bpp::AbstractTransliterator Class Reference

Partial implementation of the Transliterator interface. More...

#include <Bpp/Seq/Transliterator.h>

Inheritance diagram for bpp::AbstractTransliterator:

Collaboration diagram for bpp::AbstractTransliterator:

Public Member Functions
	AbstractTransliterator ()
virtual	~AbstractTransliterator ()
int	translate (int state) const override=0
	Translate a given state coded as a int from source alphabet to target alphabet. More...
std::string	translate (const std::string &state) const override=0
	Translate a given state coded as a string from source alphabet to target alphabet. More...
std::unique_ptr< Sequence >	translate (const SequenceInterface &sequence) const override
	Translate a whole sequence from source alphabet to target alphabet. More...
virtual std::shared_ptr< const Alphabet >	getSourceAlphabet () const =0
	Get the source alphabet. More...
virtual const Alphabet &	sourceAlphabet () const =0
	Get the source alphabet. More...
virtual std::shared_ptr< const Alphabet >	getTargetAlphabet () const =0
	Get the target alphabet. More...
virtual const Alphabet &	targetAlphabet () const =0
	Get the target alphabet. More...

Detailed Description

Partial implementation of the Transliterator interface.

Definition at line 116 of file Transliterator.h.

Constructor & Destructor Documentation

AbstractTransliterator()

bpp::AbstractTransliterator::AbstractTransliterator ( )

inline

Definition at line 120 of file Transliterator.h.

~AbstractTransliterator()

virtual bpp::AbstractTransliterator::~AbstractTransliterator ( )

inlinevirtual

Definition at line 121 of file Transliterator.h.

Member Function Documentation

getSourceAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::TransliteratorInterface::getSourceAlphabet ( ) const

pure virtualinherited

Get the source alphabet.

Returns

A pointer toward the source alphabet.

Implemented in bpp::NucleicAcidsReplication, bpp::GeneticCode, bpp::DNAToRNA, and bpp::AllelicAlphabet::AllelicTransliterator.

getTargetAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::TransliteratorInterface::getTargetAlphabet ( ) const

pure virtualinherited

Get the target alphabet.

Returns

A pointer toward the target alphabet.

Implemented in bpp::NucleicAcidsReplication, bpp::GeneticCode, bpp::DNAToRNA, and bpp::AllelicAlphabet::AllelicTransliterator.

sourceAlphabet()

virtual const Alphabet& bpp::TransliteratorInterface::sourceAlphabet ( ) const

pure virtualinherited

Get the source alphabet.

Returns

A reference toward the source alphabet.

Implemented in bpp::NucleicAcidsReplication, bpp::GeneticCode, and bpp::DNAToRNA.

targetAlphabet()

virtual const Alphabet& bpp::TransliteratorInterface::targetAlphabet ( ) const

pure virtualinherited

Get the target alphabet.

Returns

A reference toward the target alphabet.

Implemented in bpp::NucleicAcidsReplication, bpp::GeneticCode, and bpp::DNAToRNA.

translate() [1/3]

unique_ptr< Sequence > AbstractTransliterator::translate ( const SequenceInterface &  sequence ) const

overridevirtual

Translate a whole sequence from source alphabet to target alphabet.

Parameters

sequence

A sequence in source alphabet.

Returns

The corresponding sequence in target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 13 of file Transliterator.cpp.

References bpp::CruxSymbolListInterface::alphabet(), bpp::CruxSymbolListInterface::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::Commentable::getComments(), bpp::CoreSequenceInterface::getName(), bpp::TemplateCoreSymbolListInterface< T >::getValue(), and bpp::CruxSymbolListInterface::size().

translate() [2/3]

std::string bpp::AbstractTransliterator::translate ( const std::string &  state ) const

overridepure virtual

Translate a given state coded as a string from source alphabet to target alphabet.

Parameters

state

A state in source alphabet.

Returns

The corresponding state in target alphabet.

Implements bpp::TransliteratorInterface.

Implemented in bpp::GeneticCode, bpp::DNAToRNA, and bpp::AllelicAlphabet::AllelicTransliterator.

translate() [3/3]

int bpp::AbstractTransliterator::translate ( int  state ) const

overridepure virtual

Translate a given state coded as a int from source alphabet to target alphabet.

Parameters

state

A state in source alphabet.

Returns

The corresponding state in target alphabet.

Implements bpp::TransliteratorInterface.

Implemented in bpp::GeneticCode, bpp::DNAToRNA, and bpp::AllelicAlphabet::AllelicTransliterator.

Referenced by bpp::AllelicAlphabet::AllelicTransliterator::translate(), bpp::DNAToRNA::translate(), and bpp::GeneticCode::translate().

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

• Bpp/Seq/Transliterator.h
• Bpp/Seq/Transliterator.cpp