Reverse iterator to convert RNA to DNA. More...

#include <Bpp/Seq/DNAToRNA.h>

Inheritance diagram for bpp::DNAToRNA:

Collaboration diagram for bpp::DNAToRNA:

Public Member Functions
	DNAToRNA ()

	DNAToRNA (const DNAToRNA &d2r)

DNAToRNA &	operator= (const DNAToRNA &d2r)

virtual	~DNAToRNA ()

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

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

int	translate (int state) const throw (BadIntException)
	Translate a given state coded as a int from source alphabet to target alphabet. More...

std::string	translate (const std::string &state) const throw (BadCharException)
	Translate a given state coded as a string from source alphabet to target alphabet. More...

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

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

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

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

Private Attributes
const Alphabet *	dna_

const Alphabet *	rna_

Detailed Description

Reverse iterator to convert RNA to DNA.

This only changes U to T characters.

See also: NucleicAcidsReplication

Definition at line 58 of file DNAToRNA.h.

Constructor & Destructor Documentation

◆ DNAToRNA() [1/2]

bpp::DNAToRNA::DNAToRNA ( )

inline

Definition at line 65 of file DNAToRNA.h.

◆ DNAToRNA() [2/2]

bpp::DNAToRNA::DNAToRNA ( const DNAToRNA & d2r )

inline

Definition at line 67 of file DNAToRNA.h.

◆ ~DNAToRNA()

virtual bpp::DNAToRNA::~DNAToRNA ( )

inlinevirtual

Definition at line 77 of file DNAToRNA.h.

Member Function Documentation

◆ getSourceAlphabet()

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

inlinevirtual

Get the source alphabet.

Returns: The source alphabet.

Implements bpp::AbstractReverseTransliterator.

Definition at line 80 of file DNAToRNA.h.

References dna_.

◆ getTargetAlphabet()

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

inlinevirtual

Get the target alphabet.

Returns: The target alphabet.

Implements bpp::AbstractReverseTransliterator.

Definition at line 81 of file DNAToRNA.h.

References rna_.

◆ operator=()

DNAToRNA& bpp::DNAToRNA::operator= ( const DNAToRNA & d2r )

inline

Definition at line 69 of file DNAToRNA.h.

References dna_, and rna_.

◆ reverse() [1/3]

int DNAToRNA::reverse	(	int	state	)	const
throw	(	BadIntException
	)

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::AbstractReverseTransliterator.

Definition at line 63 of file DNAToRNA.cpp.

◆ reverse() [2/3]

string DNAToRNA::reverse	(	const std::string &	state	)	const
throw	(	BadCharException
	)

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::AbstractReverseTransliterator.

Definition at line 71 of file DNAToRNA.cpp.

◆ reverse() [3/3]

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

inlinevirtual

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.

Reimplemented from bpp::AbstractReverseTransliterator.

Definition at line 90 of file DNAToRNA.h.

References bpp::AbstractReverseTransliterator::reverse().

◆ translate() [1/3]

int DNAToRNA::translate	(	int	state	)	const
throw	(	BadIntException
	)

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::AbstractTransliterator.

Definition at line 47 of file DNAToRNA.cpp.

◆ translate() [2/3]

string DNAToRNA::translate	(	const std::string &	state	)	const
throw	(	BadCharException
	)

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::AbstractTransliterator.

Definition at line 55 of file DNAToRNA.cpp.

◆ translate() [3/3]

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

inlinevirtual

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.

Reimplemented from bpp::AbstractTransliterator.

Definition at line 84 of file DNAToRNA.h.

References bpp::AbstractTransliterator::translate().

Member Data Documentation

◆ dna_

const Alphabet* bpp::DNAToRNA::dna_

private

Definition at line 62 of file DNAToRNA.h.

Referenced by getSourceAlphabet(), and operator=().

◆ rna_

const Alphabet * bpp::DNAToRNA::rna_

private

Definition at line 62 of file DNAToRNA.h.

Referenced by getTargetAlphabet(), and operator=().

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

Bpp/Seq/DNAToRNA.h
Bpp/Seq/DNAToRNA.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DNAToRNA() [1/2]

◆ DNAToRNA() [2/2]

◆ ~DNAToRNA()

Member Function Documentation

◆ getSourceAlphabet()

◆ getTargetAlphabet()

◆ operator=()

◆ reverse() [1/3]

◆ reverse() [2/3]

◆ reverse() [3/3]

◆ translate() [1/3]

◆ translate() [2/3]

◆ translate() [3/3]

Member Data Documentation

◆ dna_

◆ rna_