Codon alphabet class. More...

#include <Bpp/Seq/Alphabet/CodonAlphabet.h>

Inheritance diagram for bpp::CodonAlphabet:

Collaboration diagram for bpp::CodonAlphabet:

Public Member Functions
	CodonAlphabet (const NucleicAlphabet *alpha)
	Builds a new codon alphabet from a nucleic alphabet. More...

	CodonAlphabet (const CodonAlphabet &bia)

CodonAlphabet &	operator= (const CodonAlphabet &bia)

CodonAlphabet *	clone () const

virtual	~CodonAlphabet ()

std::string	getAlphabetType () const
	Identification method. More...

bool	hasUniqueAlphabet () const
	Returns True if the Alphabet of the letters in the word are the same type. More...

unsigned int	getLength () const
	Returns the length of the word. More...

unsigned int	getNumberOfTypes () const
	Returns the number of resolved states + one for unresolved. More...

int	getUnknownCharacterCode () const

bool	isUnresolved (int state) const

bool	isUnresolved (const std::string &state) const

std::vector< int >	getAlias (int state) const throw (BadIntException)
	Get all resolved states that match a generic state. More...

std::vector< std::string >	getAlias (const std::string &state) const throw (BadCharException)
	Get all resolved states that match a generic state. More...

int	getGeneric (const std::vector< int > &states) const throw (BadIntException)
	Get the generic state that match a set of states. More...

std::string	getGeneric (const std::vector< std::string > &states) const throw (BadCharException)
	Get the generic state that match a set of states. More...

Codon specific methods
virtual int	getCodon (int pos1, int pos2, int pos3) const throw (BadIntException)
	Get the int code for a codon given the int code of the three underlying positions. More...

virtual std::string	getCodon (const std::string &pos1, const std::string &pos2, const std::string &pos3) const throw (BadCharException)
	Get the char code for a codon given the char code of the three underlying positions. More...

virtual int	getFirstPosition (int codon) const throw (BadIntException)
	Get the int code of the first position of a codon given its int description. More...

virtual int	getSecondPosition (int codon) const throw (BadIntException)
	Get the int code of the second position of a codon given its int description. More...

virtual int	getThirdPosition (int codon) const throw (BadIntException)
	Get the int code of the third position of a codon given its int description. More...

virtual std::string	getFirstPosition (const std::string &codon) const throw (BadCharException)
	Get the char code of the first position of a codon given its char description. More...

virtual std::string	getSecondPosition (const std::string &codon) const throw (BadCharException)
	Get the char code of the second position of a codon given its char description. More...

virtual std::string	getThirdPosition (const std::string &codon) const throw (BadCharException)
	Get the char code of the third position of a codon given its char description. More...

virtual const NucleicAlphabet *const	getNucleicAlphabet () const

Methods redefined from Alphabet
std::string	getName (const std::string &state) const throw (BadCharException)
	Get the complete name of a state given its string description. More...

int	charToInt (const std::string &state) const throw (BadCharException)
	Give the int description of a state given its string description. More...

unsigned int	getSize () const
	Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases. More...

Implement these methods from the Alphabet interface.
std::string	getName (int state) const throw (BadIntException)
	Get the complete name of a state given its int description. More...

size_t	getNumberOfStates () const
	This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int. More...

unsigned int	getNumberOfChars () const
	Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet). More...

std::string	intToChar (int state) const throw (BadIntException)
	Give the string description of a state given its int description. More...

bool	isIntInAlphabet (int state) const
	Tell if a state (specified by its int description) is allowed by the the alphabet. More...

bool	isCharInAlphabet (const std::string &state) const
	Tell if a state (specified by its string description) is allowed by the the alphabet. More...

const std::vector< int > &	getSupportedInts () const

const std::vector< std::string > &	getSupportedChars () const

int	getGapCharacterCode () const

bool	isGap (int state) const

bool	isGap (const std::string &state) const

Word specific methods
const Alphabet *	getNAlphabet (size_t n) const
	Get the pointer to the Alphabet of the n-position. More...

virtual int	getWord (const std::vector< int > &vint, size_t pos=0) const throw (IndexOutOfBoundsException)
	Get the int code for a word given the int code of the underlying positions. More...

virtual std::string	getWord (const std::vector< std::string > &vpos, size_t pos=0) const throw (IndexOutOfBoundsException, BadCharException)
	Get the char code for a word given the char code of the underlying positions. More...

int	getNPosition (int word, size_t n) const throw (BadIntException)
	Get the int code of the n-position of a word given its int description. More...

std::string	getNPosition (const std::string &word, size_t n) const throw (BadCharException)
	Get the char code of the n-position of a word given its char description. More...

std::vector< int >	getPositions (int word) const throw (BadIntException)
	Get the int codes of each position of a word given its int description. More...

std::vector< std::string >	getPositions (const std::string &word) const throw (BadCharException)
	Get the char codes of each position of a word given its char description. More...

Sequence *	translate (const Sequence &sequence, size_t=0) const throw (AlphabetMismatchException, Exception)
	Translate a whole sequence from letters alphabet to words alphabet. More...

Sequence *	reverse (const Sequence &sequence) const throw (AlphabetMismatchException, Exception)
	Translate a whole sequence from words alphabet to letters alphabet. More...

Overloaded AbstractAlphabet methods.
unsigned int	getStateCodingSize () const
	Get the size of the string coding a state. More...

Specific methods to access AlphabetState
virtual AlphabetState &	getStateAt (size_t stateIndex) throw (IndexOutOfBoundsException)
	Get a state at a position in the alphabet_ vector. More...

virtual const AlphabetState &	getStateAt (size_t stateIndex) const throw (IndexOutOfBoundsException)
	Get a state at a position in the alphabet_ vector. More...

const AlphabetState &	getState (const std::string &letter) const throw (BadCharException)
	Get a state by its letter. More...

AlphabetState &	getState (const std::string &letter) throw (BadCharException)

const AlphabetState &	getState (int num) const throw (BadIntException)
	Get a state by its num. More...

AlphabetState &	getState (int num) throw (BadIntException)

int	getIntCodeAt (size_t stateIndex) const throw (IndexOutOfBoundsException)

const std::string &	getCharCodeAt (size_t stateIndex) const throw (IndexOutOfBoundsException)

size_t	getStateIndex (int state) const throw (BadIntException)

size_t	getStateIndex (const std::string &state) const throw (BadCharException)

Protected Member Functions
virtual void	registerState (AlphabetState *st) throw (Exception)
	Add a state to the Alphabet. More...

virtual void	setState (size_t pos, AlphabetState *st) throw (Exception, IndexOutOfBoundsException)
	Set a state in the Alphabet. More...

void	resize (size_t size)
	Resize the private alphabet_ vector. More...

void	remap ()
	Re-update the maps using the alphabet_ vector content. More...

bool	equals (const Alphabet &alphabet) const
	Comparison of alphabets. More...

Protected Attributes
std::vector< const Alphabet *>	vAbsAlph_

Available codes
These vectors will be computed the first time you call the getAvailableInts or getAvailableChars method.
std::vector< std::string >	charList_

std::vector< int >	intList_

Detailed Description

Codon alphabet class.

Author: Laurent Guéguen, Julien Dutheil

A codon alphabet object is a particular case of WordAlphabet with three letters. Since codons are made of 3 nucleic bases (RNA or DNA), this class has a NucleicAlphabet field used to check char description. This nucleic alphabet is passed to the constructor. This class also adds some methods specific to codon manipulation.

Definition at line 63 of file CodonAlphabet.h.

Constructor & Destructor Documentation

◆ CodonAlphabet() [1/2]

bpp::CodonAlphabet::CodonAlphabet ( const NucleicAlphabet * alpha )

inline

Builds a new codon alphabet from a nucleic alphabet.

Parameters

alpha The nucleic alphabet to be used.

Definition at line 73 of file CodonAlphabet.h.

Referenced by clone().

◆ CodonAlphabet() [2/2]

bpp::CodonAlphabet::CodonAlphabet ( const CodonAlphabet & bia )

inline

Definition at line 76 of file CodonAlphabet.h.

◆ ~CodonAlphabet()

virtual bpp::CodonAlphabet::~CodonAlphabet ( )

inlinevirtual

Definition at line 89 of file CodonAlphabet.h.

Member Function Documentation

◆ charToInt()

int bpp::WordAlphabet::charToInt	(	const std::string &	state	)	const
throw	(	BadCharException
	)

inlinevirtualinherited

Give the int description of a state given its string description.

Parameters

state The string description.

Returns: The int description.

Exceptions

BadCharException When state is not a valid char description.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 127 of file WordAlphabet.h.

References bpp::AbstractAlphabet::charToInt(), bpp::WordAlphabet::containsGap(), bpp::WordAlphabet::containsUnresolved(), bpp::WordAlphabet::getSize(), and bpp::WordAlphabet::vAbsAlph_.

Referenced by bpp::WordAlphabet::getNPosition(), bpp::WordAlphabet::getPositions(), bpp::EchinodermMitochondrialGeneticCode::isAltStart(), bpp::InvertebrateMitochondrialGeneticCode::isAltStart(), bpp::YeastMitochondrialGeneticCode::isAltStart(), bpp::MoldMitochondrialGeneticCode::isAltStart(), bpp::StandardGeneticCode::isAltStart(), bpp::VertebrateMitochondrialGeneticCode::isAltStart(), bpp::AscidianMitochondrialGeneticCode::isAltStart(), bpp::GeneticCode::isStart(), bpp::EchinodermMitochondrialGeneticCode::isStop(), bpp::MoldMitochondrialGeneticCode::isStop(), bpp::InvertebrateMitochondrialGeneticCode::isStop(), bpp::YeastMitochondrialGeneticCode::isStop(), bpp::StandardGeneticCode::isStop(), bpp::AscidianMitochondrialGeneticCode::isStop(), bpp::VertebrateMitochondrialGeneticCode::isStop(), and bpp::WordAlphabet::isUnresolved().

◆ clone()

CodonAlphabet* bpp::CodonAlphabet::clone ( ) const

inlinevirtual

Implements bpp::AbstractAlphabet.

Definition at line 84 of file CodonAlphabet.h.

References CodonAlphabet().

◆ equals()

bool bpp::AbstractAlphabet::equals ( const Alphabet & alphabet ) const

inlineprotectedvirtualinherited

Comparison of alphabets.

Returns: true If the two instances are of the same class.

Implements bpp::Alphabet.

Definition at line 268 of file AbstractAlphabet.h.

References bpp::Alphabet::getAlphabetType().

◆ getAlias() [1/2]

std::vector< int > WordAlphabet::getAlias	(	int	state	)	const
throw	(	BadIntException
	)

virtualinherited

Get all resolved states that match a generic state.

If the given state is not a generic code then the output vector will contain this unique code.

Parameters

state The alias to resolve.

Returns: A vector of resolved states.

Exceptions

BadIntException When state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 206 of file WordAlphabet.cpp.

◆ getAlias() [2/2]

std::vector< std::string > WordAlphabet::getAlias	(	const std::string &	state	)	const
throw	(	BadCharException
	)

virtualinherited

Get all resolved states that match a generic state.

If the given state is not a generic code then the output vector will contain this unique code.

Parameters

state The alias to resolve.

Returns: A vector of resolved states.

Exceptions

BadCharException When state is not a valid char description.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 230 of file WordAlphabet.cpp.

◆ getAlphabetType()

std::string bpp::CodonAlphabet::getAlphabetType ( ) const

inlinevirtual

Identification method.

Used to tell if two alphabets describe the same type of sequences. For instance, this method is used by sequence containers to compare two alphabets and allow or deny addition of sequences.

Returns: A text describing the alphabet.

Implements bpp::Alphabet.

Definition at line 91 of file CodonAlphabet.h.

References bpp::WordAlphabet::vAbsAlph_.

◆ getCharCodeAt()

const std::string& bpp::AbstractAlphabet::getCharCodeAt	(	size_t	stateIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtualinherited

Returns: The char code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 220 of file AbstractAlphabet.h.

References bpp::AlphabetState::getLetter(), and bpp::AbstractAlphabet::getStateAt().

◆ getCodon() [1/2]

int CodonAlphabet::getCodon	(	int	pos1,
		int	pos2,
		int	pos3
	)		const
throw	(	BadIntException
	)

virtual

Get the int code for a codon given the int code of the three underlying positions.

The int code of each position must match the nucleic alphabet specified for this alphabet.

Parameters

pos1	Int description for position 1.
pos2	Int description for position 2.
pos3	Int description for position 3.

Returns: The int code of the codon.

Definition at line 52 of file CodonAlphabet.cpp.

Referenced by bpp::GeneticCode::isFourFoldDegenerated(), bpp::CodonSiteTools::numberOfSynonymousDifferences(), and bpp::CodonSiteTools::numberOfSynonymousPositions().

◆ getCodon() [2/2]

string CodonAlphabet::getCodon	(	const std::string &	pos1,
		const std::string &	pos2,
		const std::string &	pos3
	)		const
throw	(	BadCharException
	)

virtual

Get the char code for a codon given the char code of the three underlying positions.

The char code of each position must match the nucleic alphabet specified for this alphabet. NB: This performs pos1 + pos2 + pos3 after checking for each position validity.

Parameters

pos1	Char description for position 1.
pos2	Char description for position 2.
pos3	Char description for position 3.

Returns: The Char code of the codon.

Definition at line 65 of file CodonAlphabet.cpp.

◆ getFirstPosition() [1/2]

int CodonAlphabet::getFirstPosition	(	int	codon	)	const
throw	(	BadIntException
	)

virtual

Get the int code of the first position of a codon given its int description.

Parameters

codon The int description of the codon.

Returns: The int description of the first position of the codon.

Definition at line 78 of file CodonAlphabet.cpp.

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::numberOfDifferences(), and bpp::CodonSiteTools::numberOfSubsitutions().

◆ getFirstPosition() [2/2]

string CodonAlphabet::getFirstPosition	(	const std::string &	codon	)	const
throw	(	BadCharException
	)

virtual

Get the char code of the first position of a codon given its char description.

Parameters

codon The char description of the codon.

Returns: The char description of the first position of the codon.

Definition at line 99 of file CodonAlphabet.cpp.

◆ getGapCharacterCode()

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 159 of file AbstractAlphabet.h.

Referenced by bpp::SequenceTools::replaceStopsWithGaps().

◆ getGeneric() [1/2]

int WordAlphabet::getGeneric	(	const std::vector< int > &	states	)	const
throw	(	BadIntException
	)

virtualinherited

Get the generic state that match a set of states.

If the given states contain generic code, each generic code is first resolved and then the new generic state is returned. If only a single resolved state is given the function return this state.

Parameters

states A vector of states to resolve.

Returns: A int code for the computed state.

Exceptions

BadIntException When a state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 262 of file WordAlphabet.cpp.

◆ getGeneric() [2/2]

std::string WordAlphabet::getGeneric	(	const std::vector< std::string > &	states	)	const
throw	(	BadCharException
	)

virtualinherited

Get the generic state that match a set of states.

If the given states contain generic code, each generic code is first resolved and then the new generic state is returned. If only a single resolved state is given the function return this state.

Parameters

states A vector of states to resolve.

Returns: A string code for the computed state.

Exceptions

BadCharException	when a state is not a valid char description.
CharStateNotSupportedException	when the alphabet does not support Char state for unresolved state.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 269 of file WordAlphabet.cpp.

◆ getIntCodeAt()

int bpp::AbstractAlphabet::getIntCodeAt	(	size_t	stateIndex	)	const
throw	(	IndexOutOfBoundsException
	)

inlinevirtualinherited

Returns: The int code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 216 of file AbstractAlphabet.h.

References bpp::AlphabetState::getNum(), and bpp::AbstractAlphabet::getStateAt().

◆ getLength()

unsigned int bpp::WordAlphabet::getLength ( ) const

inlineinherited

Returns the length of the word.

Definition at line 156 of file WordAlphabet.h.

References bpp::WordAlphabet::vAbsAlph_.

◆ getNAlphabet()

const Alphabet* bpp::WordAlphabet::getNAlphabet ( size_t n ) const

inlineinherited

Get the pointer to the Alphabet of the n-position.

Parameters

n	The position in the word (starting at 0).

Returns: The pointer to the Alphabet of the n-position.

Definition at line 210 of file WordAlphabet.h.

References bpp::WordAlphabet::vAbsAlph_.

◆ getName() [1/2]

std::string WordAlphabet::getName	(	const std::string &	state	)	const
throw	(	BadCharException
	)

virtualinherited

Get the complete name of a state given its string description.

In case of undefined characters (i.e. N and X for nucleic alphabets), this method will return the name of the undefined word.

Parameters

state The string description of the given state.

Returns: The name of the state.

Exceptions

BadCharException When state is not a valid char description.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 192 of file WordAlphabet.cpp.

References bpp::AbstractAlphabet::getName().

◆ getName() [2/2]

std::string AbstractAlphabet::getName	(	int	state	)	const
throw	(	BadIntException
	)

virtualinherited

Get the complete name of a state given its int description.

In case of several states with identical number (i.e. N and X for nucleic alphabets), this method returns the name of the first found in the vector.

Parameters

state The int description of the given state.

Returns: The name of the state.

Exceptions

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Definition at line 171 of file AbstractAlphabet.cpp.

◆ getNPosition() [1/2]

int bpp::WordAlphabet::getNPosition	(	int	word,
		size_t	n
	)		const
throw	(	BadIntException
	)

inlineinherited

Get the int code of the n-position of a word given its int description.

Parameters

word	The int description of the word.
n	The position in the word (starting at 0).

Returns: The int description of the n-position of the word.

Definition at line 248 of file WordAlphabet.h.

References bpp::AbstractAlphabet::intToChar(), and bpp::WordAlphabet::vAbsAlph_.

Referenced by bpp::SequenceContainerTools::getCodonPosition().

◆ getNPosition() [2/2]

std::string bpp::WordAlphabet::getNPosition	(	const std::string &	word,
		size_t	n
	)		const
throw	(	BadCharException
	)

inlineinherited

Get the char code of the n-position of a word given its char description.

Parameters

word	The char description of the word.
n	The position in the word (starting at 0).

Returns: The char description of the n-position of the word.

Definition at line 282 of file WordAlphabet.h.

References bpp::WordAlphabet::charToInt(), and bpp::WordAlphabet::vAbsAlph_.

◆ getNucleicAlphabet()

virtual const NucleicAlphabet* const bpp::CodonAlphabet::getNucleicAlphabet ( ) const

inlinevirtual

Returns: The nucleic alphabet associated to this codon alphabet.

Definition at line 179 of file CodonAlphabet.h.

