bpp-seq3  3.0.0
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
 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
 Translate a given state coded as a string from target alphabet to source alphabet. More...
 
virtual Sequence * reverse (const Sequence &sequence) const =0
 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
 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

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

Definition at line 102 of file Transliterator.h.

Constructor & Destructor Documentation

◆ ReverseTransliterator()

bpp::ReverseTransliterator::ReverseTransliterator ( )
inline

Definition at line 106 of file Transliterator.h.

◆ ~ReverseTransliterator()

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

Definition at line 107 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::NucleicAcidsReplication, bpp::GeneticCode, bpp::DNAToRNA, and bpp::AllelicAlphabet::AllelicTransliterator.

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

◆ getTargetAlphabet()

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

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().

◆ reverse() [1/3]

virtual Sequence* bpp::ReverseTransliterator::reverse ( const Sequence &  sequence) const
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.

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

◆ reverse() [2/3]

virtual std::string bpp::ReverseTransliterator::reverse ( const std::string &  state) const
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.

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

◆ reverse() [3/3]

virtual int bpp::ReverseTransliterator::reverse ( int  state) const
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.

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

◆ translate() [1/3]

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

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 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.

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 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.

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

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