The base class for allelic alphabets. More...

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

Inheritance diagram for bpp::AllelicAlphabet:

Collaboration diagram for bpp::AllelicAlphabet:

Classes
class	AllelicTransliterator

Public Member Functions
	AllelicAlphabet (std::shared_ptr< const Alphabet > alph, unsigned int nbAlleles)
	Builds a new word alphabet from an Alphabet. More...

	AllelicAlphabet (const AllelicAlphabet &bia)

AllelicAlphabet *	clone () const override

virtual	~AllelicAlphabet ()

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

unsigned int	getNbAlleles () const
	Returns the number of alleles. More...

std::shared_ptr< const Alphabet >	getStateAlphabet () const
	Returns Base Alphabet. More...

const Alphabet &	stateAlphabet () const

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

int	getUnknownCharacterCode () const override

bool	isUnresolved (int state) const override

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

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...

std::unique_ptr< ProbabilisticSequence >	convertFromStateAlphabet (const CoreSequenceInterface &sequence) const
	Convert a CoreSequence in StateAlphabet to a ProbabilisticSequence of the likelihoods of the di-allelic Alphabet (so if counts are not on only two states, the likelihood is null). More...

void	computeLikelihoods (const Vdouble &counts, Vdouble &likelihoods) const
	Fills the vector of the likelihoods of a vector of counts in the states alphabet, given the di-alleless. More...

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

unsigned int	getSize () const override
	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 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...

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 Alphabet >	alph_

unsigned int	nbAlleles_
	the number of alleles. More...

int	nbUnknown_
	the unknown state number More...

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...

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

The base class for allelic alphabets.

These alphabets are made of unoriented pairs (element from an alphabet, N)^2, such that both numbers sum a given constant number of individuals. The construction is made from a shared_pointer to an AbstractAlphabet.

The strings of the AllelicAlphabet are pairs of the strings of the Alphabets, with the attributed numbers, such that the first element is before the second element in the base Alphabet (such as A3C4, and not C4A3). They are made from the resolved letters of the Alphabets.

The letters are numbered as:

-1 : gap

0 -> alphabet size: alphabet states

(i * (alphabet size) + j) * (nbAlleles-1) + size + k -1 : state

(alphabet size)^2 * (nbAlleles -1) : Unknown "?N?0"

For nucleotides with three alleles, the underlying states are for instance:

_3_0 (-1), A3_0 (0), C3_0 (1), G3_0 (2), T3_0 (3), A2C1 (6), A1C2 (7), A2G1 (8), A1G2 (9), A2T1 (10), A1T2 (11), C2G1 (16), C1G2 (17), C2T1 (18), C1T2 (19), G2T1 (26), G1T2 (27), ?3_0 (32)

Definition at line 49 of file AllelicAlphabet.h.

Constructor & Destructor Documentation

◆ AllelicAlphabet() [1/2]

AllelicAlphabet::AllelicAlphabet	(	std::shared_ptr< const Alphabet >	alph,
		unsigned int	nbAlleles
	)

Builds a new word alphabet from an Alphabet.

Definition at line 16 of file AllelicAlphabet.cpp.

References alph_, nbAlleles_, nbUnknown_, and bpp::AbstractAlphabet::registerState().

Referenced by clone().

◆ AllelicAlphabet() [2/2]

bpp::AllelicAlphabet::AllelicAlphabet ( const AllelicAlphabet & bia )

inline

Definition at line 72 of file AllelicAlphabet.h.

◆ ~AllelicAlphabet()

virtual bpp::AllelicAlphabet::~AllelicAlphabet ( )

inlinevirtual

Definition at line 84 of file AllelicAlphabet.h.

Member Function Documentation

◆ charToInt()

int bpp::AllelicAlphabet::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 92 of file AllelicAlphabet.h.

References bpp::AbstractAlphabet::charToInt(), and getStateCodingSize().

Referenced by isUnresolved(), and bpp::AllelicAlphabet::AllelicTransliterator::translate().

◆ clone()

AllelicAlphabet* bpp::AllelicAlphabet::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractAlphabet.

Definition at line 79 of file AllelicAlphabet.h.

References AllelicAlphabet().

◆ computeLikelihoods()

void AllelicAlphabet::computeLikelihoods	(	const Vdouble &	counts,
		Vdouble &	likelihoods
	)		const

Fills the vector of the likelihoods of a vector of counts in the states alphabet, given the di-alleless.

Definition at line 189 of file AllelicAlphabet.cpp.

References getSize(), getStateAlphabet(), nbAlleles_, and bpp::NumConstants::TINY().

Referenced by convertFromStateAlphabet().

◆ convertFromStateAlphabet()

std::unique_ptr< ProbabilisticSequence > AllelicAlphabet::convertFromStateAlphabet ( const CoreSequenceInterface & sequence ) const

Convert a CoreSequence in StateAlphabet to a ProbabilisticSequence of the likelihoods of the di-allelic Alphabet (so if counts are not on only two states, the likelihood is null).

Parameters

sequence the CoreSequence to be converted.

Gaps are directly translated in vectors of 1.

Definition at line 125 of file AllelicAlphabet.cpp.

References computeLikelihoods(), getAlphabetType(), bpp::Commentable::getComments(), bpp::CoreSequenceInterface::getName(), getSize(), and getStateAlphabet().

◆ 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 > AllelicAlphabet::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 111 of file AllelicAlphabet.cpp.

References bpp::AbstractAlphabet::getState(), bpp::AbstractAlphabet::getSupportedChars(), bpp::AbstractAlphabet::isCharInAlphabet(), nbUnknown_, and bpp::TextTools::toUpper().

