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

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

Inheritance diagram for bpp::NucleicAlphabetState:

Collaboration diagram for bpp::NucleicAlphabetState:

Public Member Functions
	NucleicAlphabetState (int num, const std::string &letter, unsigned char code, const std::string &name)

virtual	~NucleicAlphabetState ()

NucleicAlphabetState *	clone () const

int	getBinaryCode () const
	Get the state's binary representation. More...

void	setBinaryCode (int code)
	Set the state's binary representation. 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
int	binCode_

int	num_

std::string	letter_

std::string	name_

Detailed Description

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

This class store a binary code for each state. This binary code is of length 4, one bit per nucleotid. For DNA alphabet, this code looks like this:

Letter	Binary code	int value
-	0000	0
A	0001	1
C	0010	2
G	0100	4
T	1000	8
N	1111	15
...
M	0011	3
W	1001	9
...
V	0111	7

This notation allows the use of bitwize operations like:

build a generic state from to states
A | G = R <=> 0001 | 0100 = 0101
extract a state from an unresolved one by subtraction of an other state
S & ~ C = G <=> 0110 & ~ 0010 = 0100

The binary code is stored as a char because it's the smallest memory word that can be allocated. A char is 8 bits long allowing the use of this class with Alphabet of at least 8 resolved states (enough for known nucleic alphabets!).

Author: Sylvain Gaillard

Definition at line 52 of file NucleicAlphabetState.h.

Constructor & Destructor Documentation

◆ NucleicAlphabetState()

bpp::NucleicAlphabetState::NucleicAlphabetState	(	int	num,
		const std::string &	letter,
		unsigned char	code,
		const std::string &	name
	)

inline

Definition at line 58 of file NucleicAlphabetState.h.

Referenced by clone().

◆ ~NucleicAlphabetState()

virtual bpp::NucleicAlphabetState::~NucleicAlphabetState ( )

inlinevirtual

Definition at line 62 of file NucleicAlphabetState.h.

Member Function Documentation

◆ clone()

NucleicAlphabetState* bpp::NucleicAlphabetState::clone ( ) const

inlinevirtual

Reimplemented from bpp::AlphabetState.

Definition at line 65 of file NucleicAlphabetState.h.

References NucleicAlphabetState().

◆ getBinaryCode()

int bpp::NucleicAlphabetState::getBinaryCode ( ) const

inline

Get the state's binary representation.

Returns: The state's binary representation.

Definition at line 74 of file NucleicAlphabetState.h.

References binCode_.

Referenced by bpp::DNA::getAlias(), bpp::RNA::getAlias(), bpp::DNA::isResolvedIn(), bpp::RNA::isResolvedIn(), and bpp::NucleicAlphabet::updateBinMaps_().

◆ 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 63 of file AlphabetState.h.

References bpp::AlphabetState::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

inlineinherited

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 bpp::AlphabetState::name_.

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

◆ 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 47 of file AlphabetState.h.

References bpp::AlphabetState::num_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::AlphabetTools::checkAlphabetCodingSize(), bpp::AbstractAlphabet::getIntCodeAt(), bpp::NucleicAlphabet::getOverlap(), bpp::AlphabetState::operator==(), bpp::LetterAlphabet::registerState(), bpp::LetterAlphabet::setState(), 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 89 of file AlphabetState.h.

References bpp::AlphabetState::getNum().

◆ setBinaryCode()

void bpp::NucleicAlphabetState::setBinaryCode ( int code )

inline

Set the state's binary representation.

Parameters

code	The state's binary representation.

Definition at line 80 of file NucleicAlphabetState.h.

References binCode_.

◆ 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 69 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 82 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 53 of file AlphabetState.h.

References bpp::AlphabetState::num_.

Member Data Documentation

◆ binCode_

int bpp::NucleicAlphabetState::binCode_

private

Definition at line 55 of file NucleicAlphabetState.h.

Referenced by getBinaryCode(), and setBinaryCode().

◆ letter_

std::string bpp::AlphabetState::letter_

privateinherited

Definition at line 25 of file AlphabetState.h.

Referenced by bpp::AlphabetState::getLetter(), and bpp::AlphabetState::setLetter().

◆ name_

std::string bpp::AlphabetState::name_

privateinherited

Definition at line 26 of file AlphabetState.h.

Referenced by bpp::AlphabetState::getName(), and bpp::AlphabetState::setName().

◆ num_

int bpp::AlphabetState::num_

privateinherited

Definition at line 24 of file AlphabetState.h.

Referenced by bpp::AlphabetState::getNum(), and bpp::AlphabetState::setNum().

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

Bpp/Seq/Alphabet/NucleicAlphabetState.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NucleicAlphabetState()

◆ ~NucleicAlphabetState()

Member Function Documentation

◆ clone()

◆ getBinaryCode()

◆ getLetter()

◆ getName()

◆ getNum()

◆ operator==()

◆ setBinaryCode()

◆ setLetter()

◆ setName()

◆ setNum()

Member Data Documentation

◆ binCode_

◆ letter_

◆ name_

◆ num_