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 (std::shared_ptr< const NucleicAlphabet > alphabet)

virtual	~GeneticCode ()

virtual GeneticCode *	clone () const override=0

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 size_t	getNumberOfStopCodons () const =0

virtual std::vector< int >	getStopCodonsAsInt () const =0

virtual std::vector< std::string >	getStopCodonsAsChar () const =0

virtual bool	isStop (int state) const =0
	Tells is a particular codon is a stop codon. More...

virtual bool	isStop (const std::string &state) const =0
	Tells is a particular codon is a stop codon. 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...

virtual bool	isAltStart (int state) const =0
	Tells is a particular codon is an alternative start codon. More...

virtual bool	isAltStart (const std::string &state) const =0
	Tells is a particular codon is an alternative 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_

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 47 of file GeneticCode.h.

Constructor & Destructor Documentation

◆ GeneticCode()

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

inline

Definition at line 57 of file GeneticCode.h.

◆ ~GeneticCode()

virtual bpp::GeneticCode::~GeneticCode ( )

inlinevirtual

Definition at line 64 of file GeneticCode.h.

Member Function Documentation

◆ areSynonymous() [1/2]

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

inline

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 translate().

◆ areSynonymous() [2/2]

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

inline

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 translate().

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

◆ clone()

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

overridepure virtual

Implements bpp::Clonable.

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

◆ codonAlphabet()

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

inlinevirtual

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 codonAlphabet_.

◆ getCodingSequence()

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

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

◆ getCodonAlphabet()

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

inlinevirtual

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 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()

virtual size_t bpp::GeneticCode::getNumberOfStopCodons ( ) const

pure virtual

Returns: The number of stop codons.

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

◆ getProteicAlphabet()

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

inlinevirtual

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 proteicAlphabet_.

◆ getSourceAlphabet()

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

inlineoverridevirtual

Get the source alphabet.

Returns: A pointer toward the source alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 74 of file GeneticCode.h.

References codonAlphabet_.

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

◆ getStopCodonsAsChar()

virtual std::vector<std::string> bpp::GeneticCode::getStopCodonsAsChar ( ) const

pure virtual

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

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

◆ getStopCodonsAsInt()

virtual std::vector<int> bpp::GeneticCode::getStopCodonsAsInt ( ) const

pure virtual

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

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

◆ getSynonymous() [1/2]

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

Definition at line 63 of file GeneticCode.cpp.

References codonAlphabet_, proteicAlphabet_, and translate().

◆ getSynonymous() [2/2]

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

Definition at line 42 of file GeneticCode.cpp.

References codonAlphabet_, proteicAlphabet_, and translate().

◆ getTargetAlphabet()

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

inlineoverridevirtual

Get the target alphabet.

Returns: A pointer toward the target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 78 of file GeneticCode.h.

References proteicAlphabet_.

◆ isAltStart() [1/2]

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

pure virtual

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.

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

◆ isAltStart() [2/2]

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

pure virtual

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.

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

◆ isFourFoldDegenerated()

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 84 of file GeneticCode.cpp.

References codonAlphabet_, isStop(), and translate().

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

◆ isStart() [1/2]

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

inlinevirtual

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 codonAlphabet_, and isStart().

◆ isStart() [2/2]

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

inlinevirtual

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 codonAlphabet_.

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

◆ isStop() [1/2]

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

pure virtual

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.

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

◆ isStop() [2/2]

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

pure virtual

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.

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

Referenced by bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SequenceTools::getCDS(), getCodingSequence(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::CodonSiteTools::hasStop(), isFourFoldDegenerated(), bpp::CodonSiteTools::numberOfSynonymousDifferences(), bpp::CodonSiteTools::numberOfSynonymousPositions(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), and translate().

◆ proteicAlphabet()

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

inlinevirtual

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 proteicAlphabet_.

◆ sourceAlphabet()

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

inlineoverridevirtual

Get the source alphabet.

Returns: A reference toward the source alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 76 of file GeneticCode.h.

References 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

inlineoverridevirtual

Get the target alphabet.

Returns: A reference toward the target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 80 of file GeneticCode.h.

References proteicAlphabet_.

◆ translate() [1/3]

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

inlineoverridevirtual

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

overridevirtual

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 codonAlphabet_, proteicAlphabet_, and translate().

◆ translate() [3/3]

int GeneticCode::translate ( int state ) const

overridevirtual

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 codonAlphabet_, isStop(), and tlnTable_.

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

Member Data Documentation

◆ codonAlphabet_

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

protected

Definition at line 52 of file GeneticCode.h.

◆ proteicAlphabet_

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

protected

Definition at line 53 of file GeneticCode.h.

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

◆ tlnTable_

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

protected

Definition at line 54 of file GeneticCode.h.

Referenced by translate().

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

◆ GeneticCode()

◆ ~GeneticCode()

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()

◆ 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_