The base class for word alphabets. More...

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

Inheritance diagram for bpp::WordAlphabet:

Collaboration diagram for bpp::WordAlphabet:

Public Member Functions
	WordAlphabet (const std::vector< const Alphabet * > &vAlpha)
	Builds a new word alphabet from a vector of Alphabets.
	WordAlphabet (const Alphabet *pAlpha, unsigned int num)
	Builds a new word alphabet from a pointer to number of Alphabets.
virtual	~WordAlphabet ()
bool	hasUniqueAlphabet () const
	Returns True if the Alphabet of the letters in the word are the same type.
unsigned int	getLength () const
	Returns the length of the word.
unsigned int	getNumberOfTypes () const
	Returns the number of resolved states + one for unresolved.
std::string	getAlphabetType () const
	Identification method.
int	getUnknownCharacterCode () const
bool	isUnresolved (int state) const
bool	isUnresolved (const std::string &state) const
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 (BadCharException)
	Get the generic state that match a set of states.
Methods redefined from Alphabet
std::string	getName (const std::string &state) const throw (BadCharException)
	Get the complete name of a state given its string description.
int	charToInt (const std::string &state) const throw (BadCharException)
	Give the int description of a state given its string description.
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.
Word specific methods
const Alphabet *	getNAlphabet (size_t n) const
	Get the pointer to the Alphabet of the n-position.
virtual int	getWord (const std::vector< int > &vint, size_t pos=0) const throw (IndexOutOfBoundsException)
	Get the int code for a word given the int code of the underlying positions.
virtual std::string	getWord (const std::vector< std::string > &vpos, size_t pos=0) const throw (IndexOutOfBoundsException, BadCharException)
	Get the char code for a word given the char code of the underlying positions.
int	getNPosition (int word, size_t n) const throw (BadIntException)
	Get the int code of the n-position of a word given its int description.
std::vector< int >	getPositions (int word) const throw (BadIntException)
	Get the int codes of each position of a word given its int description.
std::string	getNPosition (const std::string &word, size_t n) const throw (BadCharException)
	Get the char code of the n-position of a word given its char description.
std::vector< std::string >	getPositions (const std::string &word) const throw (BadCharException)
	Get the char codes of each position of a word given its char description.
Sequence *	translate (const Sequence &sequence, size_t=0) const throw (AlphabetMismatchException, Exception)
	Translate a whole sequence from letters alphabet to words alphabet.
Sequence *	reverse (const Sequence &sequence) const throw (AlphabetMismatchException, Exception)
	Translate a whole sequence from words alphabet to letters alphabet.
Overloaded AbstractAlphabet methods.
unsigned int	getStateCodingSize () const
	Get the size of the string coding a state.
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 (int state) const throw (BadIntException)
	Get the complete name of a state given its int 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.
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.
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.
Protected Attributes
std::vector< const Alphabet * >	vAbsAlph_
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
Inner utilitary functions
bool	containsUnresolved (const std::string &state) const throw (BadCharException)
bool	containsGap (const std::string &state) const throw (BadCharException)
void	build_ ()

Detailed Description

The base class for word alphabets.

These alphabets are compounds of several alphabets. The only constraint on these alphabets is that their words have length one (so it is not possible to make WordAlphabets from other WordAlphabets). The construction is made from a vector of pointers to AbstractAlphabets.

The strings of the WordAlphabet are concatenations of the strings of the Alphabets. They are made from the resolved letters of the Alphabets.

Definition at line 66 of file WordAlphabet.h.

Constructor & Destructor Documentation

WordAlphabet::WordAlphabet ( const std::vector< const Alphabet * > & vAlpha )

Builds a new word alphabet from a vector of Alphabets.

The unit alphabets are not owned by the world alphabet, and won't be destroyed when this instance is destroyed.

Parameters:

vAlpha The vector of Alphabets to be used.

Definition at line 51 of file WordAlphabet.cpp.

References build_().

WordAlphabet::WordAlphabet	(	const Alphabet *	pAlpha,
		unsigned int	num
	)

Builds a new word alphabet from a pointer to number of Alphabets.

Parameters:

pAlpha	The Pointer to the Alphabet to be used.
num	the length of the words.

Definition at line 58 of file WordAlphabet.cpp.

References build_(), and vAbsAlph_.

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

Definition at line 93 of file WordAlphabet.h.

Member Function Documentation

void WordAlphabet::build_ ( ) [private]

Definition at line 70 of file WordAlphabet.cpp.

References getSize(), bpp::AbstractAlphabet::getStateAt(), bpp::AbstractAlphabet::remap(), bpp::AbstractAlphabet::resize(), bpp::AlphabetState::setLetter(), bpp::AbstractAlphabet::setState(), and vAbsAlph_.

Referenced by WordAlphabet().

int bpp::WordAlphabet::charToInt ( const std::string & state ) const throw (BadCharException) [inline, 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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 113 of file WordAlphabet.h.

References containsGap(), containsUnresolved(), getSize(), and vAbsAlph_.

Referenced by bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), getNPosition(), getPositions(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::CodonAlphabet::isInit(), isUnresolved(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

bool WordAlphabet::containsGap ( const std::string & state ) const throw (BadCharException) [private]

Definition at line 169 of file WordAlphabet.cpp.

Referenced by charToInt().

bool WordAlphabet::containsUnresolved ( const std::string & state ) const throw (BadCharException) [private]

Definition at line 151 of file WordAlphabet.cpp.

Referenced by charToInt().

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

Get all resolved states that match a generic state.

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

Parameters:

state The alias to resolve.

Returns:: A vector of resolved states.

Exceptions:

BadIntException When state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 200 of file WordAlphabet.cpp.

std::vector< std::string > WordAlphabet::getAlias ( const std::string & state ) const throw (BadCharException) [virtual]

Get all resolved states that match a generic state.

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

Parameters:

state The alias to resolve.

Returns:: A vector of resolved states.

Exceptions:

BadCharException When state is not a valid char description.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 224 of file WordAlphabet.cpp.

References bpp::TextTools::toUpper().

std::string WordAlphabet::getAlphabetType ( ) const [virtual]

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.

Reimplemented in bpp::CodonAlphabet, bpp::InvertebrateMitochondrialCodonAlphabet, bpp::YeastMitochondrialCodonAlphabet, bpp::EchinodermMitochondrialCodonAlphabet, bpp::VertebrateMitochondrialCodonAlphabet, and bpp::StandardCodonAlphabet.

Definition at line 129 of file WordAlphabet.cpp.

References vAbsAlph_.

Referenced by hasUniqueAlphabet().

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

Returns:: The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 132 of file AbstractAlphabet.h.

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

int WordAlphabet::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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 256 of file WordAlphabet.cpp.

std::string WordAlphabet::getGeneric ( const std::vector< std::string > & states ) const throw (BadCharException) [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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 263 of file WordAlphabet.cpp.

unsigned int bpp::WordAlphabet::getLength ( ) const [inline]

Returns the length of the word.

Definition at line 142 of file WordAlphabet.h.

References vAbsAlph_.

const Alphabet* bpp::WordAlphabet::getNAlphabet ( size_t n ) const [inline]

Get the pointer to the Alphabet of the n-position.

Parameters:

n	The position in the word (starting at 0).

Returns:: The pointer to the Alphabet of the n-position.

Definition at line 195 of file WordAlphabet.h.

References vAbsAlph_.

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

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

In case of undefined characters (i.e. N and X for nucleic alphabets), this method will return the name of the undefined word.

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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 186 of file WordAlphabet.cpp.

References bpp::AbstractAlphabet::getName().

Referenced by bpp::CodonAlphabet::isStop().

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

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.

int bpp::WordAlphabet::getNPosition	(	int	word,
		size_t	n
	)		const throw (BadIntException) `[inline]`

Get the int code of the n-position of a word given its int description.

Parameters:

word	The int description of the word.
n	The position in the word (starting at 0).

Returns:: The int description of the n-position of the word.

Definition at line 233 of file WordAlphabet.h.

References bpp::AbstractAlphabet::intToChar(), and vAbsAlph_.

Referenced by bpp::SequenceContainerTools::getCodonPosition().

std::string bpp::WordAlphabet::getNPosition	(	const std::string &	word,
		size_t	n
	)		const throw (BadCharException) `[inline]`

Get the char code of the n-position of a word given its char description.

Parameters:

word	The char description of the word.
n	The position in the word (starting at 0).

Returns:: The char description of the n-position of the word.

Definition at line 267 of file WordAlphabet.h.

References charToInt(), and vAbsAlph_.

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

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(), getNumberOfTypes(), getSize(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::NucleicAlphabet::registerState(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

unsigned int bpp::WordAlphabet::getNumberOfTypes ( ) const [inline, virtual]

Returns the number of resolved states + one for unresolved.

Implements bpp::Alphabet.

Definition at line 152 of file WordAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars().

std::vector<int> bpp::WordAlphabet::getPositions ( int word ) const throw (BadIntException) [inline]

Get the int codes of each position of a word given its int description.

Parameters:

word	The int description of the word.

Returns:: The int description of the positions of the codon.

Definition at line 249 of file WordAlphabet.h.

References charToInt(), bpp::AbstractAlphabet::intToChar(), and vAbsAlph_.

Referenced by bpp::GeneticCode::isFourFoldDegenerated(), bpp::CodonSiteTools::numberOfSynonymousDifferences(), and bpp::CodonSiteTools::numberOfSynonymousPositions().

std::vector<std::string> bpp::WordAlphabet::getPositions ( const std::string & word ) const throw (BadCharException) [inline]

Get the char codes of each position of a word given its char description.

Parameters:

word	The char description of the word.

Returns:: The char description of the three positions of the word.

Definition at line 285 of file WordAlphabet.h.

References charToInt().

unsigned int bpp::WordAlphabet::getSize ( ) const [inline, virtual]

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

Returns:: The number of resolved states.

Implements bpp::Alphabet.

Definition at line 124 of file WordAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars().

Referenced by build_(), charToInt(), and getUnknownCharacterCode().

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

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, inherited]

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, inherited]

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 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, inherited]

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::WordAlphabet::getStateCodingSize ( ) const [inline, 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

Reimplemented from bpp::AbstractAlphabet.

Definition at line 324 of file WordAlphabet.h.

References vAbsAlph_.

const std::vector< std::string > & AbstractAlphabet::getSupportedChars ( ) const [virtual, inherited]

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, inherited]

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.

int bpp::WordAlphabet::getUnknownCharacterCode ( ) const [inline, virtual]

Returns:: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 158 of file WordAlphabet.h.

References getSize().

Referenced by isUnresolved().

int WordAlphabet::getWord	(	const std::vector< int > &	vint,
		size_t	pos = `0`
	)		const throw (IndexOutOfBoundsException) `[virtual]`

Get the int code for a word given the int code of the underlying positions.

The int code of each position must match the corresponding alphabet specified at this position.

Parameters:

vint	description for all the positions.
pos	the start position to match in the vector.

Returns:: The int code of the word.

Exceptions:

IndexOutOfBoundsException In case of wrong position.

Definition at line 270 of file WordAlphabet.cpp.

std::string WordAlphabet::getWord	(	const std::vector< std::string > &	vpos,
		size_t	pos = `0`
	)		const throw (IndexOutOfBoundsException, BadCharException) `[virtual]`

Get the char code for a word given the char code of the underlying positions.

The char code of each position must match the corresponding alphabet specified at this position.

Parameters:

vpos	vector description for all the positions.
pos	the start position to match in the vector.

Returns:: The string of the word.

Exceptions:

IndexOutOfBoundsException In case of wrong position.

Definition at line 286 of file WordAlphabet.cpp.

bool WordAlphabet::hasUniqueAlphabet ( ) const

Returns True if the Alphabet of the letters in the word are the same type.

Definition at line 140 of file WordAlphabet.cpp.

References getAlphabetType(), and vAbsAlph_.

std::string AbstractAlphabet::intToChar ( int state ) const throw (BadIntException) [virtual, inherited]

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.

Referenced by bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), bpp::RNY::getAlias(), bpp::GeneticCode::getCodingSequence(), getNPosition(), bpp::NucleicAlphabet::getOverlap(), getPositions(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::CodonAlphabet::isStop(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::NucleicAlphabet::subtract(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

bool AbstractAlphabet::isCharInAlphabet ( const std::string & state ) const [virtual, inherited]

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 161 of file AbstractAlphabet.cpp.

bool bpp::AbstractAlphabet::isGap ( int state ) const [inline, virtual, inherited]

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 [inline, virtual, inherited]

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 [virtual, inherited]

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.

bool bpp::WordAlphabet::isUnresolved ( int state ) const [inline, virtual]

Parameters:

state The state to test.

Returns:: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 163 of file WordAlphabet.h.

References getUnknownCharacterCode().

Referenced by bpp::CodonSiteTools::numberOfSynonymousPositions().

bool bpp::WordAlphabet::isUnresolved ( const std::string & state ) const [inline, virtual]

Parameters:

state The state to test.

Returns:: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 164 of file WordAlphabet.h.

References charToInt(), and getUnknownCharacterCode().

void AbstractAlphabet::registerState ( const AlphabetState & st ) [protected, virtual, inherited]

Add a state to the Alphabet.

Parameters:

st	The state to add.

Reimplemented in bpp::LetterAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

Definition at line 65 of file AbstractAlphabet.cpp.

References bpp::AlphabetState::clone().

void bpp::AbstractAlphabet::remap ( ) [inline, protected, inherited]

Re-update the maps using the alphabet_ vector content.

Definition at line 207 of file AbstractAlphabet.h.

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

Referenced by build_().

void bpp::AbstractAlphabet::resize ( unsigned int size ) [inline, protected, inherited]

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(), build_(), bpp::DefaultAlphabet::DefaultAlphabet(), and bpp::RNY::RNY().

Sequence * WordAlphabet::reverse ( const Sequence & sequence ) const throw (AlphabetMismatchException, Exception)

Translate a whole sequence from words alphabet to letters alphabet.

Parameters:

sequence A sequence in words alphabet.

Returns:: The corresponding sequence in letters alphabet.

Exceptions:

AlphabetMismatchException	If the sequence alphabet do not match the target alphabet.
Exception	Other kind of error, depending on the implementation.

Definition at line 327 of file WordAlphabet.cpp.

References bpp::Sequence::append(), and bpp::BasicSymbolList::size().

void AbstractAlphabet::setState	(	size_t	pos,
		const AlphabetState &	st
	)		throw (IndexOutOfBoundsException) `[protected, virtual, inherited]`

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 in bpp::LetterAlphabet.

Definition at line 74 of file AbstractAlphabet.cpp.

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

Sequence * WordAlphabet::translate	(	const Sequence &	sequence,
		size_t	pos = `0`
	)		const throw (AlphabetMismatchException, Exception)

Translate a whole sequence from letters alphabet to words alphabet.

Parameters:

sequence	A sequence in letters alphabet.
pos	the start postion (default 0)

Returns:: The corresponding sequence in words alphabet.

Exceptions:

AlphabetMismatchException	If the sequence alphabet do not match the source alphabet.
Exception	Other kind of error, depending on the implementation.

Definition at line 303 of file WordAlphabet.cpp.

Member Data Documentation

std::vector<std::string> bpp::AbstractAlphabet::charList_ [mutable, protected, inherited]

Definition at line 99 of file AbstractAlphabet.h.

std::vector<int> bpp::AbstractAlphabet::intList_ [mutable, protected, inherited]

Definition at line 100 of file AbstractAlphabet.h.

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

Bpp/Seq/Alphabet/WordAlphabet.h
Bpp/Seq/Alphabet/WordAlphabet.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation