Specialized partial implementation of Alphabet using single letters. More...

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

Inheritance diagram for bpp::LetterAlphabet:

Collaboration diagram for bpp::LetterAlphabet:

Public Member Functions
	LetterAlphabet (bool caseSensitive=false)

virtual	~LetterAlphabet ()

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...

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

Implement these methods from the Alphabet interface.
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
const AlphabetState &	getState (const std::string &letter) const throw (BadCharException)
	Get a state by its letter. More...

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

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
void	registerState (const AlphabetState &st)
	Add a state to the Alphabet. More...

void	setState (size_t pos, const AlphabetState &st) throw (IndexOutOfBoundsException)
	Set a state in the Alphabet. More...

void	resize (unsigned int size)
	Resize the private alphabet_ vector. More...

virtual AlphabetState &	getStateAt (size_t pos) throw (IndexOutOfBoundsException)
	Get a state at a position in the alphabet_ vector. More...

virtual const AlphabetState &	getStateAt (size_t pos) const throw (IndexOutOfBoundsException)
	Get a state at a position in the 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...

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
std::vector< int >	letters_

bool	caseSensitive_

Static Private Attributes
static const int	LETTER_UNDEF_VALUE = -99

Detailed Description

Specialized partial implementation of Alphabet using single letters.

Author: Sylvain Gaillard

Definition at line 57 of file LetterAlphabet.h.

Constructor & Destructor Documentation

bpp::LetterAlphabet::LetterAlphabet ( bool caseSensitive = false )

inline

Definition at line 66 of file LetterAlphabet.h.

virtual bpp::LetterAlphabet::~LetterAlphabet ( )

inlinevirtual

Definition at line 67 of file LetterAlphabet.h.

Member Function Documentation

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

inlinevirtual

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 76 of file LetterAlphabet.h.

References isCharInAlphabet(), and letters_.

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::DNA, and bpp::RNA.

Definition at line 171 of file AbstractAlphabet.cpp.

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::DNA, and bpp::RNA.

Definition at line 181 of file AbstractAlphabet.cpp.

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::CodonAlphabet, bpp::RNY, bpp::CaseMaskedAlphabet, bpp::DNA, bpp::RNA, bpp::DefaultAlphabet, bpp::BinaryAlphabet, bpp::InvertebrateMitochondrialCodonAlphabet, bpp::YeastMitochondrialCodonAlphabet, bpp::EchinodermMitochondrialCodonAlphabet, bpp::VertebrateMitochondrialCodonAlphabet, and bpp::StandardCodonAlphabet.

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

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 132 of file AbstractAlphabet.h.

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

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 191 of file AbstractAlphabet.cpp.

References bpp::MapTools::getKeys(), and bpp::TextTools::toString().

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 217 of file AbstractAlphabet.cpp.

References bpp::MapTools::getKeys(), and bpp::TextTools::toString().

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 123 of file AbstractAlphabet.cpp.

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

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 130 of file AbstractAlphabet.cpp.

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 119 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), bpp::WordAlphabet::getNumberOfTypes(), bpp::WordAlphabet::getSize(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::NucleicAlphabet::registerState(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

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::CaseMaskedAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

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

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::CaseMaskedAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

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

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 89 of file AbstractAlphabet.cpp.

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

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 98 of file AbstractAlphabet.cpp.

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

protectedvirtualinherited

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

pos	The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If pos is out of the vector.

Definition at line 107 of file AbstractAlphabet.cpp.

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

protectedvirtualinherited

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

pos	The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If pos is out of the vector.

Definition at line 115 of file AbstractAlphabet.cpp.

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 213 of file AbstractAlphabet.h.

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 260 of file AbstractAlphabet.cpp.

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

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 243 of file AbstractAlphabet.cpp.

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::CaseMaskedAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

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

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 144 of file AbstractAlphabet.cpp.

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

inline

Definition at line 70 of file LetterAlphabet.h.

References LETTER_UNDEF_VALUE, and letters_.

Referenced by charToInt(), and isCharInAlphabet().

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

inlinevirtual

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 73 of file LetterAlphabet.h.

References isCharInAlphabet().

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.

Definition at line 133 of file AbstractAlphabet.h.

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 134 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

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 151 of file AbstractAlphabet.cpp.

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::CaseMaskedAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

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

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::CaseMaskedAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

void bpp::LetterAlphabet::registerState ( const AlphabetState & st )

inlineprotectedvirtual

Add a state to the Alphabet.

Parameters

st	The state to add.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 83 of file LetterAlphabet.h.

References caseSensitive_, bpp::AlphabetState::getLetter(), bpp::AlphabetState::getLetter(), bpp::AlphabetState::getLetter(), bpp::AlphabetState::getNum(), bpp::AlphabetState::getNum(), bpp::AlphabetState::getNum(), letters_, letters_, letters_, and bpp::AbstractAlphabet::registerState().

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

void bpp::AbstractAlphabet::remap ( )

inlineprotectedinherited

Re-update the maps using the alphabet_ vector content.

Definition at line 207 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_, bpp::AbstractAlphabet::alphabet_, and bpp::AbstractAlphabet::updateMaps_().

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

void bpp::AbstractAlphabet::resize ( unsigned int size )

inlineprotectedinherited

Resize the private alphabet_ vector.

Parameters

size	The new size of the Alphabet.

Definition at line 182 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::BinaryAlphabet::BinaryAlphabet(), bpp::WordAlphabet::build_(), bpp::DefaultAlphabet::DefaultAlphabet(), and bpp::RNY::RNY().

void bpp::LetterAlphabet::setState	(	size_t	pos,
		const AlphabetState &	st
	)		throw (IndexOutOfBoundsException)

inlineprotectedvirtual

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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 93 of file LetterAlphabet.h.

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

Referenced by bpp::DefaultAlphabet::DefaultAlphabet(), bpp::DefaultAlphabet::DefaultAlphabet(), and bpp::NucleicAlphabet::setState().

Member Data Documentation

bool bpp::LetterAlphabet::caseSensitive_

private

Definition at line 63 of file LetterAlphabet.h.

Referenced by registerState(), and setState().

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

mutableprotectedinherited

Definition at line 99 of file AbstractAlphabet.h.

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

mutableprotectedinherited

Definition at line 100 of file AbstractAlphabet.h.

const int bpp::LetterAlphabet::LETTER_UNDEF_VALUE = -99

staticprivate

Definition at line 61 of file LetterAlphabet.h.

Referenced by isCharInAlphabet().

std::vector<int> bpp::LetterAlphabet::letters_

private

Definition at line 62 of file LetterAlphabet.h.

Referenced by charToInt(), isCharInAlphabet(), registerState(), registerState(), registerState(), setState(), setState(), and setState().

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

Bpp/Seq/Alphabet/LetterAlphabet.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation