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

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

Inheritance diagram for bpp::AbstractAlphabet:

Collaboration diagram for bpp::AbstractAlphabet:

Public Member Functions
	AbstractAlphabet ()
virtual	~AbstractAlphabet ()
virtual std::string	getAlphabetType () const =0
	Identification method.
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).
std::string	getName (const std::string &state) const throw (BadCharException)
	Get the complete name of a state given its string description.
std::string	getName (int state) const throw (BadIntException)
	Get the complete name of a state given its int description.
int	charToInt (const std::string &state) const throw (BadCharException)
	Give the int description of a state given its string description.
std::string	intToChar (int state) const throw (BadIntException)
	Give the string description of a state given its int description.
bool	isIntInAlphabet (int state) const
	Tell if a state (specified by its int description) is allowed by the the alphabet.
bool	isCharInAlphabet (const std::string &state) const
	Tell if a state (specified by its string description) is allowed by the the alphabet.
std::vector< int >	getAlias (int state) const throw (BadIntException)
	Get all resolved states that match a generic state.
std::vector< std::string >	getAlias (const std::string &state) const throw (BadCharException)
	Get all resolved states that match a generic state.
int	getGeneric (const std::vector< int > &states) const throw (BadIntException)
	Get the generic state that match a set of states.
std::string	getGeneric (const std::vector< std::string > &states) const throw (AlphabetException)
	Get the generic state that match a set of states.
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.
const AlphabetState &	getState (int num) const throw (BadIntException)
	Get a state by its num.
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.
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.
Utilitary methods
virtual int	getUnknownCharacterCode () const =0
virtual bool	isUnresolved (int state) const =0
virtual bool	isUnresolved (const std::string &state) const =0
Protected Member Functions
virtual void	registerState (const AlphabetState &st)
	Add a state to the Alphabet.
virtual void	setState (size_t pos, const AlphabetState &st) throw (IndexOutOfBoundsException)
	Set a state in the Alphabet.
void	resize (unsigned int size)
	Resize the private alphabet_ vector.
virtual AlphabetState &	getStateAt (size_t pos) throw (IndexOutOfBoundsException)
	Get a state at a position in the alphabet_ vector.
virtual const AlphabetState &	getStateAt (size_t pos) const throw (IndexOutOfBoundsException)
	Get a state at a position in the alphabet_ vector.
void	remap ()
	Re-update the maps using the alphabet_ vector content.
unsigned int	getStateCodingSize () const
	Get the size of the string coding a state.
Protected Attributes
Available codes
These vectors will be computed the first time you call the getAvailableInts or getAvailableChars method.
std::vector< std::string >	charList_
std::vector< int >	intList_
Private Member Functions
void	updateMaps_ (size_t pos, const AlphabetState &st)
	Update the private maps letters_ and nums_ when adding a state.
Private Attributes
std::vector< AlphabetState * >	alphabet_
	Alphabet: vector of AlphabetState.
maps used to quick search for letter and num.
std::map< std::string, size_t >	letters_
std::map< int, size_t >	nums_

Detailed Description

A partial implementation of the Alphabet interface.

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

See also:: Alphabet

Definition at line 67 of file AbstractAlphabet.h.

Constructor & Destructor Documentation

bpp::AbstractAlphabet::AbstractAlphabet ( ) [inline]

Definition at line 105 of file AbstractAlphabet.h.

virtual bpp::AbstractAlphabet::~AbstractAlphabet ( ) [inline, virtual]

Definition at line 107 of file AbstractAlphabet.h.

References alphabet_.

Member Function Documentation

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

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

Parameters:

state The string description.

Returns:: The int description.

Exceptions:

BadCharException When state is not a valid char description.

Implements bpp::Alphabet.

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

Definition at line 137 of file AbstractAlphabet.cpp.

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

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

Get all resolved states that match a generic state.

If the given state is not a generic code then the output vector will contain this unique code.

Parameters:

state The alias to resolve.

Returns:: A vector of resolved states.

Exceptions:

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::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) [virtual]

Get all resolved states that match a generic state.

If the given state is not a generic code then the output vector will contain this unique code.

Parameters:

state The alias to resolve.

Returns:: A vector of resolved states.

Exceptions:

BadCharException When state is not a valid char description.

Implements bpp::Alphabet.

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

Definition at line 181 of file AbstractAlphabet.cpp.

virtual std::string bpp::Alphabet::getAlphabetType ( ) const [pure virtual, inherited]

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(), and bpp::SequenceTools::invertComplement().

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const [inline, virtual]

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) [virtual]

Get the generic state that match a set of states.

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

Parameters:

states A vector of states to resolve.

Returns:: A int code for the computed state.

Exceptions:

BadIntException When a state is not a valid integer.

Implements bpp::Alphabet.

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

Definition at line 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) [virtual]

Get the generic state that match a set of states.

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

Parameters:

states A vector of states to resolve.

Returns:: A string code for the computed state.

Exceptions:

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

Implements bpp::Alphabet.

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

Definition at line 217 of file AbstractAlphabet.cpp.

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

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

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

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

Parameters:

state The string description of the given state.

Returns:: The name of the state.

Exceptions:

BadCharException When state is not a valid char description.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 123 of file AbstractAlphabet.cpp.

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

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

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

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

Parameters:

state The int description of the given state.

Returns:: The name of the state.

Exceptions:

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Definition at line 130 of file AbstractAlphabet.cpp.

unsigned int bpp::AbstractAlphabet::getNumberOfChars ( ) const [inline, virtual]

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 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 virtual, inherited]

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 virtual, inherited]

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::UserAlphabetIndex1::getIndex(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::CaseMaskedAlphabet::getSize(), bpp::UserAlphabetIndex1::setIndex(), and bpp::SimpleScore::SimpleScore().

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

Get a state by its letter.

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

Parameters:

letter The letter of the state to find.

Exceptions:

BadCharException If the letter is not in the Alphabet.

Implements bpp::Alphabet.

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

Definition at line 89 of file AbstractAlphabet.cpp.

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

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

Get a state by its num.

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

Parameters:

num	The num of the state to find.

Exceptions:

BadIntException If the num is not in the Alphabet.

Implements bpp::Alphabet.

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

Definition at line 98 of file AbstractAlphabet.cpp.

AlphabetState & AbstractAlphabet::getStateAt ( size_t pos ) throw (IndexOutOfBoundsException) [protected, 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:

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.

Referenced by bpp::WordAlphabet::build_(), bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

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

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 [inline, protected, virtual]

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 [virtual]

Returns:: A list of all supported character codes.

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

Implements bpp::Alphabet.

Definition at line 260 of file AbstractAlphabet.cpp.

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

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

Returns:: A list of all supported int codes.

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

Implements bpp::Alphabet.

Definition at line 243 of file AbstractAlphabet.cpp.

virtual int bpp::Alphabet::getUnknownCharacterCode ( ) const [pure virtual, inherited]