::SubstitutionRegister::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::GCSynonymousSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::SelectedSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::CompleteSubstitutionRegister, bpp::TotalSubstitutionRegister, and bpp::CategorySubstitutionRegister.

Referenced by bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), and bpp::CompleteSubstitutionRegister::getTypeName().

operator=()

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

inline

Definition at line 136 of file SubstitutionRegister.h.

References model_.

Referenced by bpp::CompleteSubstitutionRegister::operator=(), bpp::GeneralSubstitutionRegister::operator=(), bpp::DnDsSubstitutionRegister::operator=(), and bpp::GCSynonymousSubstitutionRegister::operator=().

Member Data Documentation

model_

const SubstitutionModel* bpp::AbstractSubstitutionRegister::model_

protected

Definition at line 125 of file SubstitutionRegister.h.

Referenced by getAlphabet(), bpp::CategorySubstitutionRegister::getCategory(), getSubstitutionModel(), bpp::CategorySubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), operator=(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), and bpp::CategorySubstitutionRegister::setCategories().

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

• Bpp/Phyl/Mapping/SubstitutionRegister.h