bpp::GeneticCode Class Reference

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 (const NucleicAlphabet *alphabet)
virtual	~GeneticCode ()
virtual GeneticCode *	clone () const =0
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 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 throw (BadIntException)
	Tells is a particular codon is a stop codon. More...
virtual bool	isStop (const std::string &state) const =0 throw (BadCharException)
	Tells is a particular codon is a stop codon. More...
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...
virtual bool	isAltStart (int state) const =0 throw (BadIntException)
	Tells is a particular codon is an alternative start codon. More...
virtual bool	isAltStart (const std::string &state) const =0 throw (BadCharException)
	Tells is a particular codon is an alternative 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

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

GeneticCode()

bpp::GeneticCode::GeneticCode ( const NucleicAlphabet *  alphabet )

inline

Definition at line 89 of file GeneticCode.h.

~GeneticCode()

virtual bpp::GeneticCode::~GeneticCode ( )

inlinevirtual

Definition at line 96 of file GeneticCode.h.

Member Function Documentation

areSynonymous() [1/2]

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

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.

Exceptions

BadIntException

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

Definition at line 206 of file GeneticCode.h.

References translate().

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

areSynonymous() [2/2]

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

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.

Exceptions

BadCharException

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

Definition at line 219 of file GeneticCode.h.

References translate().

clone()

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

pure virtual

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

getCodingSequence()

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 149 of file GeneticCode.cpp.

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

getNumberOfStopCodons()

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

pure virtual

Returns

The number of stop codons.

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

getSourceAlphabet()

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

inlinevirtual

Get the source alphabet.

Returns

The source alphabet.

Implements bpp::Transliterator.

Definition at line 106 of file GeneticCode.h.

References codonAlphabet_.

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

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

getStopCodonsAsInt()

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

pure virtual

Returns

A vector will all int codes for stop codons.

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

getSynonymous() [1/2]

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

Definition at line 77 of file GeneticCode.cpp.

getSynonymous() [2/2]

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

Definition at line 98 of file GeneticCode.cpp.

getTargetAlphabet()

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

inlinevirtual

Get the target alphabet.

Returns

The target alphabet.

Implements bpp::Transliterator.

Definition at line 107 of file GeneticCode.h.

References proteicAlphabet_.

isAltStart() [1/2]

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

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.

Exceptions

BadIntException

if the state is not supported by the alphabet.

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

isAltStart() [2/2]

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

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.

Exceptions

BadCharException

if the state is not supported by the alphabet.

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

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 119 of file GeneticCode.cpp.

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

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

isStart() [1/2]

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

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.

Exceptions

BadIntException

if the state is not supported by the alphabet.

Definition at line 163 of file GeneticCode.h.

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

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

isStart() [2/2]

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

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.

Exceptions

BadCharException

if the state is not supported by the alphabet.

Definition at line 176 of file GeneticCode.h.

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

isStop() [1/2]

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

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.

Exceptions

BadIntException

if the state is not supported by the alphabet.

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

Referenced by bpp::SequenceTools::getCDS(), isFourFoldDegenerated(), and bpp::CodonSiteTools::numberOfSynonymousDifferences().

isStop() [2/2]

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

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.

Exceptions

BadCharException

if the state is not supported by the alphabet.

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

translate() [1/3]

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

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.

Definition at line 55 of file GeneticCode.cpp.

Referenced by areSynonymous(), and isFourFoldDegenerated().

translate() [2/3]

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

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.

Definition at line 69 of file GeneticCode.cpp.

translate() [3/3]

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

inlinevirtual

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_

protected

Definition at line 84 of file GeneticCode.h.

Referenced by bpp::AscidianMitochondrialGeneticCode::AscidianMitochondrialGeneticCode(), bpp::EchinodermMitochondrialGeneticCode::EchinodermMitochondrialGeneticCode(), getSourceAlphabet(), bpp::InvertebrateMitochondrialGeneticCode::InvertebrateMitochondrialGeneticCode(), bpp::EchinodermMitochondrialGeneticCode::isAltStart(), bpp::StandardGeneticCode::isAltStart(), bpp::InvertebrateMitochondrialGeneticCode::isAltStart(), bpp::YeastMitochondrialGeneticCode::isAltStart(), bpp::MoldMitochondrialGeneticCode::isAltStart(), bpp::AscidianMitochondrialGeneticCode::isAltStart(), bpp::VertebrateMitochondrialGeneticCode::isAltStart(), isFourFoldDegenerated(), isStart(), bpp::EchinodermMitochondrialGeneticCode::isStop(), bpp::StandardGeneticCode::isStop(), bpp::InvertebrateMitochondrialGeneticCode::isStop(), bpp::YeastMitochondrialGeneticCode::isStop(), bpp::MoldMitochondrialGeneticCode::isStop(), bpp::VertebrateMitochondrialGeneticCode::isStop(), bpp::AscidianMitochondrialGeneticCode::isStop(), bpp::MoldMitochondrialGeneticCode::MoldMitochondrialGeneticCode(), bpp::StandardGeneticCode::StandardGeneticCode(), bpp::VertebrateMitochondrialGeneticCode::VertebrateMitochondrialGeneticCode(), and bpp::YeastMitochondrialGeneticCode::YeastMitochondrialGeneticCode().

proteicAlphabet_

ProteicAlphabet bpp::GeneticCode::proteicAlphabet_

protected

Definition at line 85 of file GeneticCode.h.

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

tlnTable_

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

protected

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(), bpp::VertebrateMitochondrialGeneticCode::VertebrateMitochondrialGeneticCode(), and bpp::YeastMitochondrialGeneticCode::YeastMitochondrialGeneticCode().

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

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