This class implements the standard genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1. More...

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

Inheritance diagram for bpp::StandardGeneticCode:

Collaboration diagram for bpp::StandardGeneticCode:

Public Member Functions
	StandardGeneticCode (std::shared_ptr< const NucleicAlphabet > alphabet)

virtual	~StandardGeneticCode ()

virtual StandardGeneticCode *	clone () const

size_t	getNumberOfStopCodons () const

std::vector< int >	getStopCodonsAsInt () const

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

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

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

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

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

Methods form the Transliterator interface.
std::shared_ptr< const Alphabet >	getSourceAlphabet () const override
	Get the source alphabet. More...

const Alphabet &	sourceAlphabet () const override
	Get the source alphabet. More...

std::shared_ptr< const Alphabet >	getTargetAlphabet () const override
	Get the target alphabet. More...

const Alphabet &	targetAlphabet () const override
	Get the target alphabet. More...

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

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

std::unique_ptr< Sequence >	translate (const SequenceInterface &sequence) const override
	Translate a whole sequence from source alphabet to target alphabet. More...

Specific methods.
virtual std::shared_ptr< const CodonAlphabet >	getCodonAlphabet () const
	Alias for getSourceAlphabet return a pointer toward a CodonAlphabet. More...

virtual const CodonAlphabet &	codonAlphabet () const
	Alias for getSourceAlphabet return a pointer toward a CodonAlphabet. More...

virtual std::shared_ptr< const ProteicAlphabet >	getProteicAlphabet () const
	Alias for getTargetAlphabet return a pointer toward a ProteicAlphabet. More...

virtual const ProteicAlphabet &	proteicAlphabet () const
	Alias for getTargetAlphabet return a pointer toward a ProteicAlphabet. More...

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

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

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

std::vector< int >	getSynonymous (int aminoacid) const

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

bool	isFourFoldDegenerated (int codon) const

std::unique_ptr< Sequence >	getCodingSequence (const SequenceInterface &sequence, bool lookForInitCodon=false, bool includeInitCodon=false) const
	Get the subsequence corresponding to the coding part of a given sequence. More...

Protected Attributes
std::shared_ptr< const CodonAlphabet >	codonAlphabet_

std::shared_ptr< const ProteicAlphabet >	proteicAlphabet_

std::map< int, int >	tlnTable_

Private Member Functions
void	init_ ()

Detailed Description

This class implements the standard genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1.

Definition at line 18 of file StandardGeneticCode.h.

Constructor & Destructor Documentation

◆ StandardGeneticCode()

bpp::StandardGeneticCode::StandardGeneticCode ( std::shared_ptr< const NucleicAlphabet > alphabet )

inline

Definition at line 22 of file StandardGeneticCode.h.

References init_().

Referenced by clone().

◆ ~StandardGeneticCode()

virtual bpp::StandardGeneticCode::~StandardGeneticCode ( )

inlinevirtual

Definition at line 28 of file StandardGeneticCode.h.

Member Function Documentation

◆ areSynonymous() [1/2]

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

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.

Definition at line 217 of file GeneticCode.h.

References bpp::GeneticCode::translate().

◆ areSynonymous() [2/2]

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

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.

Definition at line 205 of file GeneticCode.h.

References bpp::GeneticCode::translate().

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

◆ clone()

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

inlinevirtual

Implements bpp::GeneticCode.

Definition at line 30 of file StandardGeneticCode.h.

References StandardGeneticCode().

◆ codonAlphabet()

virtual const CodonAlphabet& bpp::GeneticCode::codonAlphabet ( ) const

inlinevirtualinherited

Alias for getSourceAlphabet return a pointer toward a CodonAlphabet.

Returns: A reference toward the codon alphabet.

Definition at line 111 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

◆ getCodingSequence()

unique_ptr< Sequence > GeneticCode::getCodingSequence	(	const SequenceInterface &	sequence,
		bool	lookForInitCodon = `false`,
		bool	includeInitCodon = `false`
	)		const

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 beginning 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 114 of file GeneticCode.cpp.

References bpp::CruxSymbolListInterface::alphabet(), bpp::GeneticCode::codonAlphabet_, bpp::AlphabetTools::isCodonAlphabet(), bpp::AlphabetTools::isNucleicAlphabet(), bpp::GeneticCode::isStop(), and bpp::CruxSymbolListInterface::size().

◆ getCodonAlphabet()

virtual std::shared_ptr<const CodonAlphabet> bpp::GeneticCode::getCodonAlphabet ( ) const

inlinevirtualinherited

Alias for getSourceAlphabet return a pointer toward a CodonAlphabet.

