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

Inheritance diagram for bpp::NumericAlphabet:

Collaboration diagram for bpp::NumericAlphabet:

Public Member Functions
	NumericAlphabet (const UniformDiscreteDistribution &)

virtual	~NumericAlphabet ()

	NumericAlphabet (const NumericAlphabet &)

NumericAlphabet &	operator= (const NumericAlphabet &)

NumericAlphabet *	clone () const

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

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

bool	containsGap (const std::string &state) const throw (BadCharException)

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

unsigned int	getNumberOfTypes () const
	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...

int	getUnknownCharacterCode () const

bool	isGap (int state) const

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

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

bool	isUnresolved (int state) const

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

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

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

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

double	getDelta () const
	Returns the difference between successive values. More...

double	intToValue (int state) const throw (BadIntException)
	Returns the value for the character number. More...

size_t	getValueIndex (double value) const
	Returns the CategoryIndex of the category to which the value belongs. More...

void	remap ()
	Re-update the maps. 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...

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 (const std::string &state) const

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

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

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

AlphabetState &	getState (int num) throw (BadIntException)

int	getIntCodeAt (size_t stateIndex) const throw (IndexOutOfBoundsException)

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

size_t	getStateIndex (int state) const throw (BadIntException)

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

Protected Member Functions
void	resize (size_t size)
	Resize the private alphabet_ vector. 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 Attributes
const UniformDiscreteDistribution *	pdd_

std::map< double, size_t >	values_

Detailed Description

Definition at line 58 of file NumericAlphabet.h.

Constructor & Destructor Documentation

◆ NumericAlphabet() [1/2]

NumericAlphabet::NumericAlphabet ( const UniformDiscreteDistribution & pd )

Definition at line 52 of file NumericAlphabet.cpp.

References pdd_, and registerState().

Referenced by clone().

◆ ~NumericAlphabet()

virtual bpp::NumericAlphabet::~NumericAlphabet ( )

inlinevirtual

Definition at line 69 of file NumericAlphabet.h.

References pdd_.

◆ NumericAlphabet() [2/2]

NumericAlphabet::NumericAlphabet ( const NumericAlphabet & na )

Definition at line 66 of file NumericAlphabet.cpp.

Member Function Documentation

◆ charToInt()

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

virtualinherited

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 bpp::AbstractAlphabet::isGap().

◆ clone()

NumericAlphabet* bpp::NumericAlphabet::clone ( ) const

inlinevirtual

Implements bpp::AbstractAlphabet.

Definition at line 75 of file NumericAlphabet.h.

References NumericAlphabet().

◆ containsGap()

bool NumericAlphabet::containsGap	(	const std::string &	state	)	const
throw	(	BadCharException
	)

Definition at line 127 of file NumericAlphabet.cpp.

◆ equals()

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

inlineprotectedvirtualinherited

Comparison of alphabets.

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

Implements bpp::Alphabet.

Definition at line 268 of file AbstractAlphabet.h.

References bpp::Alphabet::getAlphabetType().

◆ getAlias() [1/2]

vector< int > NumericAlphabet::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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 106 of file NumericAlphabet.cpp.

◆ getAlias() [2/2]

vector< string > NumericAlphabet::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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 113 of file NumericAlphabet.cpp.

◆ getAlphabetType()

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

inlinevirtual

Identification method.

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

Returns: A text describing the alphabet.

Implements bpp::Alphabet.

Definition at line 95 of file NumericAlphabet.h.

◆ getCharCodeAt()

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

inlinevirtualinherited

Returns: The char code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 220 of file AbstractAlphabet.h.

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

◆ getDelta()

double NumericAlphabet::getDelta ( ) const

Returns the difference between successive values.

@ brief Specific methods

Definition at line 165 of file NumericAlphabet.cpp.

References pdd_.

◆ getGapCharacterCode()

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 159 of file AbstractAlphabet.h.

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

◆ getGeneric() [1/2]

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

virtualinherited

Get the generic state that match a set of states.

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

Parameters

states A vector of states to resolve.

Returns: A int code for the computed state.

Exceptions

BadIntException When a state is not a valid integer.

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
	)

virtualinherited

Get the generic state that match a set of states.

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

Parameters

states A vector of states to resolve.

Returns: A string code for the computed state.

Exceptions

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

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
	)

inlinevirtualinherited

Returns: The int code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 216 of file AbstractAlphabet.h.

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

◆ getName() [1/2]

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

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 164 of file AbstractAlphabet.cpp.

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

◆ getName() [2/2]

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

virtualinherited

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

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

Parameters

state The int description of the given state.

Returns: The name of the state.

Exceptions

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Definition at line 171 of file AbstractAlphabet.cpp.

◆ getNumberOfChars()

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

inlinevirtualinherited

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

Returns: The total number of supported character descriptions.

Implements bpp::Alphabet.

Definition at line 146 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

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

◆ getNumberOfStates()

size_t bpp::AbstractAlphabet::getNumberOfStates ( ) const

inlinevirtualinherited

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

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

Implements bpp::Alphabet.

Definition at line 145 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

◆ getNumberOfTypes()

unsigned int NumericAlphabet::getNumberOfTypes ( ) const

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.

Implements bpp::Alphabet.

Definition at line 147 of file NumericAlphabet.cpp.

References values_.

◆ getSize()

unsigned int NumericAlphabet::getSize ( ) const

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.

Implements bpp::Alphabet.

Definition at line 142 of file NumericAlphabet.cpp.

References values_.

Referenced by remap().

◆ getState() [1/4]

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

virtualinherited

Get a state by its letter.

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

Parameters

letter The letter of the state to find.

Exceptions

BadCharException If the letter is not in the Alphabet.

Implements bpp::Alphabet.

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

Definition at line 94 of file AbstractAlphabet.cpp.

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

◆ getState() [2/4]

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

inherited

Definition at line 130 of file AbstractAlphabet.cpp.

◆ getState() [3/4]

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

virtualinherited

Get a state by its num.

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

Parameters

num	The num of the state to find.

Exceptions

BadIntException If the num is not in the Alphabet.

Implements bpp::Alphabet.

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

Definition at line 112 of file AbstractAlphabet.cpp.

◆ getState() [4/4]

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

inherited

Definition at line 139 of file AbstractAlphabet.cpp.

◆ getStateAt() [1/2]

AlphabetNumericState & NumericAlphabet::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 from bpp::AbstractAlphabet.

Definition at line 181 of file NumericAlphabet.cpp.

References bpp::AbstractAlphabet::getStateAt().

Referenced by remap().

◆ getStateAt() [2/2]

const AlphabetNumericState & NumericAlphabet::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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 186 of file NumericAlphabet.cpp.

References bpp::AbstractAlphabet::getStateAt().

◆ getStateCodingSize()

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

inlineprotectedvirtualinherited

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
	)

virtualinherited

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

Implements bpp::Alphabet.

Definition at line 121 of file AbstractAlphabet.cpp.

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

◆ getStateIndex() [2/2]

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

virtualinherited

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

Implements bpp::Alphabet.

Definition at line 103 of file AbstractAlphabet.cpp.

◆ getSupportedChars()

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

virtualinherited

Returns: A list of all supported character codes.

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

Implements bpp::Alphabet.

Definition at line 301 of file AbstractAlphabet.cpp.

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

◆ getSupportedInts()

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

virtualinherited

Returns: A list of all supported int codes.

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

Implements bpp::Alphabet.

Definition at line 284 of file AbstractAlphabet.cpp.

◆ getUnknownCharacterCode()

int bpp::NumericAlphabet::getUnknownCharacterCode ( ) const

inlinevirtual

Returns: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 88 of file NumericAlphabet.h.

◆ getValueIndex()

size_t NumericAlphabet::getValueIndex ( double value ) const

Returns the CategoryIndex of the category to which the value belongs.

Definition at line 175 of file NumericAlphabet.cpp.

References pdd_, and values_.

◆ intToChar()

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

virtualinherited

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

Parameters

state The int description.

Returns: The string description.

Exceptions

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY.

Definition at line 185 of file AbstractAlphabet.cpp.