References bpp::WordAlphabet::vAbsAlph_.

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::CodonSiteTools::isMonoSitePolymorphic(), and bpp::CodonSiteTools::numberOfSubsitutions().

◆ getNumberOfChars()

unsigned int bpp::AbstractAlphabet::getNumberOfChars ( ) const

inlinevirtualinherited

Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet).

Returns: The total number of supported character descriptions.

Implements bpp::Alphabet.

Definition at line 146 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::WordAlphabet::getNumberOfTypes(), bpp::WordAlphabet::getSize(), and bpp::NucleicAlphabet::registerState().

◆ getNumberOfStates()

size_t bpp::AbstractAlphabet::getNumberOfStates ( ) const

inlinevirtualinherited

This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int.

This funcion is typically used il loops over all states of an alphabet.

Implements bpp::Alphabet.

Definition at line 145 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

◆ getNumberOfTypes()

unsigned int bpp::WordAlphabet::getNumberOfTypes ( ) const

inlinevirtualinherited

Returns the number of resolved states + one for unresolved.

Implements bpp::Alphabet.

Definition at line 166 of file WordAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars().

◆ getPositions() [1/2]

std::vector<int> bpp::WordAlphabet::getPositions	(	int	word	)	const
throw	(	BadIntException
	)

inlineinherited

Get the int codes of each position of a word given its int description.

Parameters

word	The int description of the word.

Returns: The int description of the positions of the codon.

Definition at line 264 of file WordAlphabet.h.

References bpp::WordAlphabet::charToInt(), bpp::AbstractAlphabet::intToChar(), and bpp::WordAlphabet::vAbsAlph_.

Referenced by bpp::GeneticCode::isFourFoldDegenerated(), bpp::CodonSiteTools::numberOfSynonymousDifferences(), and bpp::CodonSiteTools::numberOfSynonymousPositions().

◆ getPositions() [2/2]

std::vector<std::string> bpp::WordAlphabet::getPositions	(	const std::string &	word	)	const
throw	(	BadCharException
	)

inlineinherited

Get the char codes of each position of a word given its char description.

Parameters

word	The char description of the word.

Returns: The char description of the three positions of the word.

Definition at line 300 of file WordAlphabet.h.

References bpp::WordAlphabet::charToInt().

◆ getSecondPosition() [1/2]

int CodonAlphabet::getSecondPosition	(	int	codon	)	const
throw	(	BadIntException
	)

virtual

Get the int code of the second position of a codon given its int description.

Parameters

codon The int description of the codon.

Returns: The int description of the second position of the codon.

Definition at line 85 of file CodonAlphabet.cpp.

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::numberOfDifferences(), and bpp::CodonSiteTools::numberOfSubsitutions().

◆ getSecondPosition() [2/2]

string CodonAlphabet::getSecondPosition	(	const std::string &	codon	)	const
throw	(	BadCharException
	)

virtual

Get the char code of the second position of a codon given its char description.

Parameters

codon The char description of the codon.

Returns: The char description of the second position of the codon.

Definition at line 107 of file CodonAlphabet.cpp.

◆ getSize()

unsigned int bpp::WordAlphabet::getSize ( ) const

inlinevirtualinherited

Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases.

Returns: The number of resolved states.

Implements bpp::Alphabet.

Definition at line 138 of file WordAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars().

Referenced by bpp::WordAlphabet::build_(), bpp::WordAlphabet::charToInt(), and bpp::WordAlphabet::getUnknownCharacterCode().

◆ getState() [1/4]

const AlphabetState & AbstractAlphabet::getState	(	const std::string &	letter	)	const
throw	(	BadCharException
	)

virtualinherited

Get a state by its letter.

This method must be overloaded in specialized classes to send back a reference of the corect type.

Parameters

letter The letter of the state to find.

Exceptions

BadCharException If the letter is not in the Alphabet.

Implements bpp::Alphabet.

Reimplemented in bpp::NucleicAlphabet, and bpp::ProteicAlphabet.

Definition at line 94 of file AbstractAlphabet.cpp.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::ProteicAlphabet::getState(), and bpp::NucleicAlphabet::getState().

◆ getState() [2/4]

AlphabetState & AbstractAlphabet::getState	(	const std::string &	letter	)
throw	(	BadCharException
	)

inherited

Definition at line 130 of file AbstractAlphabet.cpp.

◆ getState() [3/4]

const AlphabetState & AbstractAlphabet::getState	(	int	num	)	const
throw	(	BadIntException
	)

virtualinherited

Get a state by its num.

This method must be overloaded in specialized classes to send back a reference of the corect type.

Parameters

num	The num of the state to find.

Exceptions

BadIntException If the num is not in the Alphabet.

Implements bpp::Alphabet.

Reimplemented in bpp::NucleicAlphabet, and bpp::ProteicAlphabet.