Returns: A pointer toward the codon alphabet.

Definition at line 104 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSynonymousDifferences(), bpp::CodonSiteTools::numberOfSynonymousPositions(), bpp::CodonSiteTools::piNonSynonymous(), and bpp::CodonSiteTools::piSynonymous().

◆ getNumberOfStopCodons()

size_t bpp::StandardGeneticCode::getNumberOfStopCodons ( ) const

inlinevirtual

Returns: The number of stop codons.

Implements bpp::GeneticCode.

Definition at line 36 of file StandardGeneticCode.h.

◆ getProteicAlphabet()

virtual std::shared_ptr<const ProteicAlphabet> bpp::GeneticCode::getProteicAlphabet ( ) const

inlinevirtualinherited

Alias for getTargetAlphabet return a pointer toward a ProteicAlphabet.

Returns: A pointer toward the protein alphabet.

Definition at line 118 of file GeneticCode.h.

References bpp::GeneticCode::proteicAlphabet_.

◆ getSourceAlphabet()

std::shared_ptr<const Alphabet> bpp::GeneticCode::getSourceAlphabet ( ) const

inlineoverridevirtualinherited

Get the source alphabet.

Returns: A pointer toward the source alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 74 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

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

◆ getStopCodonsAsChar()

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

inlinevirtual

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

Implements bpp::GeneticCode.

Definition at line 43 of file StandardGeneticCode.h.

◆ getStopCodonsAsInt()

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

inlinevirtual

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

Implements bpp::GeneticCode.

Definition at line 38 of file StandardGeneticCode.h.

◆ getSynonymous() [1/2]

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

inherited

Definition at line 63 of file GeneticCode.cpp.

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

◆ getSynonymous() [2/2]

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

inherited

Definition at line 42 of file GeneticCode.cpp.

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

◆ getTargetAlphabet()

std::shared_ptr<const Alphabet> bpp::GeneticCode::getTargetAlphabet ( ) const

inlineoverridevirtualinherited

Get the target alphabet.

Returns: A pointer toward the target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 78 of file GeneticCode.h.

References bpp::GeneticCode::proteicAlphabet_.

◆ init_()

void StandardGeneticCode::init_ ( )

private

Definition at line 13 of file StandardGeneticCode.cpp.

Referenced by StandardGeneticCode().

◆ isAltStart() [1/2]

bool bpp::StandardGeneticCode::isAltStart ( const std::string & state ) const

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.

Implements bpp::GeneticCode.

Definition at line 68 of file StandardGeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

◆ isAltStart() [2/2]

bool bpp::StandardGeneticCode::isAltStart ( int state ) const

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.

Implements bpp::GeneticCode.

Definition at line 61 of file StandardGeneticCode.h.

References 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 84 of file GeneticCode.cpp.

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

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

◆ isStart() [1/2]

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

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.

Definition at line 177 of file GeneticCode.h.

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

◆ isStart() [2/2]

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

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.

Definition at line 164 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

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

◆ isStop() [1/2]

bool bpp::StandardGeneticCode::isStop ( const std::string & state ) const

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.

Implements bpp::GeneticCode.

Definition at line 55 of file StandardGeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

◆ isStop() [2/2]

bool bpp::StandardGeneticCode::isStop ( int state ) const

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.

Implements bpp::GeneticCode.

Definition at line 48 of file StandardGeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

◆ proteicAlphabet()

virtual const ProteicAlphabet& bpp::GeneticCode::proteicAlphabet ( ) const

inlinevirtualinherited

Alias for getTargetAlphabet return a pointer toward a ProteicAlphabet.

Returns: A reference toward the protein alphabet.

Definition at line 125 of file GeneticCode.h.

References bpp::GeneticCode::proteicAlphabet_.

◆ sourceAlphabet()

const Alphabet& bpp::GeneticCode::sourceAlphabet ( ) const

inlineoverridevirtualinherited

Get the source alphabet.

Returns: A reference toward the source alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 76 of file GeneticCode.h.

References bpp::GeneticCode::codonAlphabet_.

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::piNonSynonymous(), and bpp::CodonSiteTools::piSynonymous().

◆ targetAlphabet()

const Alphabet& bpp::GeneticCode::targetAlphabet ( ) const

inlineoverridevirtualinherited

Get the target alphabet.

Returns: A reference toward the target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 80 of file GeneticCode.h.

References bpp::GeneticCode::proteicAlphabet_.

◆ translate() [1/3]

std::unique_ptr<Sequence> bpp::GeneticCode::translate ( const SequenceInterface & sequence ) const

inlineoverridevirtualinherited

Translate a whole sequence from source alphabet to target alphabet.

