Partial implementation of the ReverseTransliterator interface. More...

#include <Bpp/Seq/Transliterator.h>

Inheritance diagram for bpp::AbstractReverseTransliterator:

Collaboration diagram for bpp::AbstractReverseTransliterator:

Public Member Functions
	AbstractReverseTransliterator ()

virtual	~AbstractReverseTransliterator ()

virtual const Alphabet *	getSourceAlphabet () const =0
	Get the source alphabet. More...

virtual const Alphabet *	getTargetAlphabet () const =0
	Get the target alphabet. More...

virtual int	reverse (int state) const =0 throw (BadIntException, Exception)
	Translate a given state coded as a int from target alphabet to source alphabet. More...

virtual std::string	reverse (const std::string &state) const =0 throw (BadCharException, Exception)
	Translate a given state coded as a string from target alphabet to source alphabet. More...

virtual Sequence *	reverse (const Sequence &sequence) const throw (AlphabetMismatchException, Exception)
	Translate a whole sequence from target alphabet to source 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...

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...

Detailed Description

Partial implementation of the ReverseTransliterator interface.

Definition at line 167 of file Transliterator.h.

Constructor & Destructor Documentation

◆ AbstractReverseTransliterator()

bpp::AbstractReverseTransliterator::AbstractReverseTransliterator ( )

inline

Definition at line 172 of file Transliterator.h.

◆ ~AbstractReverseTransliterator()

virtual bpp::AbstractReverseTransliterator::~AbstractReverseTransliterator ( )

inlinevirtual

Definition at line 173 of file Transliterator.h.

Member Function Documentation

◆ getSourceAlphabet()

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

pure virtual

Get the source alphabet.

Returns: The source alphabet.

Implements bpp::Transliterator.

Implemented in bpp::DNAToRNA.

◆ getTargetAlphabet()

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

pure virtual

Get the target alphabet.

Returns: The target alphabet.

Implements bpp::Transliterator.

Implemented in bpp::DNAToRNA.

◆ reverse() [1/3]

virtual int bpp::AbstractReverseTransliterator::reverse	(	int	state	)	const
throw	(	BadIntException,
		Exception
	)

pure virtual

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

Parameters

state A state in target alphabet.

Returns: The corresponding state in source alphabet.

Exceptions

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

Implements bpp::ReverseTransliterator.

Implemented in bpp::DNAToRNA.

Referenced by bpp::DNAToRNA::reverse().

◆ reverse() [2/3]

virtual std::string bpp::AbstractReverseTransliterator::reverse	(	const std::string &	state	)	const
throw	(	BadCharException,
		Exception
	)

pure virtual

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

Parameters

state A state in target alphabet.

Returns: The corresponding state in source alphabet.

Exceptions

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

Implements bpp::ReverseTransliterator.

Implemented in bpp::DNAToRNA.

◆ reverse() [3/3]

Sequence * AbstractReverseTransliterator::reverse	(	const Sequence &	sequence	)	const
throw	(	AlphabetMismatchException,
		Exception
	)

virtual

Translate a whole sequence from target alphabet to source alphabet.

Parameters

sequence A sequence in target alphabet.

Returns: The corresponding sequence in source alphabet.

Exceptions

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

Implements bpp::ReverseTransliterator.

Reimplemented in bpp::DNAToRNA.

Definition at line 61 of file Transliterator.cpp.

References bpp::SymbolList::addElement().

◆ translate() [1/6]

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

pure virtualinherited

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() [2/6]

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

pure virtualinherited

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() [3/6]

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

pure virtualinherited

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.

◆ translate() [4/6]

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

pure virtualinherited

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() [5/6]

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

pure virtualinherited

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() [6/6]

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

virtualinherited

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().

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

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

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AbstractReverseTransliterator()

◆ ~AbstractReverseTransliterator()

Member Function Documentation

◆ getSourceAlphabet()

◆ getTargetAlphabet()

◆ reverse() [1/3]

◆ reverse() [2/3]

◆ reverse() [3/3]

◆ translate() [1/6]

◆ translate() [2/6]

◆ translate() [3/6]

◆ translate() [4/6]

◆ translate() [5/6]

◆ translate() [6/6]