A partial implementation of the Alphabet interface. More...

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

Inheritance diagram for bpp::AbstractAlphabet:

Collaboration diagram for bpp::AbstractAlphabet:

Public Member Functions
	AbstractAlphabet ()

	AbstractAlphabet (const AbstractAlphabet &alph)

AbstractAlphabet &	operator= (const AbstractAlphabet &alph)

virtual AbstractAlphabet *	clone () const =0

virtual	~AbstractAlphabet ()

virtual std::string	getAlphabetType () const =0
	Identification method. 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 throw (BadCharException)
	Get the complete name of a state given its string description. More...

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

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

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 (AlphabetException)
	Get the generic state that match a set of states. 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

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)

Sizes.
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 int	getUnknownCharacterCode () const =0

virtual bool	isUnresolved (int state) const =0

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

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...

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

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

Protected Attributes
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...

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

A partial implementation of the Alphabet interface.

It contains a vector of AlphabetState. All methods are based uppon this vector but do not provide any method to initialize it. This is up to each constructor of the derived classes.

See also: Alphabet

Definition at line 67 of file AbstractAlphabet.h.

Constructor & Destructor Documentation

◆ AbstractAlphabet() [1/2]

bpp::AbstractAlphabet::AbstractAlphabet ( )

inline

Definition at line 105 of file AbstractAlphabet.h.

◆ AbstractAlphabet() [2/2]

bpp::AbstractAlphabet::AbstractAlphabet ( const AbstractAlphabet & alph )

inline

Definition at line 107 of file AbstractAlphabet.h.

References alphabet_.

◆ ~AbstractAlphabet()

virtual bpp::AbstractAlphabet::~AbstractAlphabet ( )

inlinevirtual

Definition at line 133 of file AbstractAlphabet.h.

References alphabet_.

Member Function Documentation

◆ charToInt()

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

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::LetterAlphabet, and bpp::RNY.

Definition at line 178 of file AbstractAlphabet.cpp.

Referenced by bpp::RNY::charToInt(), bpp::WordAlphabet::charToInt(), and isGap().

◆ clone()

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

pure virtual

Implements bpp::Alphabet.

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

◆ equals()

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

inlineprotectedvirtual

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 > AbstractAlphabet::getAlias	(	int	state	)	const
throw	(	BadIntException
	)

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::NumericAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 212 of file AbstractAlphabet.cpp.

◆ getAlias() [2/2]

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

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::NumericAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 222 of file AbstractAlphabet.cpp.

◆ getAlphabetType()

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

pure virtualinherited

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::ProteicAlphabet, bpp::RNY, bpp::NumericAlphabet, bpp::CodonAlphabet, bpp::DNA, bpp::DefaultAlphabet, bpp::RNA, bpp::CaseMaskedAlphabet, bpp::IntegerAlphabet, and bpp::BinaryAlphabet.

Referenced by bpp::SiteTools::areSitesIdentical(), equals(), and bpp::SequenceTools::invertComplement().

◆ getCharCodeAt()

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

inlinevirtual

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 getStateAt().

◆ getGapCharacterCode()

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtual

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

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 232 of file AbstractAlphabet.cpp.

◆ getGeneric() [2/2]

std::string AbstractAlphabet::getGeneric	(	const std::vector< std::string > &	states	)	const
throw	(	AlphabetException
	)

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 258 of file AbstractAlphabet.cpp.

◆ getIntCodeAt()

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

inlinevirtual

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 getStateAt().

◆ getName() [1/2]

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

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 164 of file AbstractAlphabet.cpp.

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

◆ getName() [2/2]

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

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.

Implements bpp::Alphabet.

Definition at line 171 of file AbstractAlphabet.cpp.

◆ getNumberOfChars()

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

inlinevirtual

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 alphabet_.

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

◆ getNumberOfStates()

size_t bpp::AbstractAlphabet::getNumberOfStates ( ) const

inlinevirtual

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 alphabet_.

◆ getNumberOfTypes()

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

pure virtualinherited

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::NucleicAlphabet, bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::DefaultAlphabet, bpp::NumericAlphabet, bpp::CaseMaskedAlphabet, bpp::IntegerAlphabet, and bpp::BinaryAlphabet.

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

◆ getSize()

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

pure virtualinherited

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::NucleicAlphabet, bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::DefaultAlphabet, bpp::NumericAlphabet, bpp::CaseMaskedAlphabet, bpp::IntegerAlphabet, and bpp::BinaryAlphabet.

Referenced by bpp::SequenceTools::bowkerTest(), bpp::SequenceContainerTools::getFrequencies(), bpp::SequenceTools::getRandomSequence(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::CaseMaskedAlphabet::getSize(), and bpp::SimpleScore::SimpleScore().

◆ getState() [1/4]

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

virtual

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
	)

Definition at line 130 of file AbstractAlphabet.cpp.

◆ getState() [3/4]

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

virtual

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
	)

Definition at line 139 of file AbstractAlphabet.cpp.

◆ getStateAt() [1/2]

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

virtual

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

◆ getStateAt() [2/2]

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

virtual

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::AbstractAlphabet::getStateCodingSize ( ) const

inlineprotectedvirtual

Get the size of the string coding a state.

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

Author: Sylvain Gaillard

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 266 of file AbstractAlphabet.h.

