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 ()
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 throw (AlphabetMismatchException, Exception)
	Translate a whole sequence from source alphabet to target alphabet. More...
virtual const Alphabet *	getSourceAlphabet () const =0
	Get the source alphabet. More...
virtual const Alphabet *	getTargetAlphabet () const =0
	Get the target alphabet. More...

Detailed Description

Partial implementation of the Transliterator interface.

Definition at line 151 of file Transliterator.h.

Constructor & Destructor Documentation

AbstractTransliterator()

bpp::AbstractTransliterator::AbstractTransliterator ( )

inline

Definition at line 155 of file Transliterator.h.

~AbstractTransliterator()

virtual bpp::AbstractTransliterator::~AbstractTransliterator ( )

inlinevirtual

Definition at line 156 of file Transliterator.h.

Member Function Documentation

getSourceAlphabet()

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

pure virtualinherited

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 virtualinherited

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::AbstractTransliterator::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.

Implements bpp::Transliterator.

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

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

translate() [2/3]

virtual std::string bpp::AbstractTransliterator::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.

Implements bpp::Transliterator.

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

translate() [3/3]

Sequence * AbstractTransliterator::translate ( const Sequence &  sequence ) const throw ( AlphabetMismatchException, Exception )

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.

Implements bpp::Transliterator.

Reimplemented in bpp::GeneticCode, and bpp::DNAToRNA.

Definition at line 44 of file Transliterator.cpp.

References bpp::SymbolList::addElement(), bpp::BasicSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

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

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