Parameters

sequence A sequence in source alphabet.

Returns: The corresponding sequence in target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 86 of file GeneticCode.h.

References bpp::AbstractTransliterator::translate().

◆ translate() [2/3]

std::string GeneticCode::translate ( const std::string & state ) const

overridevirtualinherited

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.

Implements bpp::AbstractTransliterator.

Definition at line 34 of file GeneticCode.cpp.

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

◆ translate() [3/3]

int GeneticCode::translate ( int state ) const

overridevirtualinherited

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.

Implements bpp::AbstractTransliterator.

Definition at line 20 of file GeneticCode.cpp.

References bpp::GeneticCode::codonAlphabet_, bpp::GeneticCode::isStop(), and bpp::GeneticCode::tlnTable_.

Referenced by bpp::GeneticCode::areSynonymous(), bpp::GeneticCode::getSynonymous(), bpp::GeneticCode::isFourFoldDegenerated(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::CodonSiteTools::numberOfSynonymousPositions(), and bpp::GeneticCode::translate().

Member Data Documentation

◆ codonAlphabet_

std::shared_ptr<const CodonAlphabet> bpp::GeneticCode::codonAlphabet_

protectedinherited

Definition at line 52 of file GeneticCode.h.

Referenced by bpp::GeneticCode::codonAlphabet(), bpp::GeneticCode::getCodingSequence(), bpp::GeneticCode::getCodonAlphabet(), bpp::GeneticCode::getSourceAlphabet(), bpp::GeneticCode::getSynonymous(), bpp::AscidianMitochondrialGeneticCode::isAltStart(), bpp::CiliateNuclearGeneticCode::isAltStart(), bpp::EchinodermMitochondrialGeneticCode::isAltStart(), bpp::InvertebrateMitochondrialGeneticCode::isAltStart(), bpp::MoldMitochondrialGeneticCode::isAltStart(), isAltStart(), bpp::VertebrateMitochondrialGeneticCode::isAltStart(), bpp::YeastMitochondrialGeneticCode::isAltStart(), bpp::GeneticCode::isFourFoldDegenerated(), bpp::GeneticCode::isStart(), bpp::AscidianMitochondrialGeneticCode::isStop(), bpp::CiliateNuclearGeneticCode::isStop(), bpp::EchinodermMitochondrialGeneticCode::isStop(), bpp::InvertebrateMitochondrialGeneticCode::isStop(), bpp::MoldMitochondrialGeneticCode::isStop(), isStop(), bpp::VertebrateMitochondrialGeneticCode::isStop(), bpp::YeastMitochondrialGeneticCode::isStop(), bpp::GeneticCode::sourceAlphabet(), and bpp::GeneticCode::translate().

◆ proteicAlphabet_

std::shared_ptr<const ProteicAlphabet> bpp::GeneticCode::proteicAlphabet_

protectedinherited

Definition at line 53 of file GeneticCode.h.

Referenced by bpp::GeneticCode::getProteicAlphabet(), bpp::GeneticCode::getSynonymous(), bpp::GeneticCode::getTargetAlphabet(), bpp::GeneticCode::proteicAlphabet(), bpp::GeneticCode::targetAlphabet(), and bpp::GeneticCode::translate().

◆ tlnTable_

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

protectedinherited

Definition at line 54 of file GeneticCode.h.

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

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

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

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ StandardGeneticCode()

◆ ~StandardGeneticCode()

Member Function Documentation

◆ areSynonymous() [1/2]

◆ areSynonymous() [2/2]

◆ clone()

◆ codonAlphabet()

◆ getCodingSequence()

◆ getCodonAlphabet()

◆ getNumberOfStopCodons()

◆ getProteicAlphabet()

◆ getSourceAlphabet()

◆ getStopCodonsAsChar()

◆ getStopCodonsAsInt()

◆ getSynonymous() [1/2]

◆ getSynonymous() [2/2]

◆ getTargetAlphabet()

◆ init_()

◆ isAltStart() [1/2]

◆ isAltStart() [2/2]

◆ isFourFoldDegenerated()

◆ isStart() [1/2]

◆ isStart() [2/2]

◆ isStop() [1/2]

◆ isStop() [2/2]

◆ proteicAlphabet()

◆ sourceAlphabet()

◆ targetAlphabet()

◆ translate() [1/3]

◆ translate() [2/3]

◆ translate() [3/3]

Member Data Documentation

◆ codonAlphabet_

◆ proteicAlphabet_

◆ tlnTable_