Codon alphabet class. More...

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

Inheritance diagram for bpp::CodonAlphabet:

Collaboration diagram for bpp::CodonAlphabet:

Public Member Functions
	CodonAlphabet (std::shared_ptr< 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 override

virtual	~CodonAlphabet ()

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

From AbstractAlphabet
unsigned int	getNumberOfTypes () const override
	Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number of integers used for state description. More...

unsigned int	getSize () const override

int	getUnknownCharacterCode () const override

bool	isUnresolved (int state) const override

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

bool	isResolvedIn (int state1, int state2) const override
	Tells if a given (potentially unresolved) state can be resolved in another resolved state. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

From CoreWordAlphabet
unsigned int	getLength () const override

bool	hasUniqueAlphabet () const override

std::shared_ptr< const Alphabet >	getNAlphabet (size_t n) const override

int	getWord (const Sequence &seq, size_t pos=0) const override

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

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

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

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

std::string	getNPosition (const std::string &codon, size_t pos) const override
	Get the char code of the Nth position of a codon given its char description. More...

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

std::unique_ptr< SequenceInterface >	translate (const SequenceInterface &sequence, size_t=0) const override
	Translate a whole sequence from letters alphabet to words alphabet. More...

std::unique_ptr< SequenceInterface >	reverse (const SequenceInterface &sequence) const override
	Translate a whole sequence from words alphabet to letters alphabet. More...

int	getGCinCodon (int codon) const
	Get the number of G+C in codon. More...

std::shared_ptr< const NucleicAlphabet >	getNucleicAlphabet () const

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

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

std::string	getName (int state) const
	Get the complete name of a state given its int description. More...

std::string	intToChar (int state) const
	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

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

int	getGapCharacterCode () const

bool	isGap (int state) const

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

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

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

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

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

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

AlphabetState &	getState (int num)

int	getIntCodeAt (size_t stateIndex) const

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

size_t	getStateIndex (int state) const

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

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

virtual void	setState (size_t pos, AlphabetState *st)
	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::shared_ptr< const NucleicAlphabet >	nAlph_

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_

Private Member Functions
void	updateMaps_ (size_t pos, const AlphabetState &st)
	Update the private maps letters_ and nums_ when adding a state. More...

Inner utilitary functions
bool	containsUnresolved (const std::string &state) const override

bool	containsGap (const std::string &state) const override

void	build_ ()

Private Attributes
std::vector< AlphabetState * >	alphabet_
	Alphabet: vector of AlphabetState. More...

maps used to quick search for letter and num.
std::map< std::string, size_t >	letters_

std::map< int, size_t >	nums_

Detailed Description

Codon alphabet class.

Author: Laurent Guéguen, Julien Dutheil

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 28 of file CodonAlphabet.h.

Constructor & Destructor Documentation

◆ CodonAlphabet() [1/2]

bpp::CodonAlphabet::CodonAlphabet ( std::shared_ptr< const NucleicAlphabet > alpha )

inline

Builds a new codon alphabet from a nucleic alphabet.

Parameters

alpha The nucleic alphabet to be used.

Definition at line 43 of file CodonAlphabet.h.

References build_().

Referenced by clone().

◆ CodonAlphabet() [2/2]

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

inline

Definition at line 50 of file CodonAlphabet.h.

◆ ~CodonAlphabet()

virtual bpp::CodonAlphabet::~CodonAlphabet ( )

inlinevirtual

Definition at line 68 of file CodonAlphabet.h.

Member Function Documentation

◆ build_()

void CodonAlphabet::build_ ( )

private

Definition at line 17 of file CodonAlphabet.cpp.

Referenced by CodonAlphabet().

◆ charToInt()

int bpp::CodonAlphabet::charToInt ( const std::string & state ) const

inlineoverridevirtual

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 134 of file CodonAlphabet.h.

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

Referenced by isUnresolved().

◆ clone()

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

inlineoverridevirtual

Implements bpp::AbstractAlphabet.

Definition at line 63 of file CodonAlphabet.h.

References CodonAlphabet().

◆ containsGap()

bool CodonAlphabet::containsGap ( const std::string & state ) const

overrideprivatevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 80 of file CodonAlphabet.cpp.

Referenced by charToInt().