Definition at line 112 of file AbstractAlphabet.cpp.

◆ getState() [4/4]

AlphabetState & AbstractAlphabet::getState	(	int	num	)
throw	(	BadIntException
	)

inherited

Definition at line 139 of file AbstractAlphabet.cpp.

◆ getStateAt() [1/2]

AlphabetState & AbstractAlphabet::getStateAt	(	size_t	stateIndex	)
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Get a state at a position in the alphabet_ vector.

This method must be overloaded in specialized classes to send back a reference of the corect type.

Parameters

stateIndex The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If the index is invalid.

Reimplemented in bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::ProteicAlphabet.

Definition at line 148 of file AbstractAlphabet.cpp.

Referenced by bpp::AbstractAlphabet::getCharCodeAt(), bpp::AbstractAlphabet::getIntCodeAt(), bpp::ProteicAlphabet::getStateAt(), bpp::NumericAlphabet::getStateAt(), and bpp::NucleicAlphabet::getStateAt().

◆ getStateAt() [2/2]

const AlphabetState & AbstractAlphabet::getStateAt	(	size_t	stateIndex	)	const
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Get a state at a position in the alphabet_ vector.

This method must be overloaded in specialized classes to send back a reference of the corect type.

Parameters

stateIndex The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If the index is invalid.

Implements bpp::Alphabet.

Reimplemented in bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::ProteicAlphabet.

Definition at line 156 of file AbstractAlphabet.cpp.

◆ getStateCodingSize()

unsigned int bpp::WordAlphabet::getStateCodingSize ( ) const

inlinevirtualinherited

Get the size of the string coding a state.

Returns: The size of the tring coding each states in the Alphabet.

Author: Sylvain Gaillard

Reimplemented from bpp::AbstractAlphabet.

Definition at line 339 of file WordAlphabet.h.

References bpp::WordAlphabet::vAbsAlph_.

◆ getStateIndex() [1/2]

size_t AbstractAlphabet::getStateIndex	(	int	state	)	const
throw	(	BadIntException
	)

virtualinherited

Returns: The indices of the states with corresponding int code.

Implements bpp::Alphabet.

Definition at line 121 of file AbstractAlphabet.cpp.

Referenced by bpp::AAIndex2Entry::getIndex().

◆ getStateIndex() [2/2]

size_t AbstractAlphabet::getStateIndex	(	const std::string &	state	)	const
throw	(	BadCharException
	)

virtualinherited

Returns: The index of the state with corresponding char code.

Implements bpp::Alphabet.

Definition at line 103 of file AbstractAlphabet.cpp.

◆ getSupportedChars()

const std::vector< std::string > & AbstractAlphabet::getSupportedChars ( ) const

virtualinherited

Returns: A list of all supported character codes.

Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.

Implements bpp::Alphabet.

Definition at line 301 of file AbstractAlphabet.cpp.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet().

◆ getSupportedInts()

const std::vector< int > & AbstractAlphabet::getSupportedInts ( ) const

virtualinherited

Returns: A list of all supported int codes.

Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.

Implements bpp::Alphabet.

Definition at line 284 of file AbstractAlphabet.cpp.

◆ getThirdPosition() [1/2]

int CodonAlphabet::getThirdPosition	(	int	codon	)	const
throw	(	BadIntException
	)

virtual

Get the int code of the third position of a codon given its int description.

Parameters

codon The int description of the codon.

Returns: The int description of the third position of the codon.

Definition at line 92 of file CodonAlphabet.cpp.

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::numberOfDifferences(), and bpp::CodonSiteTools::numberOfSubsitutions().

◆ getThirdPosition() [2/2]

string CodonAlphabet::getThirdPosition	(	const std::string &	codon	)	const
throw	(	BadCharException
	)

virtual

Get the char code of the third position of a codon given its char description.

Parameters

codon The char description of the codon.

Returns: The char description of the third position of the codon.

Definition at line 115 of file CodonAlphabet.cpp.

◆ getUnknownCharacterCode()

int bpp::WordAlphabet::getUnknownCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 173 of file WordAlphabet.h.

References bpp::WordAlphabet::getSize().

◆ getWord() [1/2]

int WordAlphabet::getWord	(	const std::vector< int > &	vint,
		size_t	pos = `0`
	)		const
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Get the int code for a word given the int code of the underlying positions.

The int code of each position must match the corresponding alphabet specified at this position.

Parameters

vint	description for all the positions.
pos	the start position to match in the vector.

Returns: The int code of the word.

Exceptions

IndexOutOfBoundsException In case of wrong position.

Definition at line 276 of file WordAlphabet.cpp.

◆ getWord() [2/2]

std::string WordAlphabet::getWord	(	const std::vector< std::string > &	vpos,
		size_t	pos = `0`
	)		const
throw	(	IndexOutOfBoundsException,
		BadCharException
	)

virtualinherited

Get the char code for a word given the char code of the underlying positions.

The char code of each position must match the corresponding alphabet specified at this position.

Parameters

vpos	vector description for all the positions.
pos	the start position to match in the vector.

Returns: The string of the word.

Exceptions

IndexOutOfBoundsException In case of wrong position.

Definition at line 292 of file WordAlphabet.cpp.

◆ hasUniqueAlphabet()

bool WordAlphabet::hasUniqueAlphabet ( ) const

inherited

Returns True if the Alphabet of the letters in the word are the same type.

Definition at line 146 of file WordAlphabet.cpp.

References bpp::WordAlphabet::getAlphabetType(), and bpp::WordAlphabet::vAbsAlph_.

◆ intToChar()

std::string AbstractAlphabet::intToChar	(	int	state	)	const
throw	(	BadIntException
	)

virtualinherited

Give the string description of a state given its int description.

Parameters

state The int description.

Returns: The string description.

Exceptions

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY.

Definition at line 185 of file AbstractAlphabet.cpp.

◆ isCharInAlphabet()

bool AbstractAlphabet::isCharInAlphabet ( const std::string & state ) const

virtualinherited

Tell if a state (specified by its string description) is allowed by the the alphabet.

Parameters

state The string description.

Returns: 'true' if the state in known.

Implements bpp::Alphabet.

Reimplemented in bpp::LetterAlphabet.

Definition at line 202 of file AbstractAlphabet.cpp.

◆ isGap() [1/2]

bool bpp::AbstractAlphabet::isGap ( int state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is a gap.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY, and bpp::NumericAlphabet.

Definition at line 160 of file AbstractAlphabet.h.

◆ isGap() [2/2]

bool bpp::AbstractAlphabet::isGap ( const std::string & state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is a gap.

Implements bpp::Alphabet.

Definition at line 161 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

◆ isIntInAlphabet()

bool AbstractAlphabet::isIntInAlphabet ( int state ) const

virtualinherited

Tell if a state (specified by its int description) is allowed by the the alphabet.

Parameters

state The int description.

Returns: 'true' if the state in known.

Implements bpp::Alphabet.

Definition at line 192 of file AbstractAlphabet.cpp.

◆ isUnresolved() [1/2]

bool bpp::WordAlphabet::isUnresolved ( int state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 178 of file WordAlphabet.h.

References bpp::WordAlphabet::getUnknownCharacterCode().

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

◆ isUnresolved() [2/2]

bool bpp::WordAlphabet::isUnresolved ( const std::string & state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 179 of file WordAlphabet.h.

References bpp::WordAlphabet::charToInt(), and bpp::WordAlphabet::getUnknownCharacterCode().

◆ operator=()

CodonAlphabet& bpp::CodonAlphabet::operator= ( const CodonAlphabet & bia )

inline

Definition at line 78 of file CodonAlphabet.h.

References bpp::WordAlphabet::operator=().

◆ registerState()

void AbstractAlphabet::registerState	(	AlphabetState *	st	)
throw	(	Exception
	)

protectedvirtualinherited

Add a state to the Alphabet.

Parameters

st	The state to add.

Exceptions

Exception If a wrong alphabet state is provided.

Reimplemented in bpp::LetterAlphabet, bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::DefaultAlphabet.

Definition at line 70 of file AbstractAlphabet.cpp.

Referenced by bpp::BinaryAlphabet::BinaryAlphabet(), bpp::WordAlphabet::build_(), bpp::IntegerAlphabet::IntegerAlphabet(), bpp::DefaultAlphabet::registerState(), bpp::NumericAlphabet::registerState(), bpp::LetterAlphabet::registerState(), and bpp::RNY::RNY().

◆ remap()

void bpp::AbstractAlphabet::remap ( )

inlineprotectedinherited

Re-update the maps using the alphabet_ vector content.

Definition at line 258 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_, bpp::AbstractAlphabet::letters_, bpp::AbstractAlphabet::nums_, and bpp::AbstractAlphabet::updateMaps_().

Referenced by bpp::NumericAlphabet::remap().

◆ resize()

void bpp::AbstractAlphabet::resize ( size_t size )

inlineprotectedinherited

Resize the private alphabet_ vector.

Parameters

size	The new size of the Alphabet.

Definition at line 253 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::IntegerAlphabet::IntegerAlphabet().

◆ reverse()

Sequence * WordAlphabet::reverse	(	const Sequence &	sequence	)	const
throw	(	AlphabetMismatchException,
		Exception
	)

inherited

Translate a whole sequence from words alphabet to letters alphabet.

Parameters

sequence A sequence in words alphabet.

Returns: The corresponding sequence in letters alphabet.