◆ intToValue()

double NumericAlphabet::intToValue	(	int	state	)	const
throw	(	BadIntException
	)

Returns the value for the character number.

Definition at line 170 of file NumericAlphabet.cpp.

◆ isCharInAlphabet()

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

virtualinherited

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

Parameters

state The string description.

Returns: 'true' if the state in known.

Implements bpp::Alphabet.

Reimplemented in bpp::LetterAlphabet.

Definition at line 202 of file AbstractAlphabet.cpp.

◆ isGap() [1/2]

bool NumericAlphabet::isGap ( int state ) const

virtual

Parameters

state The state to test.

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

Reimplemented from bpp::AbstractAlphabet.

Definition at line 122 of file NumericAlphabet.cpp.

◆ isGap() [2/2]

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

inlinevirtualinherited

Parameters

state The state to test.

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

Implements bpp::Alphabet.

Definition at line 161 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

◆ isIntInAlphabet()

bool AbstractAlphabet::isIntInAlphabet ( int state ) const

virtualinherited

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

Parameters

state The int description.

Returns: 'true' if the state in known.

Implements bpp::Alphabet.

Definition at line 192 of file AbstractAlphabet.cpp.

◆ isUnresolved() [1/2]

bool NumericAlphabet::isUnresolved ( int state ) const

virtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 137 of file NumericAlphabet.cpp.

◆ isUnresolved() [2/2]

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

virtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 132 of file NumericAlphabet.cpp.

◆ operator=()

NumericAlphabet & NumericAlphabet::operator= ( const NumericAlphabet & na )

Definition at line 72 of file NumericAlphabet.cpp.

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

◆ registerState()

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

virtual

Add a state to the Alphabet.

Parameters

st	The state to add.

Exceptions

Exception If a wrong alphabet state is provided.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 93 of file NumericAlphabet.cpp.

References bpp::AbstractAlphabet::registerState().

Referenced by NumericAlphabet().

◆ remap()

void NumericAlphabet::remap ( )

Re-update the maps.

Definition at line 152 of file NumericAlphabet.cpp.

References getSize(), getStateAt(), bpp::AlphabetNumericState::getValue(), bpp::AbstractAlphabet::remap(), and values_.

◆ resize()

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

inlineprotectedinherited

Resize the private alphabet_ vector.

Parameters

size	The new size of the Alphabet.

Definition at line 253 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

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

◆ setState()

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

virtual

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 from bpp::AbstractAlphabet.

Definition at line 81 of file NumericAlphabet.cpp.

References bpp::AbstractAlphabet::setState().

Member Data Documentation

◆ charList_

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

mutableprotectedinherited

Definition at line 99 of file AbstractAlphabet.h.

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

◆ intList_

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

mutableprotectedinherited

Definition at line 100 of file AbstractAlphabet.h.

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

◆ pdd_

const UniformDiscreteDistribution* bpp::NumericAlphabet::pdd_

private

Definition at line 61 of file NumericAlphabet.h.

Referenced by getDelta(), getValueIndex(), NumericAlphabet(), operator=(), and ~NumericAlphabet().

◆ values_

std::map<double, size_t> bpp::NumericAlphabet::values_

private

Definition at line 63 of file NumericAlphabet.h.

Referenced by getNumberOfTypes(), getSize(), getValueIndex(), and remap().

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

Bpp/Seq/Alphabet/NumericAlphabet.h
Bpp/Seq/Alphabet/NumericAlphabet.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NumericAlphabet() [1/2]

◆ ~NumericAlphabet()

◆ NumericAlphabet() [2/2]

Member Function Documentation

◆ charToInt()

◆ clone()

◆ containsGap()

◆ equals()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAlphabetType()

◆ getCharCodeAt()

◆ getDelta()

◆ 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()

◆ getValueIndex()

◆ intToChar()

◆ intToValue()

◆ isCharInAlphabet()

◆ isGap() [1/2]

◆ isGap() [2/2]

◆ isIntInAlphabet()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]

◆ operator=()

◆ registerState()

◆ remap()

◆ resize()

◆ setState()

Member Data Documentation

◆ charList_

◆ intList_

◆ pdd_

◆ values_