bpp::Transliterator Class Reference

This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA. More...

#include <Bpp/Seq/Transliterator.h>

Inheritance diagram for bpp::Transliterator:

Public Member Functions
	Transliterator ()
virtual	~Transliterator ()
virtual const Alphabet *	getSourceAlphabet () const =0
	Get the source alphabet. More...
virtual const Alphabet *	getTargetAlphabet () const =0
	Get the target alphabet. More...
virtual int	translate (int state) const =0
	Translate a given state coded as a int from source alphabet to target alphabet. More...
virtual std::string	translate (const std::string &state) const =0
	Translate a given state coded as a string from source alphabet to target alphabet. More...
virtual Sequence *	translate (const Sequence &sequence) const =0
	Translate a whole sequence from source alphabet to target alphabet. More...

Detailed Description

This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA.

Definition at line 53 of file Transliterator.h.

Constructor & Destructor Documentation

Transliterator()

bpp::Transliterator::Transliterator ( )

inline

Definition at line 56 of file Transliterator.h.

~Transliterator()

virtual bpp::Transliterator::~Transliterator ( )

inlinevirtual

Definition at line 57 of file Transliterator.h.

Member Function Documentation

getSourceAlphabet()

virtual const Alphabet* bpp::Transliterator::getSourceAlphabet ( ) const

pure virtual

Get the source alphabet.

Returns

The source alphabet.

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

Referenced by bpp::AbstractTransliterator::translate().

getTargetAlphabet()

virtual const Alphabet* bpp::Transliterator::getTargetAlphabet ( ) const

pure virtual

Get the target alphabet.

Returns

The target alphabet.

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

Referenced by bpp::AbstractTransliterator::translate().

translate() [1/3]

virtual Sequence* bpp::Transliterator::translate ( const Sequence &  sequence ) const

pure virtual

Translate a whole sequence from source alphabet to target alphabet.

Parameters

sequence

A sequence in source alphabet.

Returns

The corresponding sequence in target alphabet.

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

translate() [2/3]

virtual std::string bpp::Transliterator::translate ( const std::string &  state ) const

pure 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.

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

translate() [3/3]

virtual int bpp::Transliterator::translate ( int  state ) const

pure 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.

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

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

• Bpp/Seq/Transliterator.h