bpp::CaseMaskedAlphabet Class Reference

Case-sensitive letter alphabet. More...

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

Inheritance diagram for bpp::CaseMaskedAlphabet:

Collaboration diagram for bpp::CaseMaskedAlphabet:

Public Member Functions
	CaseMaskedAlphabet (const LetterAlphabet *nocaseAlphabet)
	CaseMaskedAlphabet (const CaseMaskedAlphabet &cma)
CaseMaskedAlphabet &	operator= (const CaseMaskedAlphabet &cma)
CaseMaskedAlphabet *	clone () const
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...
std::string	getAlphabetType () const
	Identification method. More...
int	getUnknownCharacterCode () const
bool	isUnresolved (int state) const
bool	isUnresolved (const std::string &state) const
const Alphabet *	getUnmaskedAlphabet () const
bool	isMasked (int state) const
bool	isMasked (const std::string &state) const
bool	isMasked (char state) const
int	getMaskedEquivalentState (int state) const throw (BadIntException)
	Get the masked state equivalent to the input one. More...
const std::string	getMaskedEquivalentState (const std::string &state) const throw (BadCharException, BadIntException)
	Get the masked state equivalent to the input one. More...
bool	isCharInAlphabet (char state) const
bool	isCharInAlphabet (const std::string &state) const
	Tell if a state (specified by its string description) is allowed by the the alphabet. More...
int	charToInt (const std::string &state) const throw (BadCharException)
	Give the int description of a state given its string 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 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...
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...
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)

Public Attributes
const LetterAlphabet *	nocaseAlphabet_

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

Detailed Description

Case-sensitive letter alphabet.

This alphabet is used for parsing comodity. It takes as input another LetterAlphabet and will create duplicate any aphanumerical and upper case state, by creating a lower case version of the state, also named "masked" state. Helper functions are provided to determine whether a given state is masked or unmasked.

Definition at line 59 of file CaseMaskedAlphabet.h.

Constructor & Destructor Documentation

CaseMaskedAlphabet() [1/2]

CaseMaskedAlphabet::CaseMaskedAlphabet

(

const LetterAlphabet *

nocaseAlphabet

)

Definition at line 51 of file CaseMaskedAlphabet.cpp.

References bpp::AlphabetState::clone(), bpp::AlphabetState::getLetter(), bpp::AlphabetState::getName(), bpp::AlphabetState::getNum(), bpp::AbstractAlphabet::getState(), bpp::AbstractAlphabet::getSupportedChars(), nocaseAlphabet_, and bpp::LetterAlphabet::registerState().

Referenced by clone().

CaseMaskedAlphabet() [2/2]

bpp::CaseMaskedAlphabet::CaseMaskedAlphabet ( const CaseMaskedAlphabet &  cma )

inline

Definition at line 68 of file CaseMaskedAlphabet.h.

Member Function Documentation

charToInt()

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

inlinevirtualinherited

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 93 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet(), and bpp::LetterAlphabet::letters_.

Referenced by bpp::AAIndex1Entry::getIndex(), bpp::AAMassIndex::getIndex(), bpp::AASEA1030Index::getIndex(), bpp::AASEAInf10Index::getIndex(), bpp::AASEASup30Index::getIndex(), bpp::AASurfaceIndex::getIndex(), bpp::AAChouFasmanTurnIndex::getIndex(), bpp::AAVolumeIndex::getIndex(), bpp::AAChouFasmanAHelixIndex::getIndex(), bpp::AAChouFasmanBSheetIndex::getIndex(), bpp::AAChenGuHuangHydrophobicityIndex::getIndex(), bpp::GranthamAAPolarityIndex::getIndex(), bpp::KleinAANetChargeIndex::getIndex(), bpp::GranthamAAVolumeIndex::getIndex(), bpp::AAChargeIndex::getIndex(), bpp::NucleicAlphabet::getOverlap(), bpp::ProteicAlphabet::isUnresolved(), bpp::NucleicAlphabet::isUnresolved(), and bpp::NucleicAlphabet::subtract().

clone()

CaseMaskedAlphabet* bpp::CaseMaskedAlphabet::clone ( ) const

inlinevirtual

Implements bpp::LetterAlphabet.

Definition at line 77 of file CaseMaskedAlphabet.h.

References CaseMaskedAlphabet().

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]

std::vector< int > AbstractAlphabet::getAlias ( int  state ) const throw ( BadIntException )

virtualinherited

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 )

virtualinherited

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()

std::string bpp::CaseMaskedAlphabet::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 85 of file CaseMaskedAlphabet.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().

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().

getMaskedEquivalentState() [1/2]

int CaseMaskedAlphabet::getMaskedEquivalentState	(	int	state	)	const
throw	(	BadIntException
	)

Get the masked state equivalent to the input one.

If the input state is masked, returns it "as is".

Parameters

state

The input state.

Exceptions

BadIntException

if the input state is not supported, or if there is no quivallent masked state.

Definition at line 68 of file CaseMaskedAlphabet.cpp.

getMaskedEquivalentState() [2/2]

const string CaseMaskedAlphabet::getMaskedEquivalentState	(	const std::string &	state	)	const
throw	(	BadCharException,
		BadIntException
	)

Get the masked state equivalent to the input one.

If the input state is masked, returns it "as is".

Parameters

state

The input state.

Exceptions

BadCharException	if the input state is not supported.
BadIntException	if there is no equivalent masked state.

Definition at line 82 of file CaseMaskedAlphabet.cpp.

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 bpp::CaseMaskedAlphabet::getNumberOfTypes ( ) const

inlinevirtual

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 84 of file CaseMaskedAlphabet.h.

References bpp::Alphabet::getNumberOfTypes(), and nocaseAlphabet_.

getSize()

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

inlinevirtual

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 83 of file CaseMaskedAlphabet.h.

References bpp::Alphabet::getSize(), and nocaseAlphabet_.

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 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]

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

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

getStateAt() [2/2]

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

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 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

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 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::CaseMaskedAlphabet::getUnknownCharacterCode ( ) const

inlinevirtual

Returns

The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 86 of file CaseMaskedAlphabet.h.

References bpp::Alphabet::getUnknownCharacterCode(), and nocaseAlphabet_.

getUnmaskedAlphabet()

const Alphabet* bpp::CaseMaskedAlphabet::getUnmaskedAlphabet ( ) const

inline

Definition at line 90 of file CaseMaskedAlphabet.h.

References nocaseAlphabet_.

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.

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

isCharInAlphabet() [1/2]

bool bpp::LetterAlphabet::isCharInAlphabet ( char  state ) const

inlineinherited

Definition at line 87 of file LetterAlphabet.h.

References bpp::LetterAlphabet::LETTER_UNDEF_VALUE, and bpp::LetterAlphabet::letters_.

Referenced by bpp::LetterAlphabet::charToInt(), and bpp::LetterAlphabet::isCharInAlphabet().

isCharInAlphabet() [2/2]

bool bpp::LetterAlphabet::isCharInAlphabet ( const std::string &  state ) const

inlinevirtualinherited

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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 90 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet().

isGap() [1/2]

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 160 of file AbstractAlphabet.h.

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.

isMasked() [1/3]

bool bpp::CaseMaskedAlphabet::isMasked ( int  state ) const

inline

Definition at line 92 of file CaseMaskedAlphabet.h.

Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation(), and isMasked().

isMasked() [2/3]

bool bpp::CaseMaskedAlphabet::isMasked ( const std::string &  state ) const

inline

Definition at line 93 of file CaseMaskedAlphabet.h.

References isMasked().

isMasked() [3/3]

bool bpp::CaseMaskedAlphabet::isMasked ( char  state ) const

inline

Definition at line 97 of file CaseMaskedAlphabet.h.

isUnresolved() [1/2]

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

inlinevirtual

Parameters

state

The state to test.

Returns

'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 87 of file CaseMaskedAlphabet.h.

References bpp::Alphabet::isUnresolved(), and nocaseAlphabet_.

isUnresolved() [2/2]

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

inlinevirtual

Parameters

state

The state to test.

Returns

'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 88 of file CaseMaskedAlphabet.h.

References bpp::Alphabet::isUnresolved(), and nocaseAlphabet_.

operator=()

CaseMaskedAlphabet& bpp::CaseMaskedAlphabet::operator= ( const CaseMaskedAlphabet &  cma )

inline

Definition at line 71 of file CaseMaskedAlphabet.h.

References nocaseAlphabet_, and bpp::LetterAlphabet::operator=().

registerState()

void bpp::LetterAlphabet::registerState ( AlphabetState *  st ) throw ( Exception )

inlineprotectedvirtualinherited

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.

Reimplemented in bpp::NucleicAlphabet.

Definition at line 100 of file LetterAlphabet.h.

References bpp::LetterAlphabet::caseSensitive_, bpp::LetterAlphabet::letters_, and bpp::AbstractAlphabet::registerState().

Referenced by CaseMaskedAlphabet(), and bpp::NucleicAlphabet::registerState().

remap()

void bpp::AbstractAlphabet::remap ( )

inlineprotectedinherited

Re-update the maps using the alphabet_ vector content.

Definition at line 258 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 253 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

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

setState()

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

inlineprotectedvirtualinherited

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.

Reimplemented in bpp::NucleicAlphabet.

Definition at line 110 of file LetterAlphabet.h.

References bpp::LetterAlphabet::caseSensitive_, bpp::LetterAlphabet::letters_, and bpp::AbstractAlphabet::setState().

Referenced by bpp::NucleicAlphabet::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=().

nocaseAlphabet_

const LetterAlphabet* bpp::CaseMaskedAlphabet::nocaseAlphabet_

Definition at line 63 of file CaseMaskedAlphabet.h.

Referenced by CaseMaskedAlphabet(), getNumberOfTypes(), getSize(), getUnknownCharacterCode(), getUnmaskedAlphabet(), isUnresolved(), and operator=().

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

• Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
• Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp