The abstract base class for nucleic alphabets. More...

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

Inheritance diagram for bpp::NucleicAlphabet:

Collaboration diagram for bpp::NucleicAlphabet:

Public Member Functions
	NucleicAlphabet ()

virtual	~NucleicAlphabet ()

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...

int	getUnknownCharacterCode () const

bool	isUnresolved (int state) const

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

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...

Specific methods
const NucleicAlphabetState &	getStateByBinCode (int code) const throw (BadIntException)
	Get a state by its binary representation. More...

int	subtract (int s1, int s2) const throw (BadIntException)
	Subtract states. More...

std::string	subtract (const std::string &s1, const std::string &s2) const throw (BadCharException)
	Subtract states. More...

int	getOverlap (int s1, int s2) const throw (BadIntException)
	Get the overlap between to states. More...

std::string	getOverlap (const std::string &s1, const std::string &s2) const throw (BadCharException)
	Get the overlap between to states. 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

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 Member Functions
void	updateMaps_ (int pos, const NucleicAlphabetState &st)

Private Attributes
std::map< int, unsigned int >	binCodes_

Overloaded methods from AbstractAlphabet
const NucleicAlphabetState &	getState (const std::string &letter) const throw (BadCharException)
	Get a state by its letter. More...

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

void	registerState (const NucleicAlphabetState &st)

void	setState (unsigned int pos, const NucleicAlphabetState &st)

const NucleicAlphabetState &	getStateAt (unsigned int pos) const throw (IndexOutOfBoundsException)

NucleicAlphabetState &	getStateAt (unsigned int pos) throw (IndexOutOfBoundsException)

Detailed Description

The abstract base class for nucleic alphabets.

This class only implements a few methods, it is mainly designed for methods/classes that will require to work with both RNA and DNA.

Definition at line 60 of file NucleicAlphabet.h.

Constructor & Destructor Documentation

bpp::NucleicAlphabet::NucleicAlphabet ( )

inline

Definition at line 71 of file NucleicAlphabet.h.

virtual bpp::NucleicAlphabet::~NucleicAlphabet ( )

inlinevirtual

Definition at line 73 of file NucleicAlphabet.h.

Member Function Documentation

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 76 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet(), and bpp::LetterAlphabet::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(), registerState(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

unsigned int bpp::NucleicAlphabet::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 247 of file NucleicAlphabet.h.

int bpp::NucleicAlphabet::getOverlap	(	int	s1,
		int	s2
	)		const throw (BadIntException)

inline

Get the overlap between to states.

Get the overlapping states between two steps.

int m = alpha->charToInt("M");
int r = alpha->charToInt("R");
int a = alpha->getOverlap(m, r);
cout << alpha->intToChar(a) << endl;
// should print A because M = A/C and R = A/G

Parameters

s1	the first state as an int
s2	the second state as an int

Exceptions

BadIntException if one of the states is not valid

Returns: The overlapping state

Author: Sylvain Gaillard

Definition at line 212 of file NucleicAlphabet.h.

References bpp::AlphabetState::getNum(), getState(), and getStateByBinCode().

Referenced by getOverlap().

std::string bpp::NucleicAlphabet::getOverlap	(	const std::string &	s1,
		const std::string &	s2
	)		const throw (BadCharException)

inline

Get the overlap between to states.

Get the overlapping states between two steps.

string m = "M";
string r = R;
cout << alpha->getOverlap(m, r) << endl;
// should print A because M = A/C and R = A/G

Parameters

s1	the first state as a string
s2	the second state as a string

Exceptions

BadCharException if one of the states is not valid

Returns: The overlapping state

Author: Sylvain Gaillard

Definition at line 236 of file NucleicAlphabet.h.

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

unsigned int bpp::NucleicAlphabet::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 244 of file NucleicAlphabet.h.

const NucleicAlphabetState& bpp::NucleicAlphabet::getState ( const std::string & letter ) const throw (BadCharException)

inlinevirtual

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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 107 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getState().

Referenced by getOverlap(), getOverlap(), subtract(), and subtract().

const NucleicAlphabetState& bpp::NucleicAlphabet::getState ( int num ) const throw (BadIntException)

inlinevirtual

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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 113 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getState().

const NucleicAlphabetState& bpp::NucleicAlphabet::getStateAt ( unsigned int pos ) const throw (IndexOutOfBoundsException)

inlineprotected

Definition at line 88 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getStateAt().

Referenced by getStateByBinCode().

NucleicAlphabetState& bpp::NucleicAlphabet::getStateAt ( unsigned int pos ) throw (IndexOutOfBoundsException)

inlineprotected

Definition at line 94 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getStateAt().

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.

const NucleicAlphabetState& bpp::NucleicAlphabet::getStateByBinCode ( int code ) const throw (BadIntException)

inline

Get a state by its binary representation.

Parameters

code	The binary representation as an unsigned char.

Returns: The NucleicAlphabetState.

Exceptions

BadIntException If the code is not a valide state.

Author: Sylvain Gaillard

Definition at line 134 of file NucleicAlphabet.h.

References binCodes_, binCodes_, and getStateAt().

Referenced by getOverlap(), and subtract().

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.

int bpp::NucleicAlphabet::getUnknownCharacterCode ( ) const

inlinevirtual

Returns: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 249 of file NucleicAlphabet.h.

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

inlineinherited

Definition at line 70 of file LetterAlphabet.h.

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

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

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 73 of file LetterAlphabet.h.

References bpp::LetterAlphabet::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.

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

inlinevirtual

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 251 of file NucleicAlphabet.h.

bool bpp::NucleicAlphabet::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 252 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::charToInt().

void bpp::NucleicAlphabet::registerState ( const NucleicAlphabetState & st )

inlineprotected

Definition at line 80 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::registerState(), and updateMaps_().

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

inlineprotectedvirtualinherited

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

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), and 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::NucleicAlphabet::setState	(	unsigned int	pos,
		const NucleicAlphabetState &	st
	)

inlineprotected

Definition at line 84 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::setState(), and updateMaps_().

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

Reimplemented from bpp::AbstractAlphabet.

Definition at line 93 of file LetterAlphabet.h.

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

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

int bpp::NucleicAlphabet::subtract	(	int	s1,
		int	s2
	)		const throw (BadIntException)

inline

Subtract states.

Get the remaining state when subtracting one state to another.

int a = alpha->charToInt("A");
int m = alpha->charToInt("M");
int c = alpha->subtract(m, a);
cout << alpha->intToChar(c) << endl;
// should print C because M - A = C

Parameters

s1	the first state as an int
s2	the second state as an int

Exceptions

BadIntException if one of the states is not valide.

Returns: The remaining state as an int

Author: Sylvain Gaillard

Definition at line 163 of file NucleicAlphabet.h.

References bpp::AlphabetState::getNum(), getState(), and getStateByBinCode().

Referenced by subtract().

std::string bpp::NucleicAlphabet::subtract	(	const std::string &	s1,
		const std::string &	s2
	)		const throw (BadCharException)

inline

Subtract states.

Get the remaining state when subtracting one state to another.

string a = "A";
string m = "M";
cout << alpha->subtract(m, a) << endl;
// should print C because M - A = C

Parameters

s1	the first state as a string
s2	the second state as a string

Exceptions

BadCharException if one of the states is not valide.

Returns: The remaining state as a string

Author: Sylvain Gaillard

Definition at line 187 of file NucleicAlphabet.h.

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

void bpp::NucleicAlphabet::updateMaps_	(	int	pos,
		const NucleicAlphabetState &	st
	)

inlineprivate

Definition at line 65 of file NucleicAlphabet.h.

References binCodes_, binCodes_, binCodes_, bpp::NucleicAlphabetState::getBinaryCode(), and bpp::NucleicAlphabetState::getBinaryCode().

Referenced by registerState(), and setState().

Member Data Documentation

std::map<int, unsigned int> bpp::NucleicAlphabet::binCodes_

private

Definition at line 64 of file NucleicAlphabet.h.

Referenced by getStateByBinCode(), getStateByBinCode(), updateMaps_(), updateMaps_(), and updateMaps_().

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.

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

Bpp/Seq/Alphabet/NucleicAlphabet.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Overloaded methods from AbstractAlphabet

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation