bpp-seq  2.2.0
Public Member Functions | List of all members
bpp::ReverseTransliterator Class Referenceabstract

The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;. More...

#include <Bpp/Seq/Transliterator.h>

+ Inheritance diagram for bpp::ReverseTransliterator:
+ Collaboration diagram for bpp::ReverseTransliterator:

Public Member Functions

 ReverseTransliterator ()
 
virtual ~ReverseTransliterator ()
 
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 =0 throw (AlphabetMismatchException, Exception)
 Translate a whole sequence from target alphabet to source alphabet. More...
 
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

The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;.

Definition at line 108 of file Transliterator.h.

Constructor & Destructor Documentation

◆ ReverseTransliterator()

bpp::ReverseTransliterator::ReverseTransliterator ( )
inline

Definition at line 112 of file Transliterator.h.

◆ ~ReverseTransliterator()

virtual bpp::ReverseTransliterator::~ReverseTransliterator ( )
inlinevirtual

Definition at line 113 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.

◆ reverse() [1/3]

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

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

Parameters
stateA state in target alphabet.
Returns
The corresponding state in source alphabet.
Exceptions
BadIntExceptionIf the state is not a proper state for target alphabet.
ExceptionOther kind of error, depending on the implementation.

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

◆ reverse() [2/3]

virtual std::string bpp::ReverseTransliterator::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
stateA state in target alphabet.
Returns
The corresponding state in source alphabet.
Exceptions
BadCharExceptionIf the state is not a proper state for target alphabet.
ExceptionOther kind of error, depending on the implementation.

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

◆ reverse() [3/3]

virtual Sequence* bpp::ReverseTransliterator::reverse ( const Sequence &  sequence) const
throw (AlphabetMismatchException,
Exception
)
pure virtual

Translate a whole sequence from target alphabet to source alphabet.

Parameters
sequenceA sequence in target alphabet.
Returns
The corresponding sequence in source alphabet.
Exceptions
AlphabetMismatchExceptionIf the sequence alphabet do not match the target alphabet.
ExceptionOther kind of error, depending on the implementation.

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

◆ translate() [1/3]

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
stateA state in source alphabet.
Returns
The corresponding state in target alphabet.
Exceptions
BadIntExceptionIf the state is not a proper state for source alphabet.
ExceptionOther 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 virtualinherited

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

Parameters
stateA state in source alphabet.
Returns
The corresponding state in target alphabet.
Exceptions
BadCharExceptionIf the state is not a proper state for source alphabet.
ExceptionOther 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 virtualinherited

Translate a whole sequence from source alphabet to target alphabet.

Parameters
sequenceA sequence in source alphabet.
Returns
The corresponding sequence in target alphabet.
Exceptions
AlphabetMismatchExceptionIf the sequence alphabet do not match the source alphabet.
ExceptionOther kind of error, depending on the implementation.

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

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