◆ getStateIndex() [1/2]

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

virtual

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
	)

virtual

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

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.

Implements bpp::Alphabet.

Definition at line 301 of file AbstractAlphabet.cpp.

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

◆ getSupportedInts()

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

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.

Implements bpp::Alphabet.

Definition at line 284 of file AbstractAlphabet.cpp.

◆ getUnknownCharacterCode()

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

pure virtualinherited

Returns: The int code for unknown characters.

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

Referenced by bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::CaseMaskedAlphabet::getUnknownCharacterCode(), bpp::SiteTools::hasUnknown(), and bpp::SequenceTools::subtractHaplotype().

◆ intToChar()

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

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.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY.

Definition at line 185 of file AbstractAlphabet.cpp.

Referenced by bpp::RNY::getAlias(), bpp::GeneticCode::getCodingSequence(), bpp::WordAlphabet::getNPosition(), bpp::NucleicAlphabet::getOverlap(), bpp::WordAlphabet::getPositions(), bpp::EchinodermMitochondrialGeneticCode::isAltStart(), bpp::StandardGeneticCode::isAltStart(), bpp::YeastMitochondrialGeneticCode::isAltStart(), bpp::InvertebrateMitochondrialGeneticCode::isAltStart(), bpp::MoldMitochondrialGeneticCode::isAltStart(), bpp::AscidianMitochondrialGeneticCode::isAltStart(), bpp::VertebrateMitochondrialGeneticCode::isAltStart(), bpp::GeneticCode::isStart(), bpp::EchinodermMitochondrialGeneticCode::isStop(), bpp::StandardGeneticCode::isStop(), bpp::MoldMitochondrialGeneticCode::isStop(), bpp::YeastMitochondrialGeneticCode::isStop(), bpp::InvertebrateMitochondrialGeneticCode::isStop(), bpp::AscidianMitochondrialGeneticCode::isStop(), bpp::VertebrateMitochondrialGeneticCode::isStop(), and bpp::NucleicAlphabet::subtract().

◆ isCharInAlphabet()

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

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.

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

inlinevirtual

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

inlinevirtual

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 charToInt().

◆ isIntInAlphabet()

bool AbstractAlphabet::isIntInAlphabet ( int state ) const

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.

Implements bpp::Alphabet.

Definition at line 192 of file AbstractAlphabet.cpp.

◆ isUnresolved() [1/2]

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

pure virtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

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

Referenced by bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SiteTools::isComplete(), bpp::SiteTools::isGapOrUnresolvedOnly(), bpp::CaseMaskedAlphabet::isUnresolved(), and bpp::SequenceTools::subtractHaplotype().

◆ isUnresolved() [2/2]

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

pure virtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

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

◆ operator=()

AbstractAlphabet& bpp::AbstractAlphabet::operator= ( const AbstractAlphabet & alph )

inline

Definition at line 113 of file AbstractAlphabet.h.

References alphabet_, charList_, intList_, letters_, and nums_.

Referenced by bpp::BinaryAlphabet::operator=(), bpp::IntegerAlphabet::operator=(), bpp::LetterAlphabet::operator=(), bpp::NumericAlphabet::operator=(), bpp::RNY::operator=(), and bpp::WordAlphabet::operator=().

◆ registerState()

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

protectedvirtual

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 ( )

inlineprotected

Re-update the maps using the alphabet_ vector content.

Definition at line 258 of file AbstractAlphabet.h.

References alphabet_, letters_, nums_, and updateMaps_().

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

◆ resize()

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

inlineprotected

Resize the private alphabet_ vector.

Parameters

size	The new size of the Alphabet.

Definition at line 253 of file AbstractAlphabet.h.

References alphabet_.

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

◆ setState()

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

protectedvirtual

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().

◆ updateMaps_()

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

private

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 have been added or modified

Definition at line 57 of file AbstractAlphabet.cpp.

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

Referenced by remap().

Member Data Documentation

◆ alphabet_

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

private

Alphabet: vector of AlphabetState.

Definition at line 75 of file AbstractAlphabet.h.

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

◆ charList_

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

mutableprotected

Definition at line 99 of file AbstractAlphabet.h.

Referenced by operator=().

◆ intList_

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

mutableprotected

Definition at line 100 of file AbstractAlphabet.h.

Referenced by operator=().

◆ letters_

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

private

Definition at line 80 of file AbstractAlphabet.h.

Referenced by operator=(), and remap().

◆ nums_

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

private

Definition at line 81 of file AbstractAlphabet.h.

Referenced by operator=(), and remap().

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

Bpp/Seq/Alphabet/AbstractAlphabet.h
Bpp/Seq/Alphabet/AbstractAlphabet.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractAlphabet() [1/2]

◆ AbstractAlphabet() [2/2]

◆ ~AbstractAlphabet()

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()

◆ 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()

◆ getUnknownCharacterCode()

◆ intToChar()

◆ isCharInAlphabet()

◆ isGap() [1/2]

◆ isGap() [2/2]

◆ isIntInAlphabet()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]

◆ operator=()

◆ registerState()

◆ remap()

◆ resize()

◆ setState()

◆ updateMaps_()

Member Data Documentation

◆ alphabet_

◆ charList_

◆ intList_

◆ letters_

◆ nums_