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 *alphabet)

virtual	~VertebrateMitochondrialGeneticCode ()

virtual VertebrateMitochondrialGeneticCode *	clone () const

size_t	getNumberOfStopCodons () const

std::vector< int >	getStopCodonsAsInt () const

std::vector< std::string >	getStopCodonsAsChar () const

bool	isStop (int state) const throw (BadIntException)
	Tells is a particular codon is a stop codon. More...

bool	isStop (const std::string &state) const throw (BadCharException)
	Tells is a particular codon is a stop codon. More...

bool	isAltStart (int state) const throw (BadIntException)
	Tells is a particular codon is an alternative start codon. More...

bool	isAltStart (const std::string &state) const throw (BadCharException)
	Tells is a particular codon is an alternative start codon. More...

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

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

virtual int	translate (int state) const 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 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 throw (Exception)
	Translate a whole sequence from source alphabet to target alphabet. More...

Specific methods.
virtual bool	isStart (int state) const throw (BadIntException)
	Tells is a particular codon is a start codon. More...

virtual bool	isStart (const std::string &state) const throw (BadCharException)
	Tells is a particular codon is a start codon. More...

bool	areSynonymous (int i, int j) const throw (BadIntException)
	Tell if two codons are synonymous, that is, if they encode the same amino-acid. More...

bool	areSynonymous (const std::string &i, const std::string &j) const throw (BadCharException)
	Tell if two codons are synonymous, that is, if they encode the same amino-acid. More...

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
CodonAlphabet	codonAlphabet_

ProteicAlphabet	proteicAlphabet_

std::map< int, int >	tlnTable_

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 53 of file VertebrateMitochondrialGeneticCode.h.

Constructor & Destructor Documentation

◆ VertebrateMitochondrialGeneticCode()

VertebrateMitochondrialGeneticCode::VertebrateMitochondrialGeneticCode ( const NucleicAlphabet * alphabet )

Definition at line 48 of file VertebrateMitochondrialGeneticCode.cpp.

References bpp::GeneticCode::codonAlphabet_, bpp::ProteicAlphabet::getUnknownCharacterCode(), bpp::WordAlphabet::getUnknownCharacterCode(), bpp::GeneticCode::proteicAlphabet_, and bpp::GeneticCode::tlnTable_.

Referenced by clone().

◆ ~VertebrateMitochondrialGeneticCode()

virtual bpp::VertebrateMitochondrialGeneticCode::~VertebrateMitochondrialGeneticCode ( )

inlinevirtual

Definition at line 59 of file VertebrateMitochondrialGeneticCode.h.

Member Function Documentation

◆ areSynonymous() [1/2]

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

inlineinherited

Tell if two codons are synonymous, that is, if they encode the same amino-acid.

Parameters

i	The numeric code for the first codon.
j	The numeric code for the second codon.

Returns: True if the two codons are synonymous.

Exceptions

BadIntException if at least one of the states is not supported by the alphabet.

Definition at line 206 of file GeneticCode.h.

References bpp::GeneticCode::translate().

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

◆ areSynonymous() [2/2]

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

inlineinherited

Tell if two codons are synonymous, that is, if they encode the same amino-acid.

Parameters

i	The character code for the first codon.
j	The character code for the second codon.

Returns: True if the two codons are synonymous.

Exceptions

BadCharException if at least one of the states is not supported by the alphabet.

Definition at line 219 of file GeneticCode.h.

References bpp::GeneticCode::translate().

◆ clone()

virtual VertebrateMitochondrialGeneticCode* bpp::VertebrateMitochondrialGeneticCode::clone ( ) const

inlinevirtual

Implements bpp::GeneticCode.

Definition at line 61 of file VertebrateMitochondrialGeneticCode.h.

References VertebrateMitochondrialGeneticCode().

◆ getCodingSequence()

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.

Returns: A nucleotide/codon subsequence.

Definition at line 149 of file GeneticCode.cpp.

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

◆ getNumberOfStopCodons()

size_t bpp::VertebrateMitochondrialGeneticCode::getNumberOfStopCodons ( ) const

inlinevirtual

Returns: The number of stop codons.

Implements bpp::GeneticCode.

Definition at line 66 of file VertebrateMitochondrialGeneticCode.h.

◆ getSourceAlphabet()

const CodonAlphabet* bpp::GeneticCode::getSourceAlphabet ( ) const

inlinevirtualinherited

Get the source alphabet.

Returns: The source alphabet.

Implements bpp::Transliterator.

Definition at line 106 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

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

◆ getStopCodonsAsChar()

std::vector<std::string> bpp::VertebrateMitochondrialGeneticCode::getStopCodonsAsChar ( ) const

inlinevirtual

Returns: A vector will all char codes for stop codons.

Implements bpp::GeneticCode.

Definition at line 77 of file VertebrateMitochondrialGeneticCode.h.

◆ getStopCodonsAsInt()

std::vector<int> bpp::VertebrateMitochondrialGeneticCode::getStopCodonsAsInt ( ) const

inlinevirtual

Returns: A vector will all int codes for stop codons.

Implements bpp::GeneticCode.

Definition at line 68 of file VertebrateMitochondrialGeneticCode.h.

◆ getSynonymous() [1/2]

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

inherited

Definition at line 77 of file GeneticCode.cpp.

◆ getSynonymous() [2/2]

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

inherited

Definition at line 98 of file GeneticCode.cpp.

◆ getTargetAlphabet()

const ProteicAlphabet* bpp::GeneticCode::getTargetAlphabet ( ) const

inlinevirtualinherited

Get the target alphabet.

Returns: The target alphabet.

Implements bpp::Transliterator.

Definition at line 107 of file GeneticCode.h.

References bpp::GeneticCode::proteicAlphabet_.

◆ isAltStart() [1/2]

bool bpp::VertebrateMitochondrialGeneticCode::isAltStart	(	int	state	)	const
throw	(	BadIntException
	)

inlinevirtual

Tells is a particular codon is an alternative start codon.

Parameters

state The numeric code for the state to test.

Returns: True if the state corresponds to an alternative start codon.

Exceptions

BadIntException if the state is not supported by the alphabet.

Implements bpp::GeneticCode.

Definition at line 97 of file VertebrateMitochondrialGeneticCode.h.

References bpp::GeneticCode::codonAlphabet_, and bpp::AbstractAlphabet::intToChar().

◆ isAltStart() [2/2]

bool bpp::VertebrateMitochondrialGeneticCode::isAltStart	(	const std::string &	state	)	const
throw	(	BadCharException
	)

inlinevirtual

Tells is a particular codon is an alternative start codon.

Parameters

state The character code for the state to test.

Returns: True if the state corresponds to an alternative start codon.

Exceptions

BadCharException if the state is not supported by the alphabet.

Implements bpp::GeneticCode.

Definition at line 103 of file VertebrateMitochondrialGeneticCode.h.

References bpp::WordAlphabet::charToInt(), and bpp::GeneticCode::codonAlphabet_.

◆ isFourFoldDegenerated()

bool GeneticCode::isFourFoldDegenerated ( int codon ) const

inherited

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 119 of file GeneticCode.cpp.

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

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

◆ isStart() [1/2]

virtual bool bpp::GeneticCode::isStart	(	int	state	)	const
throw	(	BadIntException
	)

inlinevirtualinherited

Tells is a particular codon is a start codon.

Parameters

state The numeric code for the state to test.

Returns: True if the state corresponds to a start codon.

Exceptions

BadIntException if the state is not supported by the alphabet.

Definition at line 163 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_, and bpp::AbstractAlphabet::intToChar().

Referenced by bpp::SequenceTools::getCDS(), and bpp::GeneticCode::isStart().

◆ isStart() [2/2]

virtual bool bpp::GeneticCode::isStart	(	const std::string &	state	)	const
throw	(	BadCharException
	)

inlinevirtualinherited

Tells is a particular codon is a start codon.

Parameters

state The character code for the state to test.

Returns: True if the state corresponds to a start codon.

Exceptions

BadCharException if the state is not supported by the alphabet.

Definition at line 176 of file GeneticCode.h.

References bpp::WordAlphabet::charToInt(), bpp::GeneticCode::codonAlphabet_, and bpp::GeneticCode::isStart().

◆ isStop() [1/2]

bool bpp::VertebrateMitochondrialGeneticCode::isStop	(	int	state	)	const
throw	(	BadIntException
	)

inlinevirtual

Tells is a particular codon is a stop codon.

Parameters

state The numeric code for the state to test.

Returns: True if the state corresponds to a stop codon.

Exceptions

BadIntException if the state is not supported by the alphabet.

Implements bpp::GeneticCode.

Definition at line 86 of file VertebrateMitochondrialGeneticCode.h.

References bpp::GeneticCode::codonAlphabet_, and bpp::AbstractAlphabet::intToChar().

◆ isStop() [2/2]

bool bpp::VertebrateMitochondrialGeneticCode::isStop	(	const std::string &	state	)	const
throw	(	BadCharException
	)

inlinevirtual

Tells is a particular codon is a stop codon.

Parameters

state The character code for the state to test.

Returns: True if the state corresponds to a stop codon.

Exceptions

BadCharException if the state is not supported by the alphabet.

Implements bpp::GeneticCode.

Definition at line 92 of file VertebrateMitochondrialGeneticCode.h.

References bpp::WordAlphabet::charToInt(), and bpp::GeneticCode::codonAlphabet_.

◆ translate() [1/3]

int GeneticCode::translate	(	int	state	)	const
throw	(	BadIntException,
		Exception
	)

virtualinherited

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 55 of file GeneticCode.cpp.

Referenced by bpp::GeneticCode::areSynonymous(), and bpp::GeneticCode::isFourFoldDegenerated().

◆ translate() [2/3]

std::string GeneticCode::translate	(	const std::string &	state	)	const
throw	(	BadCharException,
		Exception
	)

virtualinherited

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 69 of file GeneticCode.cpp.

◆ translate() [3/3]

virtual Sequence* bpp::GeneticCode::translate	(	const Sequence &	sequence	)	const
throw	(	Exception
	)

inlinevirtualinherited

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 110 of file GeneticCode.h.

References bpp::AbstractTransliterator::translate().

Member Data Documentation

◆ codonAlphabet_

CodonAlphabet bpp::GeneticCode::codonAlphabet_

protectedinherited

Definition at line 84 of file GeneticCode.h.

◆ proteicAlphabet_

ProteicAlphabet bpp::GeneticCode::proteicAlphabet_

protectedinherited

Definition at line 85 of file GeneticCode.h.

◆ tlnTable_

std::map<int, int> bpp::GeneticCode::tlnTable_

protectedinherited

Definition at line 86 of file GeneticCode.h.

Referenced by bpp::AscidianMitochondrialGeneticCode::AscidianMitochondrialGeneticCode(), bpp::EchinodermMitochondrialGeneticCode::EchinodermMitochondrialGeneticCode(), bpp::InvertebrateMitochondrialGeneticCode::InvertebrateMitochondrialGeneticCode(), bpp::MoldMitochondrialGeneticCode::MoldMitochondrialGeneticCode(), bpp::StandardGeneticCode::StandardGeneticCode(), VertebrateMitochondrialGeneticCode(), and bpp::YeastMitochondrialGeneticCode::YeastMitochondrialGeneticCode().

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

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

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VertebrateMitochondrialGeneticCode()

◆ ~VertebrateMitochondrialGeneticCode()

Member Function Documentation

◆ areSynonymous() [1/2]

◆ areSynonymous() [2/2]

◆ clone()

◆ getCodingSequence()

◆ getNumberOfStopCodons()

◆ getSourceAlphabet()

◆ getStopCodonsAsChar()

◆ getStopCodonsAsInt()

◆ getSynonymous() [1/2]

◆ getSynonymous() [2/2]

◆ getTargetAlphabet()

◆ isAltStart() [1/2]

◆ isAltStart() [2/2]

◆ isFourFoldDegenerated()

◆ isStart() [1/2]

◆ isStart() [2/2]

◆ isStop() [1/2]

◆ isStop() [2/2]

◆ translate() [1/3]

◆ translate() [2/3]

◆ translate() [3/3]

Member Data Documentation

◆ codonAlphabet_

◆ proteicAlphabet_

◆ tlnTable_