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

Inheritance diagram for bpp::Alphabet:

Collaboration diagram for bpp::Alphabet:

Public Member Functions
	Alphabet ()

virtual	~Alphabet ()=default

virtual std::string	getName (int state) const =0
	Get the complete name of a state given its int description. More...

virtual std::string	getName (const std::string &state) const =0
	Get the complete name of a state given its string description. More...

virtual int	getIntCodeAt (size_t stateIndex) const =0

virtual const std::string &	getCharCodeAt (size_t stateIndex) const =0

virtual size_t	getStateIndex (int state) const =0

virtual size_t	getStateIndex (const std::string &state) const =0

virtual std::string	getAlphabetType () const =0
	Identification method. More...

virtual unsigned int	getStateCodingSize () const =0
	Get the size of the string coding a state. More...

virtual bool	equals (const Alphabet &alphabet) const =0
	Comparison of alphabets. More...

The Clonable interface
Alphabet *	clone () const =0

Tests
virtual bool	isIntInAlphabet (int state) const =0
	Tell if a state (specified by its int description) is allowed by the the alphabet. More...

virtual bool	isCharInAlphabet (const std::string &state) const =0
	Tell if a state (specified by its string description) is allowed by the the alphabet. More...

State access
virtual const AlphabetState &	getStateAt (size_t stateIndex) const =0
	Get a state given its index. More...

virtual const AlphabetState &	getState (int state) const =0
	Get a state given its int description. More...

virtual const AlphabetState &	getState (const std::string &state) const =0
	Get a state given its string description. More...

Conversion methods
virtual std::string	intToChar (int state) const =0
	Give the string description of a state given its int description. More...

virtual int	charToInt (const std::string &state) const =0
	Give the int description of a state given its string description. More...

Sizes.
virtual size_t	getNumberOfStates () const =0
	This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int. More...

virtual unsigned int	getNumberOfChars () const =0
	Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet). More...

virtual unsigned int	getNumberOfTypes () const =0
	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...

virtual unsigned int	getSize () const =0
	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...

Utilitary methods
virtual bool	isResolvedIn (int state1, int state2) const =0
	Tells if a given (potentially unresolved) state can be resolved in another resolved state. More...

virtual std::vector< int >	getAlias (int state) const =0
	Get all resolved states that match a generic state. More...

virtual std::vector< std::string >	getAlias (const std::string &state) const =0
	Get all resolved states that match a generic state. More...

virtual int	getGeneric (const std::vector< int > &states) const =0
	Get the generic state that match a set of states. More...

virtual std::string	getGeneric (const std::vector< std::string > &states) const =0
	Get the generic state that match a set of states. More...

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

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

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

virtual int	getUnknownCharacterCode () const =0

virtual int	getGapCharacterCode () const =0

virtual bool	isGap (int state) const =0

virtual bool	isGap (const std::string &state) const =0

virtual bool	isUnresolved (int state) const =0

virtual bool	isUnresolved (const std::string &state) const =0

Detailed Description

The Alphabet interface.

An alphabet object defines all the states allowed for a particular type of sequence. These states are coded as a string and an integer. The string description is the one found in the text (human comprehensive) description of sequences, typically in sequence files. However, for computionnal needs, this is often more efficient to store the sequences as a vector of integers. The link between the two descriptions is made via the Alphabet classes, and the two methods intToChar() and charToInt(). The Alphabet interface also provides other methods, like getting the full name of the states and so on.

An Alphabet object in itself stores the states as AlphabetStates object, in a potentially arbitrary but consistent series. All states are then indexed from 0 to 'numbersOfChars'. The number of states is equal to the number of string representations, but is usually higher than the number of int representation, as several characters can correspond to the same state (for instance X, N and ? in nucleotide alphabets).

The alphabet objects may throw several exceptions derived of the AlphabetException class.

See also: AlphabetException, BadCharException, BadIntException

Definition at line 96 of file Alphabet.h.

Constructor & Destructor Documentation

◆ Alphabet()

bpp::Alphabet::Alphabet ( )

inline

Definition at line 101 of file Alphabet.h.

◆ ~Alphabet()

virtual bpp::Alphabet::~Alphabet ( )

virtualdefault

Member Function Documentation

◆ charToInt()

virtual int bpp::Alphabet::charToInt ( const std::string & state ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::LetterAlphabet, and bpp::AbstractAlphabet.

