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 throw (BadIntException, Exception)
	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 throw (BadCharException, Exception)
	Translate a given state coded as a string from source alphabet to target alphabet. More...
virtual Sequence *	translate (const Sequence &sequence) const =0 throw (AlphabetMismatchException, Exception)
	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 52 of file Transliterator.h.

Constructor & Destructor Documentation

Transliterator()

bpp::Transliterator::Transliterator ( )

inline

Definition at line 55 of file Transliterator.h.

~Transliterator()

virtual bpp::Transliterator::~Transliterator ( )

inlinevirtual

Definition at line 56 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::GeneticCode, bpp::NucleicAcidsReplication, and bpp::DNAToRNA.

getTargetAlphabet()

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

pure virtual

Get the target alphabet.

Returns

The target alphabet.

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

translate() [1/3]

virtual int bpp::Transliterator::translate ( int  state ) const throw ( BadIntException, Exception )

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.

Exceptions

BadIntException	If the state is not a proper state for source alphabet.
Exception	Other kind of error, depending on the implementation.

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

translate() [2/3]

virtual std::string bpp::Transliterator::translate ( const std::string &  state ) const throw ( BadCharException, Exception )

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.

Exceptions

BadCharException	If the state is not a proper state for source alphabet.
Exception	Other kind of error, depending on the implementation.

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

translate() [3/3]

virtual Sequence* bpp::Transliterator::translate ( const Sequence &  sequence ) const throw ( AlphabetMismatchException, Exception )

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.

Exceptions

AlphabetMismatchException	If the sequence alphabet do not match the source alphabet.
Exception	Other kind of error, depending on the implementation.

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

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

• Bpp/Seq/Transliterator.h