◆ containsUnresolved()

bool CodonAlphabet::containsUnresolved ( const std::string & state ) const

overrideprivatevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 63 of file CodonAlphabet.cpp.

Referenced by charToInt().

◆ 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 243 of file AbstractAlphabet.h.

References bpp::Alphabet::getAlphabetType().

◆ getAlias() [1/2]

std::vector< std::string > CodonAlphabet::getAlias ( const std::string & state ) const

overridevirtual

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 155 of file CodonAlphabet.cpp.

References bpp::TextTools::toUpper().

◆ getAlias() [2/2]

std::vector< int > CodonAlphabet::getAlias ( int state ) const

overridevirtual

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 132 of file CodonAlphabet.cpp.

◆ getAlphabetType()

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

inlineoverridevirtual

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 71 of file CodonAlphabet.h.

References nAlph_.

◆ getCharCodeAt()

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

inlinevirtualinherited

Returns: The char code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 192 of file AbstractAlphabet.h.

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

◆ getCodon() [1/2]

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

inline

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 183 of file CodonAlphabet.h.

◆ getCodon() [2/2]

int bpp::CodonAlphabet::getCodon	(	int	pos1,
		int	pos2,
		int	pos3
	)		const

inline

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 160 of file CodonAlphabet.h.

References getUnknownCharacterCode(), and nAlph_.

Referenced by getWord().

◆ getFirstPosition() [1/2]

std::string bpp::CodonAlphabet::getFirstPosition ( const std::string & codon ) const

inline

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 228 of file CodonAlphabet.h.

◆ getFirstPosition() [2/2]

int bpp::CodonAlphabet::getFirstPosition ( int codon ) const

inline

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 194 of file CodonAlphabet.h.

References isUnresolved(), and nAlph_.

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

◆ getGapCharacterCode()

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 130 of file AbstractAlphabet.h.

◆ getGCinCodon()

int CodonAlphabet::getGCinCodon ( int codon ) const

Get the number of G+C in codon.

Parameters

codon The int description of the codon.

Returns: The number of G+C in codon

Definition at line 47 of file CodonAlphabet.cpp.

◆ getGeneric() [1/2]

int bpp::CodonAlphabet::getGeneric ( const std::vector< int > & states ) const

inlineoverridevirtual

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 124 of file CodonAlphabet.h.

◆ getGeneric() [2/2]

std::string bpp::CodonAlphabet::getGeneric ( const std::vector< std::string > & states ) const

inlineoverridevirtual

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 129 of file CodonAlphabet.h.

◆ getIntCodeAt()

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

inlinevirtualinherited

Returns: The int code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 187 of file AbstractAlphabet.h.

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

◆ getLength()

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

inlineoverridevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 263 of file CodonAlphabet.h.

◆ getNAlphabet()

std::shared_ptr<const Alphabet> bpp::CodonAlphabet::getNAlphabet ( size_t n ) const

inlineoverridevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 273 of file CodonAlphabet.h.

References nAlph_.

◆ getName() [1/2]

std::string AbstractAlphabet::getName ( const std::string & state ) const

virtualinherited

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

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

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 139 of file AbstractAlphabet.cpp.

Referenced by bpp::WordAlphabet::getName(), and bpp::LexicalAlphabet::LexicalAlphabet().

◆ getName() [2/2]

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

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 146 of file AbstractAlphabet.cpp.

◆ getNPosition() [1/2]

std::string bpp::CodonAlphabet::getNPosition	(	const std::string &	codon,
		size_t	pos
	)		const

inlineoverridevirtual

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

Parameters

codon	The char description of the codon.
pos	the position in the codon (starting at 0)

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

Implements bpp::CoreWordAlphabet.

Definition at line 348 of file CodonAlphabet.h.

◆ getNPosition() [2/2]

int bpp::CodonAlphabet::getNPosition	(	int	word,
		size_t	n
	)		const

inlineoverridevirtual

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.

Implements bpp::CoreWordAlphabet.

Definition at line 312 of file CodonAlphabet.h.

References isUnresolved(), and nAlph_.

◆ getNucleicAlphabet()

std::shared_ptr<const NucleicAlphabet> bpp::CodonAlphabet::getNucleicAlphabet ( ) const

inline

Returns: The nucleic alphabet associated to this codon alphabet.

Definition at line 401 of file CodonAlphabet.h.

References nAlph_.

◆ 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 115 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::LexicalAlphabet::getNumberOfTypes(), bpp::AllelicAlphabet::getNumberOfTypes(), bpp::WordAlphabet::getNumberOfTypes(), bpp::LexicalAlphabet::getSize(), bpp::AllelicAlphabet::getSize(), 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 function is typically used il loops over all states of an alphabet.

Implements bpp::Alphabet.

Definition at line 114 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::LexicalAlphabet::getAlphabetType().

◆ getNumberOfTypes()

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

inlineoverridevirtual

Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number of integers used for state description.

Returns: The number of distinct states.

Implements bpp::Alphabet.

Definition at line 96 of file CodonAlphabet.h.

◆ getPositions() [1/2]

std::vector<std::string> bpp::CodonAlphabet::getPositions ( const std::string & word ) const

inlineoverridevirtual

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.

Implements bpp::CoreWordAlphabet.

Definition at line 359 of file CodonAlphabet.h.

◆ getPositions() [2/2]

std::vector<int> bpp::CodonAlphabet::getPositions ( int word ) const

inlineoverridevirtual

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.

Implements bpp::CoreWordAlphabet.

Definition at line 328 of file CodonAlphabet.h.

References isUnresolved(), and nAlph_.

◆ getResolvedChars()

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

virtualinherited

Returns: A list of all resolved 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 327 of file AbstractAlphabet.cpp.

◆ getSecondPosition() [1/2]

std::string bpp::CodonAlphabet::getSecondPosition ( const std::string & codon ) const

inline

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 240 of file CodonAlphabet.h.

◆ getSecondPosition() [2/2]

int bpp::CodonAlphabet::getSecondPosition ( int codon ) const

inline

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 205 of file CodonAlphabet.h.

References isUnresolved(), and nAlph_.

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

◆ getSize()

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

inlineoverridevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 98 of file CodonAlphabet.h.

Referenced by charToInt().

◆ getState() [1/4]

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

inherited

Definition at line 101 of file AbstractAlphabet.cpp.

◆ getState() [2/4]

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

virtualinherited

Get a state by its letter.

This method must be overloaded in specialized classes to send back a reference of the correct 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::ProteicAlphabet, and bpp::NucleicAlphabet.

Definition at line 61 of file AbstractAlphabet.cpp.

Referenced by bpp::AllelicAlphabet::getAlias(), bpp::NucleicAlphabet::getState(), bpp::ProteicAlphabet::getState(), bpp::RNY::intToChar(), and bpp::NumericAlphabet::intToValue().

◆ getState() [3/4]

AlphabetState & AbstractAlphabet::getState ( int num )

inherited

Definition at line 111 of file AbstractAlphabet.cpp.

◆ getState() [4/4]

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

virtualinherited

Get a state by its num.

This method must be overloaded in specialized classes to send back a reference of the correct 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::ProteicAlphabet, and bpp::NucleicAlphabet.

Definition at line 81 of file AbstractAlphabet.cpp.

◆ getStateAt() [1/2]

AlphabetState & AbstractAlphabet::getStateAt ( size_t stateIndex )

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 correct type.

Parameters

stateIndex The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If the index is invalid.

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

Definition at line 121 of file AbstractAlphabet.cpp.

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

◆ getStateAt() [2/2]

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

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 correct 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::NumericAlphabet, bpp::NucleicAlphabet, and bpp::ProteicAlphabet.

Definition at line 130 of file AbstractAlphabet.cpp.

◆ getStateCodingSize()

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

inlineoverridevirtual

Get the size of the string coding a state.

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

Author: Sylvain Gaillard

Reimplemented from bpp::AbstractAlphabet.

Definition at line 410 of file CodonAlphabet.h.

◆ getStateIndex() [1/2]

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

virtualinherited

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

Implements bpp::Alphabet.

Definition at line 71 of file AbstractAlphabet.cpp.

◆ getStateIndex() [2/2]

size_t AbstractAlphabet::getStateIndex ( int state ) const

virtualinherited

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

Implements bpp::Alphabet.

Definition at line 91 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 310 of file AbstractAlphabet.cpp.

Referenced by bpp::AllelicAlphabet::getAlias().

◆ 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 293 of file AbstractAlphabet.cpp.

Referenced by bpp::AllelicAlphabet::getAlias().

◆ getThirdPosition() [1/2]

std::string bpp::CodonAlphabet::getThirdPosition ( const std::string & codon ) const

inline

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 252 of file CodonAlphabet.h.

◆ getThirdPosition() [2/2]

int bpp::CodonAlphabet::getThirdPosition ( int codon ) const

inline

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 217 of file CodonAlphabet.h.

References isUnresolved(), and nAlph_.

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

◆ getUnknownCharacterCode()

int bpp::CodonAlphabet::getUnknownCharacterCode ( ) const

inlineoverridevirtual

Returns: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 103 of file CodonAlphabet.h.

Referenced by getCodon().

◆ getWord() [1/3]

int bpp::CodonAlphabet::getWord	(	const Sequence &	seq,
		size_t	pos = `0`
	)		const

inlineoverridevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 278 of file CodonAlphabet.h.

References getCodon(), and bpp::AbstractTemplateSymbolList< T >::size().

◆ getWord() [2/3]

int bpp::CodonAlphabet::getWord	(	const std::vector< int > &	vint,
		size_t	pos = `0`
	)		const

inlineoverridevirtual

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.

Implements bpp::CoreWordAlphabet.

Definition at line 303 of file CodonAlphabet.h.

References getCodon().

◆ getWord() [3/3]

std::string bpp::CodonAlphabet::getWord	(	const std::vector< std::string > &	vpos,
		size_t	pos = `0`
	)		const

inlineoverridevirtual

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.

Implements bpp::CoreWordAlphabet.

Definition at line 295 of file CodonAlphabet.h.

References getCodon().

◆ hasUniqueAlphabet()

bool bpp::CodonAlphabet::hasUniqueAlphabet ( ) const

inlineoverridevirtual

Implements bpp::CoreWordAlphabet.

Definition at line 268 of file CodonAlphabet.h.

◆ intToChar()

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

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 160 of file AbstractAlphabet.cpp.

Referenced by bpp::RNY::getAlias(), bpp::WordAlphabet::getAlias(), bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), bpp::WordAlphabet::getNPosition(), bpp::NucleicAlphabet::getOverlap(), bpp::WordAlphabet::getPositions(), bpp::WordAlphabet::getWord(), bpp::BinaryAlphabet::isResolvedIn(), and bpp::NucleicAlphabet::subtract().

◆ 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 177 of file AbstractAlphabet.cpp.

Referenced by bpp::BinaryAlphabet::getAlias(), bpp::RNY::getAlias(), bpp::AllelicAlphabet::getAlias(), and bpp::WordAlphabet::getAlias().

◆ isGap() [1/2]

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 132 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

◆ isGap() [2/2]

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 131 of file AbstractAlphabet.h.

Referenced by bpp::WordAlphabet::containsGap().

◆ 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 167 of file AbstractAlphabet.cpp.

Referenced by bpp::BinaryAlphabet::getAlias(), bpp::RNY::getAlias(), bpp::AllelicAlphabet::getAlias(), bpp::WordAlphabet::getAlias(), bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), bpp::BinaryAlphabet::isResolvedIn(), bpp::RNY::isResolvedIn(), bpp::AllelicAlphabet::isResolvedIn(), and bpp::WordAlphabet::isResolvedIn().

◆ isResolvedIn()

bool CodonAlphabet::isResolvedIn	(	int	state1,
		int	state2
	)		const

overridevirtual

Tells if a given (potentially unresolved) state can be resolved in another resolved state.

Parameters

state1	The alias to resolve.
state2	The candidate for resolution.

Returns: A boolean

Exceptions

BadIntException When state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 178 of file CodonAlphabet.cpp.

◆ isUnresolved() [1/2]

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

inlineoverridevirtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 113 of file CodonAlphabet.h.

References charToInt(), and isUnresolved().

◆ isUnresolved() [2/2]

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

inlineoverridevirtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 108 of file CodonAlphabet.h.

Referenced by getFirstPosition(), getNPosition(), getPositions(), getSecondPosition(), getThirdPosition(), and isUnresolved().

◆ operator=()

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

inline

Definition at line 55 of file CodonAlphabet.h.

References nAlph_, and bpp::AbstractAlphabet::operator=().

◆ registerState()

void AbstractAlphabet::registerState ( AlphabetState * st )

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

Definition at line 36 of file AbstractAlphabet.cpp.

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

◆ remap()

void bpp::AbstractAlphabet::remap ( )

inlineprotectedinherited

Re-update the maps using the alphabet_ vector content.

Definition at line 231 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 226 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

◆ reverse()

unique_ptr< SequenceInterface > CodonAlphabet::reverse ( const SequenceInterface & sequence ) const

overridevirtual

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.

Implements bpp::CoreWordAlphabet.

Definition at line 116 of file CodonAlphabet.cpp.

References bpp::CoreSequenceInterface::getName(), and bpp::CruxSymbolListInterface::size().

◆ setState()

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

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

Definition at line 46 of file AbstractAlphabet.cpp.

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

◆ translate()

unique_ptr< SequenceInterface > CodonAlphabet::translate	(	const SequenceInterface &	sequence,
		size_t	pos = `0`
	)		const

overridevirtual

Translate a whole sequence from letters alphabet to words alphabet.

Parameters

sequence	A sequence in letters alphabet.
pos	the start position (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.

Implements bpp::CoreWordAlphabet.

Definition at line 97 of file CodonAlphabet.cpp.

References bpp::CoreSequenceInterface::getName(), and bpp::CruxSymbolListInterface::size().

◆ updateMaps_()

void AbstractAlphabet::updateMaps_	(	size_t	pos,
		const AlphabetState &	st
	)

privateinherited

Update the private maps letters_ and nums_ when adding a state.

Parameters

pos	The index of the state in the alphabet_ vector.
st	The state that has been added or modified

Definition at line 22 of file AbstractAlphabet.cpp.

References bpp::AlphabetState::getLetter(), and bpp::AlphabetState::getNum().

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

Member Data Documentation

◆ alphabet_

std::vector<AlphabetState*> bpp::AbstractAlphabet::alphabet_

privateinherited

Alphabet: vector of AlphabetState.

Definition at line 37 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::AbstractAlphabet(), bpp::AbstractAlphabet::getNumberOfChars(), bpp::AbstractAlphabet::getNumberOfStates(), bpp::AbstractAlphabet::operator=(), bpp::AbstractAlphabet::remap(), bpp::AbstractAlphabet::resize(), and bpp::AbstractAlphabet::~AbstractAlphabet().

◆ charList_

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

mutableprotectedinherited

Definition at line 63 of file AbstractAlphabet.h.

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

◆ intList_

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

mutableprotectedinherited

Definition at line 64 of file AbstractAlphabet.h.

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

◆ letters_

std::map<std::string, size_t> bpp::AbstractAlphabet::letters_

privateinherited

Definition at line 43 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=(), and bpp::AbstractAlphabet::remap().

◆ nAlph_

std::shared_ptr<const NucleicAlphabet> bpp::CodonAlphabet::nAlph_

protected

Definition at line 33 of file CodonAlphabet.h.

Referenced by getAlphabetType(), getCodon(), getFirstPosition(), getNAlphabet(), getNPosition(), getNucleicAlphabet(), getPositions(), getSecondPosition(), getThirdPosition(), and operator=().

◆ nums_

std::map<int, size_t> bpp::AbstractAlphabet::nums_

privateinherited

Definition at line 44 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=(), and bpp::AbstractAlphabet::remap().

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

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CodonAlphabet() [1/2]

◆ CodonAlphabet() [2/2]

◆ ~CodonAlphabet()

Member Function Documentation

◆ build_()

◆ charToInt()

◆ clone()

◆ containsGap()

◆ containsUnresolved()

◆ equals()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAlphabetType()

◆ getCharCodeAt()

◆ getCodon() [1/2]

◆ getCodon() [2/2]

◆ getFirstPosition() [1/2]

◆ getFirstPosition() [2/2]

◆ getGapCharacterCode()

◆ getGCinCodon()

◆ 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]

◆ getResolvedChars()

◆ 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() [1/3]

◆ getWord() [2/3]

◆ getWord() [3/3]

◆ hasUniqueAlphabet()

◆ intToChar()

◆ isCharInAlphabet()

◆ isGap() [1/2]

◆ isGap() [2/2]

◆ isIntInAlphabet()

◆ isResolvedIn()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]

◆ operator=()

◆ registerState()

◆ remap()

◆ resize()

◆ reverse()

◆ setState()

◆ translate()

◆ updateMaps_()