◆ getAlias() [2/2]

std::vector< int > AllelicAlphabet::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 98 of file AllelicAlphabet.cpp.

References bpp::AbstractAlphabet::getSupportedInts(), bpp::AbstractAlphabet::isIntInAlphabet(), and nbUnknown_.

◆ getAlphabetType()

std::string AllelicAlphabet::getAlphabetType ( ) const

overridevirtual

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 73 of file AllelicAlphabet.cpp.

References alph_, and nbAlleles_.

Referenced by convertFromStateAlphabet().

◆ 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().

◆ 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.

◆ getGeneric() [1/2]

int bpp::AllelicAlphabet::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 152 of file AllelicAlphabet.h.

◆ getGeneric() [2/2]

std::string bpp::AllelicAlphabet::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 157 of file AllelicAlphabet.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().

◆ 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.

◆ getNbAlleles()

unsigned int bpp::AllelicAlphabet::getNbAlleles ( ) const

inline

Returns the number of alleles.

Definition at line 119 of file AllelicAlphabet.h.

References nbAlleles_.

◆ 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(), getNumberOfTypes(), bpp::WordAlphabet::getNumberOfTypes(), bpp::LexicalAlphabet::getSize(), 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::AllelicAlphabet::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 105 of file AllelicAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars().

◆ 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.

◆ getSize()

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

inlineoverridevirtual

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 100 of file AllelicAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars().

Referenced by computeLikelihoods(), and convertFromStateAlphabet().

◆ 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 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.

◆ getStateAlphabet()

std::shared_ptr<const Alphabet> bpp::AllelicAlphabet::getStateAlphabet ( ) const

inline

Returns Base Alphabet.

Definition at line 127 of file AllelicAlphabet.h.

References alph_.

Referenced by computeLikelihoods(), and convertFromStateAlphabet().

◆ 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::AllelicAlphabet::getStateCodingSize ( ) const

inlineoverrideprivatevirtual

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 232 of file AllelicAlphabet.h.

References alph_, and nbAlleles_.

Referenced by charToInt().

◆ 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 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 getAlias().

◆ getUnknownCharacterCode()

int bpp::AllelicAlphabet::getUnknownCharacterCode ( ) const

inlineoverridevirtual

Returns: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 139 of file AllelicAlphabet.h.

References nbUnknown_.

Referenced by isUnresolved().

◆ 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(), 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(), getAlias(), bpp::WordAlphabet::getAlias(), bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), bpp::BinaryAlphabet::isResolvedIn(), bpp::RNY::isResolvedIn(), isResolvedIn(), and bpp::WordAlphabet::isResolvedIn().

◆ isResolvedIn()

bool AllelicAlphabet::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 81 of file AllelicAlphabet.cpp.

References alph_, bpp::AbstractAlphabet::isIntInAlphabet(), isUnresolved(), and nbAlleles_.

◆ isUnresolved() [1/2]

bool bpp::AllelicAlphabet::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 146 of file AllelicAlphabet.h.

References charToInt(), and getUnknownCharacterCode().

◆ isUnresolved() [2/2]

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

inlineoverridevirtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 144 of file AllelicAlphabet.h.

References getUnknownCharacterCode().

Referenced by isResolvedIn().

◆ 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 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_.

◆ 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().

◆ stateAlphabet()

const Alphabet& bpp::AllelicAlphabet::stateAlphabet ( ) const

inline

Definition at line 132 of file AllelicAlphabet.h.

References alph_.

◆ 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

◆ alph_

std::shared_ptr<const Alphabet> bpp::AllelicAlphabet::alph_

protected

Definition at line 53 of file AllelicAlphabet.h.

Referenced by AllelicAlphabet(), getAlphabetType(), getStateAlphabet(), getStateCodingSize(), isResolvedIn(), and stateAlphabet().

◆ 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().

◆ nbAlleles_

unsigned int bpp::AllelicAlphabet::nbAlleles_

protected

the number of alleles.

Definition at line 58 of file AllelicAlphabet.h.

Referenced by AllelicAlphabet(), computeLikelihoods(), getAlphabetType(), getNbAlleles(), getStateCodingSize(), and isResolvedIn().

◆ nbUnknown_

int bpp::AllelicAlphabet::nbUnknown_

protected

the unknown state number

Definition at line 63 of file AllelicAlphabet.h.

Referenced by AllelicAlphabet(), getAlias(), and getUnknownCharacterCode().

◆ 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/AllelicAlphabet.h
Bpp/Seq/Alphabet/AllelicAlphabet.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AllelicAlphabet() [1/2]

◆ AllelicAlphabet() [2/2]

◆ ~AllelicAlphabet()

Member Function Documentation

◆ charToInt()

◆ clone()

◆ computeLikelihoods()

◆ convertFromStateAlphabet()

◆ equals()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAlphabetType()

◆ getCharCodeAt()

◆ getGapCharacterCode()

◆ getGeneric() [1/2]

◆ getGeneric() [2/2]

◆ getIntCodeAt()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNbAlleles()

◆ getNumberOfChars()

◆ getNumberOfStates()

◆ getNumberOfTypes()

◆ getResolvedChars()

◆ getSize()

◆ getState() [1/4]

◆ getState() [2/4]

◆ getState() [3/4]

◆ getState() [4/4]

◆ getStateAlphabet()

◆ 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()

◆ isResolvedIn()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]

◆ registerState()

◆ remap()

◆ resize()

◆ setState()

◆ stateAlphabet()

◆ updateMaps_()

Member Data Documentation

◆ alph_

◆ alphabet_

◆ charList_

◆ intList_

◆ letters_

◆ nbAlleles_

◆ nbUnknown_

◆ nums_