◆ clone()

Alphabet* bpp::Alphabet::clone ( ) const

pure virtual

Implements bpp::Clonable.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::NucleicAlphabet, bpp::LetterAlphabet, bpp::AbstractAlphabet, bpp::RNY, bpp::RNA, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DNA, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

◆ equals()

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

pure virtual

Comparison of alphabets.

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

Implemented in bpp::AbstractAlphabet.

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

◆ getAlias() [1/2]

virtual std::vector<std::string> bpp::Alphabet::getAlias ( const std::string & state ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::RNA, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::DNA, bpp::BinaryAlphabet, and bpp::AbstractAlphabet.

◆ getAlias() [2/2]

virtual std::vector<int> bpp::Alphabet::getAlias ( int state ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::RNA, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::DNA, bpp::BinaryAlphabet, and bpp::AbstractAlphabet.

◆ getAlphabetType()

virtual std::string bpp::Alphabet::getAlphabetType ( ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::RNA, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DNA, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AbstractAlphabet::equals(), bpp::SequenceTools::getPercentIdentity(), bpp::AbstractReverseTransliterator::reverse(), and bpp::AbstractTransliterator::translate().

◆ getCharCodeAt()

virtual const std::string& bpp::Alphabet::getCharCodeAt ( size_t stateIndex ) const

pure virtual

Returns: The char code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implemented in bpp::AbstractAlphabet.

◆ getGapCharacterCode()

virtual int bpp::Alphabet::getGapCharacterCode ( ) const

pure virtual

Returns: The int code for gap characters.

Implemented in bpp::AbstractAlphabet.

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

◆ getGeneric() [1/2]

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

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, bpp::RNA, bpp::ProteicAlphabet, bpp::DNA, and bpp::AbstractAlphabet.

◆ getGeneric() [2/2]

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

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, bpp::RNA, bpp::ProteicAlphabet, bpp::DNA, and bpp::AbstractAlphabet.

◆ getIntCodeAt()

virtual int bpp::Alphabet::getIntCodeAt ( size_t stateIndex ) const

pure virtual

Returns: The int code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implemented in bpp::AbstractAlphabet.

◆ getName() [1/2]

virtual std::string bpp::Alphabet::getName ( const std::string & state ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, and bpp::AbstractAlphabet.

◆ getName() [2/2]

virtual std::string bpp::Alphabet::getName ( int state ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

◆ getNumberOfChars()

virtual unsigned int bpp::Alphabet::getNumberOfChars ( ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

Referenced by bpp::AlphabetTools::checkAlphabetCodingSize().

◆ getNumberOfStates()

virtual size_t bpp::Alphabet::getNumberOfStates ( ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

◆ getNumberOfTypes()

virtual unsigned int bpp::Alphabet::getNumberOfTypes ( ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::NucleicAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

Referenced by bpp::AlphabetTools::checkAlphabetCodingSize().

◆ getResolvedChars()

virtual const std::vector<std::string>& bpp::Alphabet::getResolvedChars ( ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

◆ getSize()

virtual unsigned int bpp::Alphabet::getSize ( ) const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::NucleicAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

◆ getState() [1/2]

virtual const AlphabetState& bpp::Alphabet::getState ( const std::string & state ) const

pure virtual

Get a state given its string description.

Parameters

state The string description.

Returns: The AlphabetState.

Exceptions

BadCharException When state is not a valid string.

Implemented in bpp::ProteicAlphabet, bpp::NucleicAlphabet, and bpp::AbstractAlphabet.

◆ getState() [2/2]

virtual const AlphabetState& bpp::Alphabet::getState ( int state ) const

pure virtual

Get a state given its int description.

Note: several states can share the same int values. This function will return one.

Parameters

state The int description.

Returns: The AlphabetState.

Exceptions

BadIntException When state is not a valid integer.

Implemented in bpp::ProteicAlphabet, bpp::NucleicAlphabet, and bpp::AbstractAlphabet.

◆ getStateAt()

virtual const AlphabetState& bpp::Alphabet::getStateAt ( size_t stateIndex ) const

pure virtual

Get a state given its index.

Parameters

stateIndex The index of the state.

Returns: The AlphabetState.

Exceptions

IndexOutOfBoundsException When index is not a valid.

Implemented in bpp::NumericAlphabet, bpp::NucleicAlphabet, bpp::AbstractAlphabet, and bpp::ProteicAlphabet.

Referenced by bpp::AlphabetTools::checkAlphabetCodingSize().

◆ getStateCodingSize()

virtual unsigned int bpp::Alphabet::getStateCodingSize ( ) const

pure virtual

Get the size of the string coding a state.

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

Author: Sylvain Gaillard

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, and bpp::AbstractAlphabet.

◆ getStateIndex() [1/2]

virtual size_t bpp::Alphabet::getStateIndex ( const std::string & state ) const

pure virtual

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

Implemented in bpp::AbstractAlphabet.

◆ getStateIndex() [2/2]

virtual size_t bpp::Alphabet::getStateIndex ( int state ) const

pure virtual

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

Implemented in bpp::AbstractAlphabet.

◆ getSupportedChars()

virtual const std::vector<std::string>& bpp::Alphabet::getSupportedChars ( ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

◆ getSupportedInts()

virtual const std::vector<int>& bpp::Alphabet::getSupportedInts ( ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

◆ getUnknownCharacterCode()

virtual int bpp::Alphabet::getUnknownCharacterCode ( ) const

pure virtual

Returns: The int code for unknown characters.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::NucleicAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

◆ intToChar()

virtual std::string bpp::Alphabet::intToChar ( int state ) const

pure virtual

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.

Implemented in bpp::RNY, and bpp::AbstractAlphabet.

Referenced by bpp::AlphabetTools::checkAlphabetCodingSize(), bpp::AlphabetTools::getAlphabetCodingSize(), and bpp::RNY::getRNY().

◆ isCharInAlphabet()

virtual bool bpp::Alphabet::isCharInAlphabet ( const std::string & state ) const

pure virtual

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.

Implemented in bpp::LetterAlphabet, and bpp::AbstractAlphabet.

◆ isGap() [1/2]

virtual bool bpp::Alphabet::isGap ( const std::string & state ) const

pure virtual

Parameters

state The state to test.

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

Implemented in bpp::AbstractAlphabet.

◆ isGap() [2/2]

virtual bool bpp::Alphabet::isGap ( int state ) const

pure virtual

Parameters

state The state to test.

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

Implemented in bpp::RNY, bpp::NumericAlphabet, and bpp::AbstractAlphabet.

◆ isIntInAlphabet()

virtual bool bpp::Alphabet::isIntInAlphabet ( int state ) const

pure virtual

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.

Implemented in bpp::AbstractAlphabet.

◆ isResolvedIn()

virtual bool bpp::Alphabet::isResolvedIn	(	int	state1,
		int	state2
	)		const

pure virtual

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.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::RNA, bpp::ProteicAlphabet, bpp::DNA, bpp::BinaryAlphabet, and bpp::AbstractAlphabet.

◆ isUnresolved() [1/2]

virtual bool bpp::Alphabet::isUnresolved ( const std::string & state ) const

pure virtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::NucleicAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

◆ isUnresolved() [2/2]

virtual bool bpp::Alphabet::isUnresolved ( int state ) const

pure virtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implemented in bpp::WordAlphabet, bpp::CodonAlphabet, bpp::CaseMaskedAlphabet, bpp::AllelicAlphabet, bpp::RNY, bpp::ProteicAlphabet, bpp::NumericAlphabet, bpp::NucleicAlphabet, bpp::LexicalAlphabet, bpp::IntegerAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

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

Bpp/Seq/Alphabet/Alphabet.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ Alphabet()

◆ ~Alphabet()

Member Function Documentation

◆ charToInt()

◆ clone()

◆ equals()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAlphabetType()

◆ getCharCodeAt()

◆ getGapCharacterCode()

◆ getGeneric() [1/2]

◆ getGeneric() [2/2]

◆ getIntCodeAt()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfChars()

◆ getNumberOfStates()

◆ getNumberOfTypes()

◆ getResolvedChars()

◆ getSize()

◆ getState() [1/2]

◆ getState() [2/2]

◆ getStateAt()

◆ getStateCodingSize()

◆ getStateIndex() [1/2]

◆ getStateIndex() [2/2]

◆ getSupportedChars()

◆ getSupportedInts()

◆ getUnknownCharacterCode()

◆ intToChar()

◆ isCharInAlphabet()

◆ isGap() [1/2]

◆ isGap() [2/2]

◆ isIntInAlphabet()

◆ isResolvedIn()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]