Exceptions

AlphabetMismatchException	If the sequence alphabet do not match the target alphabet.
Exception	Other kind of error, depending on the implementation.

Definition at line 333 of file WordAlphabet.cpp.

References bpp::Sequence::append(), and bpp::BasicSymbolList::size().

◆ setState()

void AbstractAlphabet::setState	(	size_t	pos,
		AlphabetState *	st
	)
throw	(	Exception,
		IndexOutOfBoundsException
	)

protectedvirtualinherited

Set a state in the Alphabet.

Parameters

pos	The index of the state in the alphabet_ vector.
st	The new state to put in the Alphabet.

Exceptions

Exception	If a wrong alphabet state is provided.
IndexOutOfBoundsException	If an incorrect index is provided.

Reimplemented in bpp::LetterAlphabet, bpp::NucleicAlphabet, and bpp::NumericAlphabet.

Definition at line 79 of file AbstractAlphabet.cpp.

Referenced by bpp::NumericAlphabet::setState(), and bpp::LetterAlphabet::setState().

◆ translate()

Sequence * WordAlphabet::translate	(	const Sequence &	sequence,
		size_t	pos = `0`
	)		const
throw	(	AlphabetMismatchException,
		Exception
	)

inherited

Translate a whole sequence from letters alphabet to words alphabet.

Parameters

sequence	A sequence in letters alphabet.
pos	the start postion (default 0)

Returns: The corresponding sequence in words alphabet.

Exceptions

AlphabetMismatchException	If the sequence alphabet do not match the source alphabet.
Exception	Other kind of error, depending on the implementation.

Definition at line 309 of file WordAlphabet.cpp.

Member Data Documentation

◆ charList_

std::vector<std::string> bpp::AbstractAlphabet::charList_

mutableprotectedinherited

Definition at line 99 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=().

◆ intList_

std::vector<int> bpp::AbstractAlphabet::intList_

mutableprotectedinherited

Definition at line 100 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=().

◆ vAbsAlph_

std::vector<const Alphabet* > bpp::WordAlphabet::vAbsAlph_

protectedinherited

Definition at line 70 of file WordAlphabet.h.

Referenced by bpp::WordAlphabet::build_(), bpp::WordAlphabet::charToInt(), getAlphabetType(), bpp::WordAlphabet::getAlphabetType(), bpp::WordAlphabet::getLength(), bpp::WordAlphabet::getNAlphabet(), bpp::WordAlphabet::getNPosition(), getNucleicAlphabet(), bpp::WordAlphabet::getPositions(), bpp::WordAlphabet::getStateCodingSize(), bpp::WordAlphabet::hasUniqueAlphabet(), bpp::WordAlphabet::operator=(), and bpp::WordAlphabet::WordAlphabet().

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

Bpp/Seq/Alphabet/CodonAlphabet.h
Bpp/Seq/Alphabet/CodonAlphabet.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CodonAlphabet() [1/2]

◆ CodonAlphabet() [2/2]

◆ ~CodonAlphabet()

Member Function Documentation

◆ charToInt()

◆ clone()

◆ equals()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAlphabetType()

◆ getCharCodeAt()

◆ getCodon() [1/2]

◆ getCodon() [2/2]

◆ getFirstPosition() [1/2]

◆ getFirstPosition() [2/2]

◆ getGapCharacterCode()

◆ getGeneric() [1/2]

◆ getGeneric() [2/2]

◆ getIntCodeAt()

◆ getLength()

◆ getNAlphabet()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNPosition() [1/2]

◆ getNPosition() [2/2]

◆ getNucleicAlphabet()

◆ getNumberOfChars()

◆ getNumberOfStates()

◆ getNumberOfTypes()

◆ getPositions() [1/2]

◆ getPositions() [2/2]

◆ getSecondPosition() [1/2]

◆ getSecondPosition() [2/2]

◆ getSize()

◆ getState() [1/4]

◆ getState() [2/4]

◆ getState() [3/4]

◆ getState() [4/4]

◆ getStateAt() [1/2]

◆ getStateAt() [2/2]

◆ getStateCodingSize()

◆ getStateIndex() [1/2]

◆ getStateIndex() [2/2]

◆ getSupportedChars()

◆ getSupportedInts()

◆ getThirdPosition() [1/2]

◆ getThirdPosition() [2/2]

◆ getUnknownCharacterCode()

◆ getWord() [1/2]

◆ getWord() [2/2]

◆ hasUniqueAlphabet()

◆ intToChar()

◆ isCharInAlphabet()

◆ isGap() [1/2]

◆ isGap() [2/2]

◆ isIntInAlphabet()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]

◆ operator=()

◆ registerState()

◆ remap()

◆ resize()

◆ reverse()

◆ setState()

◆ translate()

Member Data Documentation

◆ charList_

◆ intList_

◆ vAbsAlph_