This class implements the vertebrate mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2. More...

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

Inheritance diagram for bpp::VertebrateMitochondrialGeneticCode:

Collaboration diagram for bpp::VertebrateMitochondrialGeneticCode:

Public Member Functions
	VertebrateMitochondrialGeneticCode (const NucleicAlphabet *alpha)

virtual	~VertebrateMitochondrialGeneticCode ()

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

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

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

Methods form the Transliterator interface.
const Alphabet *	getSourceAlphabet () const
	Get the source alphabet. More...

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

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. More...

Protected Attributes
const CodonAlphabet *	codonAlphabet_

const ProteicAlphabet *	proteicAlphabet_

Detailed Description

This class implements the vertebrate mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2.

Definition at line 54 of file VertebrateMitochondrialGeneticCode.h.

Constructor & Destructor Documentation

VertebrateMitochondrialGeneticCode::VertebrateMitochondrialGeneticCode ( const NucleicAlphabet * alpha )

Definition at line 50 of file VertebrateMitochondrialGeneticCode.cpp.

References bpp::GeneticCode::codonAlphabet_, and bpp::GeneticCode::proteicAlphabet_.

VertebrateMitochondrialGeneticCode::~VertebrateMitochondrialGeneticCode ( )

virtual

Definition at line 57 of file VertebrateMitochondrialGeneticCode.cpp.

References bpp::GeneticCode::codonAlphabet_, and bpp::GeneticCode::proteicAlphabet_.

Member Function Documentation

bool bpp::GeneticCode::areSynonymous	(	int	i,
		int	j
	)		const throw (BadIntException)

inlineinherited

Definition at line 131 of file GeneticCode.h.

References bpp::GeneticCode::translate(), and bpp::GeneticCode::translate().

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

inlineinherited

Definition at line 135 of file GeneticCode.h.

References bpp::GeneticCode::translate(), and bpp::GeneticCode::translate().

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

inherited

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.