This is the base class to describe states in a ProteicAlphabet. More...

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

Inheritance diagram for bpp::ProteicAlphabetState:

Collaboration diagram for bpp::ProteicAlphabetState:

Public Member Functions
	ProteicAlphabetState (int num, const std::string &letter, const std::string &abbr, const std::string &name)

virtual	~ProteicAlphabetState ()

ProteicAlphabetState *	clone () const

const std::string &	getAbbreviation () const
	Get the state's abbreviation. More...

void	setAbbreviation (const std::string &abbr)
	Set the state's abbreviation. More...

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...

Private Attributes
std::string	abbr_

Detailed Description

This is the base class to describe states in a ProteicAlphabet.

Author: Sylvain Gaillard

Definition at line 52 of file ProteicAlphabetState.h.

Constructor & Destructor Documentation

◆ ProteicAlphabetState()

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

inline

Definition at line 57 of file ProteicAlphabetState.h.

Referenced by clone().

◆ ~ProteicAlphabetState()

virtual bpp::ProteicAlphabetState::~ProteicAlphabetState ( )

inlinevirtual

Definition at line 60 of file ProteicAlphabetState.h.

Member Function Documentation

◆ clone()

ProteicAlphabetState* bpp::ProteicAlphabetState::clone ( ) const

inline

Definition at line 63 of file ProteicAlphabetState.h.

References ProteicAlphabetState().

◆ getAbbreviation()

const std::string& bpp::ProteicAlphabetState::getAbbreviation ( ) const

inline

Get the state's abbreviation.

Returns: The state's abbreviation.

Definition at line 71 of file ProteicAlphabetState.h.

References abbr_.

◆ getLetter()

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

inlineinherited

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 99 of file AlphabetState.h.

References bpp::AlphabetState::letter_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::AbstractAlphabet::getCharCodeAt(), and bpp::AbstractAlphabet::updateMaps_().

◆ getName()

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

inlineinherited

Get the name of the state.

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

Definition at line 112 of file AlphabetState.h.

References bpp::AlphabetState::name_.

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

◆ getNum()

int bpp::AlphabetState::getNum ( ) const

inlineinherited

Get the state's number.

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

Definition at line 83 of file AlphabetState.h.

References bpp::AlphabetState::num_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::AbstractAlphabet::getIntCodeAt(), bpp::NucleicAlphabet::getOverlap(), bpp::AlphabetState::operator==(), bpp::NucleicAlphabet::subtract(), and bpp::AbstractAlphabet::updateMaps_().

◆ operator==()

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

inlineinherited

operator ==

Comparison is done on state num

Definition at line 125 of file AlphabetState.h.

References bpp::AlphabetState::getNum().

◆ setAbbreviation()

void bpp::ProteicAlphabetState::setAbbreviation ( const std::string & abbr )

inline

Set the state's abbreviation.

Parameters

abbr	The state's abbreviation.

Definition at line 77 of file ProteicAlphabetState.h.

References abbr_.

◆ setLetter()

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

inlineinherited

Set the letter(s) of the state.

Parameters

letter The state's letter.

Definition at line 105 of file AlphabetState.h.

References bpp::AlphabetState::letter_.

◆ setName()

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

inlineinherited

Set the name of the state.

Parameters

name	The state's name

Definition at line 118 of file AlphabetState.h.

References bpp::AlphabetState::name_.

◆ setNum()

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

inlineinherited

Set the state's number.

Parameters

num	The state's number.

Definition at line 89 of file AlphabetState.h.

References bpp::AlphabetState::num_.

Member Data Documentation

◆ abbr_

std::string bpp::ProteicAlphabetState::abbr_

private

Definition at line 54 of file ProteicAlphabetState.h.

Referenced by getAbbreviation(), and setAbbreviation().

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

Bpp/Seq/Alphabet/ProteicAlphabetState.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProteicAlphabetState()

◆ ~ProteicAlphabetState()

Member Function Documentation

◆ clone()

◆ getAbbreviation()

◆ getLetter()

◆ getName()

◆ getNum()

◆ operator==()

◆ setAbbreviation()

◆ setLetter()

◆ setName()

◆ setNum()

Member Data Documentation

◆ abbr_