This alphabet is used to deal with RNA sequences. More...

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

Inheritance diagram for bpp::RNA:

Collaboration diagram for bpp::RNA:

Public Member Functions
	RNA (bool exclamationMarkCountsAsGap=false)
virtual	~RNA ()
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.
std::string	getAlphabetType () const
	Identification method.
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.
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.
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.
int	charToInt (const std::string &state) const throw (BadCharException)
	Give the int description of a state given its string description.
Specific methods
const NucleicAlphabetState &	getStateByBinCode (int code) const throw (BadIntException)
	Get a state by its binary representation.
int	subtract (int s1, int s2) const throw (BadIntException)
	Subtract states.
std::string	subtract (const std::string &s1, const std::string &s2) const throw (BadCharException)
	Subtract states.
int	getOverlap (int s1, int s2) const throw (BadIntException)
	Get the overlap between to states.
std::string	getOverlap (const std::string &s1, const std::string &s2) const throw (BadCharException)
	Get the overlap between to states.
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.
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.
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.
void	setState (size_t pos, const AlphabetState &st) throw (IndexOutOfBoundsException)
	Set a state in the Alphabet.
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	resize (unsigned int size)
	Resize the private 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_
Overloaded methods from AbstractAlphabet
const NucleicAlphabetState &	getState (const std::string &letter) const throw (BadCharException)
	Get a state by its letter.
const NucleicAlphabetState &	getState (int num) const throw (BadIntException)
	Get a state by its num.
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

This alphabet is used to deal with RNA sequences.

It supports all 4 nucleotides (A, U, G and C) with their standard denomination. Gaps are coded by '-', unresolved characters are coded by 'X, N, O, 0 or ?'. Extensive support for generic characters (e.g. 'P', 'Y', etc.) is provided.

Definition at line 58 of file RNA.h.

Constructor & Destructor Documentation

RNA::RNA ( bool exclamationMarkCountsAsGap = false )

Parameters:

exclamationMarkCountsAsGap If yes, '!' characters are replaced by gaps. Otherwise, they are counted as unknown characters.

Definition at line 55 of file RNA.cpp.

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

Definition at line 67 of file RNA.h.

Member Function Documentation

int bpp::LetterAlphabet::charToInt ( const std::string & state ) const throw (BadCharException) [inline, virtual, inherited]

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 > RNA::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 90 of file RNA.cpp.

References bpp::NucleicAlphabetState::getBinaryCode().

std::vector< std::string > RNA::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 112 of file RNA.cpp.

References bpp::TextTools::toUpper().

std::string bpp::RNA::getAlphabetType ( ) const [inline, 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.

Definition at line 74 of file RNA.h.

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 RNA::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 125 of file RNA.cpp.

std::string RNA::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 137 of file RNA.cpp.

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

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, 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.

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

unsigned int bpp::NucleicAlphabet::getNumberOfTypes ( ) const [inline, 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.

Implements bpp::Alphabet.

Definition at line 247 of file NucleicAlphabet.h.

int bpp::NucleicAlphabet::getOverlap	(	int	s1,
		int	s2
	)		const throw (BadIntException) `[inline, inherited]`

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(), bpp::NucleicAlphabet::getState(), and bpp::NucleicAlphabet::getStateByBinCode().

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

std::string bpp::NucleicAlphabet::getOverlap	(	const std::string &	s1,
		const std::string &	s2
	)		const throw (BadCharException) `[inline, inherited]`

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(), bpp::NucleicAlphabet::getOverlap(), and bpp::AbstractAlphabet::intToChar().

unsigned int bpp::NucleicAlphabet::getSize ( ) const [inline, 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.

Implements bpp::Alphabet.

Definition at line 244 of file NucleicAlphabet.h.

const NucleicAlphabetState& bpp::NucleicAlphabet::getState ( const std::string & letter ) const throw (BadCharException) [inline, 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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 107 of file NucleicAlphabet.h.

Referenced by bpp::NucleicAlphabet::getOverlap(), bpp::NucleicAlphabet::getState(), and bpp::NucleicAlphabet::subtract().

const NucleicAlphabetState& bpp::NucleicAlphabet::getState ( int num ) const throw (BadIntException) [inline, 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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 113 of file NucleicAlphabet.h.

References bpp::NucleicAlphabet::getState().

const NucleicAlphabetState& bpp::NucleicAlphabet::getStateAt ( unsigned int pos ) const throw (IndexOutOfBoundsException) [inline, protected, inherited]

Definition at line 88 of file NucleicAlphabet.h.

Referenced by bpp::NucleicAlphabet::getStateAt(), and bpp::NucleicAlphabet::getStateByBinCode().

NucleicAlphabetState& bpp::NucleicAlphabet::getStateAt ( unsigned int pos ) throw (IndexOutOfBoundsException) [inline, protected, inherited]

Definition at line 94 of file NucleicAlphabet.h.

References bpp::NucleicAlphabet::getStateAt().

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 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, 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.

const NucleicAlphabetState& bpp::NucleicAlphabet::getStateByBinCode ( int code ) const throw (BadIntException) [inline, inherited]

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 bpp::NucleicAlphabet::binCodes_, and bpp::NucleicAlphabet::getStateAt().

Referenced by bpp::NucleicAlphabet::getOverlap(), and bpp::NucleicAlphabet::subtract().

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

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, 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::NucleicAlphabet::getUnknownCharacterCode ( ) const [inline, virtual, inherited]

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) [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.

bool bpp::LetterAlphabet::isCharInAlphabet ( char state ) const [inline, inherited]

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 [inline, 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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 73 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet().

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::NucleicAlphabet::isUnresolved ( int state ) const [inline, virtual, inherited]

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 [inline, virtual, inherited]

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 ) [inline, protected, inherited]

Definition at line 80 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars(), and bpp::NucleicAlphabet::updateMaps_().

void bpp::LetterAlphabet::registerState ( const AlphabetState & st ) [inline, protected, virtual, inherited]

Add a state to the Alphabet.

Parameters:

st	The state to add.

Reimplemented from bpp::AbstractAlphabet.

Reimplemented in bpp::DefaultAlphabet.

Definition at line 83 of file LetterAlphabet.h.

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

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

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

void bpp::NucleicAlphabet::setState	(	unsigned int	pos,
		const NucleicAlphabetState &	st
	)		`[inline, protected, inherited]`

Definition at line 84 of file NucleicAlphabet.h.

References bpp::NucleicAlphabet::updateMaps_().

void bpp::LetterAlphabet::setState	(	size_t	pos,
		const AlphabetState &	st
	)		throw (IndexOutOfBoundsException) `[inline, 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 from bpp::AbstractAlphabet.

Definition at line 93 of file LetterAlphabet.h.

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

Referenced by bpp::DefaultAlphabet::DefaultAlphabet().

int bpp::NucleicAlphabet::subtract	(	int	s1,
		int	s2
	)		const throw (BadIntException) `[inline, inherited]`

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(), bpp::NucleicAlphabet::getState(), and bpp::NucleicAlphabet::getStateByBinCode().

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

std::string bpp::NucleicAlphabet::subtract	(	const std::string &	s1,
		const std::string &	s2
	)		const throw (BadCharException) `[inline, inherited]`

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(), bpp::AbstractAlphabet::intToChar(), and bpp::NucleicAlphabet::subtract().

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/RNA.h
Bpp/Seq/Alphabet/RNA.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Overloaded methods from AbstractAlphabet

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation