bpp::AlphabetState Class Reference

This is the base class to describe states in an Alphabet. More...

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

Inheritance diagram for bpp::AlphabetState:

Collaboration diagram for bpp::AlphabetState:

Public Member Functions
	AlphabetState (int num, const std::string &letter, const std::string &name)
virtual	~AlphabetState ()
int	getNum () const
	Get the state's number. More...
void	setNum (int num)
	Set the state's number. More...
const std::string &	getLetter () const
	Get the letter(s) corresponding to the state. More...
void	setLetter (const std::string &letter)
	Set the letter(s) of the state. More...
const std::string &	getName () const
	Get the name of the state. More...
void	setName (const std::string &name)
	Set the name of the state. More...
bool	operator== (AlphabetState &l2)
	operator == More...
The Clonable interface.
AlphabetState *	clone () const

Private Attributes
int	num_
std::string	letter_
std::string	name_

Detailed Description

This is the base class to describe states in an Alphabet.

Author

Sylvain Gaillard

Definition at line 21 of file AlphabetState.h.

Constructor & Destructor Documentation

AlphabetState()

bpp::AlphabetState::AlphabetState ( int  num, const std::string &  letter, const std::string &  name  )

inline

Definition at line 29 of file AlphabetState.h.

Referenced by clone().

~AlphabetState()

virtual bpp::AlphabetState::~AlphabetState ( )

inlinevirtual

Definition at line 32 of file AlphabetState.h.

Member Function Documentation

clone()

AlphabetState* bpp::AlphabetState::clone ( ) const

inlinevirtual

Implements bpp::Clonable.

Reimplemented in bpp::ProteicAlphabetState, and bpp::NucleicAlphabetState.

Definition at line 39 of file AlphabetState.h.

References AlphabetState().

getLetter()

const std::string& bpp::AlphabetState::getLetter ( ) const

inline

Get the letter(s) corresponding to the state.

The letter is a string because it may more than one char (for instance: codon).

Returns

The state's letter.

Definition at line 63 of file AlphabetState.h.

References letter_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::LexicalAlphabet::getAlphabetType(), bpp::AbstractAlphabet::getCharCodeAt(), bpp::RNY::intToChar(), bpp::LetterAlphabet::registerState(), bpp::LetterAlphabet::setState(), and bpp::AbstractAlphabet::updateMaps_().

getName()

const std::string& bpp::AlphabetState::getName ( ) const

inline

Get the name of the state.

Returns

The full name of the state (i.e. Adenine).

Definition at line 76 of file AlphabetState.h.

References name_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), and bpp::WordAlphabet::getName().

getNum()

int bpp::AlphabetState::getNum ( ) const

inline

Get the state's number.

Returns

The state's number (i.e. -1 for gap (-)).

Definition at line 47 of file AlphabetState.h.

References num_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::AlphabetTools::checkAlphabetCodingSize(), bpp::AbstractAlphabet::getIntCodeAt(), bpp::NucleicAlphabet::getOverlap(), operator==(), bpp::LetterAlphabet::registerState(), bpp::LetterAlphabet::setState(), bpp::NucleicAlphabet::subtract(), and bpp::AbstractAlphabet::updateMaps_().

operator==()

bool bpp::AlphabetState::operator== ( AlphabetState &  l2 )

inline

operator ==

Comparison is done on state num

Definition at line 89 of file AlphabetState.h.

References getNum().

setLetter()

void bpp::AlphabetState::setLetter ( const std::string &  letter )

inline

Set the letter(s) of the state.

Parameters

letter

The state's letter.

Definition at line 69 of file AlphabetState.h.

References letter_.

setName()

void bpp::AlphabetState::setName ( const std::string &  name )

inline

Set the name of the state.

Parameters

name	The state's name

Definition at line 82 of file AlphabetState.h.

References name_.

setNum()

void bpp::AlphabetState::setNum ( int  num )

inline

Set the state's number.

Parameters

num	The state's number.

Definition at line 53 of file AlphabetState.h.

References num_.

Member Data Documentation

letter_

std::string bpp::AlphabetState::letter_

private

Definition at line 25 of file AlphabetState.h.

Referenced by getLetter(), and setLetter().

name_

std::string bpp::AlphabetState::name_

private

Definition at line 26 of file AlphabetState.h.

Referenced by getName(), and setName().

num_

int bpp::AlphabetState::num_

private

Definition at line 24 of file AlphabetState.h.

Referenced by getNum(), and setNum().

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

• Bpp/Seq/Alphabet/AlphabetState.h