Partial implementation of the Transliterator interface for genetic code object. More...

#include <Bpp/Seq/GeneticCode/GeneticCode.h>

Inheritance diagram for bpp::GeneticCode:

Collaboration diagram for bpp::GeneticCode:

Public Member Functions
	GeneticCode ()
	GeneticCode (const GeneticCode &gc)
GeneticCode &	operator= (const GeneticCode &gc)
virtual	~GeneticCode ()
Methods form the Transliterator interface.
const Alphabet *	getSourceAlphabet () const
	Get the source alphabet.
const Alphabet *	getTargetAlphabet () const
	Get the target alphabet.
virtual int	translate (int state) const =0 throw (BadIntException, Exception)
	Translate a given state coded as a int from source alphabet to target alphabet.
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.
virtual Sequence *	translate (const Sequence &sequence) const throw (Exception)
	Translate a whole sequence from source alphabet to target alphabet.
Specific methods.
bool	areSynonymous (int i, int j) const throw (BadIntException)
bool	areSynonymous (const std::string &i, const std::string &j) const throw (BadCharException)
std::vector< int >	getSynonymous (int aminoacid) const throw (BadIntException)
std::vector< std::string >	getSynonymous (const std::string &aminoacid) const throw (BadCharException)
bool	isFourFoldDegenerated (int codon) const
Sequence *	getCodingSequence (const Sequence &sequence, bool lookForInitCodon=false, bool includeInitCodon=false) const throw (Exception)
	Get the subsequence corresponding to the coding part of a given sequence.
Protected Attributes
const CodonAlphabet *	codonAlphabet_
const ProteicAlphabet *	proteicAlphabet_

Detailed Description

Partial implementation of the Transliterator interface for genetic code object.

A genetic code object if a translator from a codon alphabet to a proteic alphabet. Depending on the codon alphabet used, several genetic code can be implemented.

See also:: CodonAlphabet, ProteicAlphabet

Definition at line 79 of file GeneticCode.h.

Constructor & Destructor Documentation

bpp::GeneticCode::GeneticCode ( ) [inline]

Definition at line 87 of file GeneticCode.h.

bpp::GeneticCode::GeneticCode ( const GeneticCode & gc ) [inline]

Definition at line 93 of file GeneticCode.h.

virtual bpp::GeneticCode::~GeneticCode ( ) [inline, virtual]

Definition at line 107 of file GeneticCode.h.

Member Function Documentation

bool bpp::GeneticCode::areSynonymous	(	int	i,
		int	j
	)		const throw (BadIntException) `[inline]`

Definition at line 131 of file GeneticCode.h.

References translate().

Referenced by bpp::CodonSiteTools::numberOfSynonymousDifferences().

bool bpp::GeneticCode::areSynonymous	(	const std::string &	i,
		const std::string &	j
	)		const throw (BadCharException) `[inline]`

Definition at line 135 of file GeneticCode.h.

References translate().

Sequence * GeneticCode::getCodingSequence	(	const Sequence &	sequence,
		bool	lookForInitCodon = `false`,
		bool	includeInitCodon = `false`
	)		const throw (Exception)

Get the subsequence corresponding to the coding part of a given sequence.

If lookForInitCodon if set to 'true', the subsequence will start at the first AUG motif, otherwise the subsequence will start at the begining of the sequence. The subsequence ends at the first stop codon (excluded) found, or the end of the sequence.

The sequence may have a nucleotide or codon alphabet. The subsequence has the same alphabet, name and comments of the input sequence. In case of nucleotide sequence and if the lookForInitCodon option is checked, the phase will be determined from the sequence.

Parameters:

sequence	The sequence to parse.
lookForInitCodon	Tell if the AUG codon must be found.
includeInitCodon	(if lookForInitCodon is true) tell if the init codon must be included in the subsequence.

Returns:: A nucleotide/codon subsequence.

Definition at line 128 of file GeneticCode.cpp.

References bpp::AbstractAlphabet::intToChar(), bpp::AlphabetTools::isCodonAlphabet(), bpp::AlphabetTools::isNucleicAlphabet(), bpp::SymbolList::size(), and bpp::SequenceTools::subseq().

const Alphabet* bpp::GeneticCode::getSourceAlphabet ( ) const [inline, virtual]

Get the source alphabet.

Returns:: The source alphabet.

Implements bpp::Transliterator.

Definition at line 115 of file GeneticCode.h.

References codonAlphabet_.

Referenced by bpp::CodonSiteTools::numberOfSynonymousDifferences().

vector< int > GeneticCode::getSynonymous ( int aminoacid ) const throw (BadIntException)

Definition at line 55 of file GeneticCode.cpp.

std::vector< std::string > GeneticCode::getSynonymous ( const std::string & aminoacid ) const throw (BadCharException)

Definition at line 76 of file GeneticCode.cpp.

const Alphabet* bpp::GeneticCode::getTargetAlphabet ( ) const [inline, virtual]

Get the target alphabet.

Returns:: The target alphabet.

Implements bpp::Transliterator.

Definition at line 116 of file GeneticCode.h.

References proteicAlphabet_.

bool GeneticCode::isFourFoldDegenerated ( int codon ) const

Returns:: True if the specified codon is fourfold degenerated (that is, if a mutation in the fourth position does not change the aminoacid).

Author:: Benoit Nabholz, Annabelle Haudry

Parameters:

codon The codon to test.

Definition at line 97 of file GeneticCode.cpp.

References codonAlphabet_, bpp::CodonAlphabet::getCodon(), bpp::WordAlphabet::getPositions(), bpp::CodonAlphabet::isStop(), and translate().

Referenced by bpp::CodonSiteTools::isFourFoldDegenerated().

GeneticCode& bpp::GeneticCode::operator= ( const GeneticCode & gc ) [inline]

Definition at line 99 of file GeneticCode.h.

References codonAlphabet_, and proteicAlphabet_.

virtual int bpp::GeneticCode::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::AbstractTransliterator.

Implemented in bpp::InvertebrateMitochondrialGeneticCode, bpp::YeastMitochondrialGeneticCode, bpp::EchinodermMitochondrialGeneticCode, bpp::StandardGeneticCode, and bpp::VertebrateMitochondrialGeneticCode.

Referenced by areSynonymous(), isFourFoldDegenerated(), and translate().

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

Implemented in bpp::InvertebrateMitochondrialGeneticCode, bpp::YeastMitochondrialGeneticCode, bpp::EchinodermMitochondrialGeneticCode, bpp::StandardGeneticCode, and bpp::VertebrateMitochondrialGeneticCode.

virtual Sequence* bpp::GeneticCode::translate ( const Sequence & sequence ) const throw (Exception) [inline, 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.

Reimplemented from bpp::AbstractTransliterator.

Reimplemented in bpp::InvertebrateMitochondrialGeneticCode, bpp::YeastMitochondrialGeneticCode, bpp::EchinodermMitochondrialGeneticCode, bpp::StandardGeneticCode, and bpp::VertebrateMitochondrialGeneticCode.

Definition at line 119 of file GeneticCode.h.

References translate().

Member Data Documentation

const CodonAlphabet* bpp::GeneticCode::codonAlphabet_ [protected]

Definition at line 83 of file GeneticCode.h.

const ProteicAlphabet* bpp::GeneticCode::proteicAlphabet_ [protected]

Definition at line 84 of file GeneticCode.h.

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

Bpp/Seq/GeneticCode/GeneticCode.h
Bpp/Seq/GeneticCode/GeneticCode.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation