seq::AminoAcid Class Reference

An amino acid. More...

#include <AminoAcid.h>

List of all members.

Public Member Functions
	AminoAcid ()
	Create an amino acid with value AminoAcid::X (any).
	AminoAcid (char c) throw (ParseException)
	Create an amino acid by parsing a character.
char	toChar () const
	Get the uppercase character representation for this amino acid.
std::string	tla () const
	Get the three letter abbreviation for this amino acid.
int	intRep () const
	Get the internal representation.
bool	operator== (const AminoAcid other) const
	Are two amino acids identical ?
bool	operator!= (const AminoAcid other) const
	Are two amino acids different ?
bool	operator< (const AminoAcid other) const
	So that you can use it as a key for STL containers.
Static Public Member Functions
static AminoAcid	fromRep (int rep)
	Create an amino acid using the internal representation directly.
Static Public Attributes
Constants used in the internal representation.
See also: intRep() and fromRep(int).
static const int	AA_A = 0
static const int	AA_C = 1
static const int	AA_D = 2
static const int	AA_E = 3
static const int	AA_F = 4
static const int	AA_G = 5
static const int	AA_H = 6
static const int	AA_I = 7
static const int	AA_K = 8
static const int	AA_L = 9
static const int	AA_M = 10
static const int	AA_N = 11
static const int	AA_P = 12
static const int	AA_Q = 13
static const int	AA_R = 14
static const int	AA_S = 15
static const int	AA_T = 16
static const int	AA_V = 17
static const int	AA_W = 18
static const int	AA_Y = 19
static const int	AA_STP = 20
static const int	AA_GAP = 21
static const int	AA_Z = 22
static const int	AA_U = 23
static const int	AA_B = 24
static const int	AA_X = 25
AminoAcid constants.
static const AminoAcid	A
static const AminoAcid	C
static const AminoAcid	D
static const AminoAcid	E
static const AminoAcid	F
static const AminoAcid	G
static const AminoAcid	H
static const AminoAcid	I
static const AminoAcid	K
static const AminoAcid	L
static const AminoAcid	M
static const AminoAcid	N
static const AminoAcid	P
static const AminoAcid	Q
static const AminoAcid	R
static const AminoAcid	S
static const AminoAcid	T
static const AminoAcid	V
static const AminoAcid	W
static const AminoAcid	Y
static const AminoAcid	STP
static const AminoAcid	GAP
static const AminoAcid	Z
static const AminoAcid	U
static const AminoAcid	B
static const AminoAcid	X

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Detailed Description

An amino acid.

The amino acid is represented internally using an integer representation. This may be helpful for e.g. indexing into an array. Therefore, it is possible to both retrieve this internal representation with intRep() and construct an AminoAcid from an internal representation directly with fromRep(int).

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Constructor & Destructor Documentation

seq::AminoAcid::AminoAcid (   )

Create an amino acid with value AminoAcid::X (any).

seq::AminoAcid::AminoAcid (  char  c  )  throw (ParseException)

Create an amino acid by parsing a character. Accepted are the characters from the FASTA file definition. See also: toChar()

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Member Function Documentation

static AminoAcid seq::AminoAcid::fromRep (  int  rep  )  [inline, static]

Create an amino acid using the internal representation directly. Only valid representations are accepted, see the AA_* constants. Illegal representations are fenced off by an assert() statement. See also: intRep()

int seq::AminoAcid::intRep (   )  const [inline]

Get the internal representation. See also: fromRep(int)

bool seq::AminoAcid::operator!= (  const AminoAcid  other  )  const [inline]

Are two amino acids different ?

bool seq::AminoAcid::operator< (  const AminoAcid  other  )  const [inline]

So that you can use it as a key for STL containers.

bool seq::AminoAcid::operator== (  const AminoAcid  other  )  const [inline]

Are two amino acids identical ?

std::string seq::AminoAcid::tla (   )  const

Get the three letter abbreviation for this amino acid. Note that AminoAcid::B and AminoAcid::Z are combinations of two amino acids, and represented as "One/Two". See also: toChar()

char seq::AminoAcid::toChar (   )  const [inline]

Get the uppercase character representation for this amino acid. See also: AminoAcid(char)

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Member Data Documentation

const AminoAcid seq::AminoAcid::A [static]

const int seq::AminoAcid::AA_A = 0 [static]

const int seq::AminoAcid::AA_B = 24 [static]

const int seq::AminoAcid::AA_C = 1 [static]

const int seq::AminoAcid::AA_D = 2 [static]

const int seq::AminoAcid::AA_E = 3 [static]

const int seq::AminoAcid::AA_F = 4 [static]

const int seq::AminoAcid::AA_G = 5 [static]

const int seq::AminoAcid::AA_GAP = 21 [static]

const int seq::AminoAcid::AA_H = 6 [static]

const int seq::AminoAcid::AA_I = 7 [static]

const int seq::AminoAcid::AA_K = 8 [static]

const int seq::AminoAcid::AA_L = 9 [static]

const int seq::AminoAcid::AA_M = 10 [static]

const int seq::AminoAcid::AA_N = 11 [static]

const int seq::AminoAcid::AA_P = 12 [static]

const int seq::AminoAcid::AA_Q = 13 [static]

const int seq::AminoAcid::AA_R = 14 [static]

const int seq::AminoAcid::AA_S = 15 [static]

const int seq::AminoAcid::AA_STP = 20 [static]

const int seq::AminoAcid::AA_T = 16 [static]

const int seq::AminoAcid::AA_U = 23 [static]

const int seq::AminoAcid::AA_V = 17 [static]

const int seq::AminoAcid::AA_W = 18 [static]

const int seq::AminoAcid::AA_X = 25 [static]

const int seq::AminoAcid::AA_Y = 19 [static]

const int seq::AminoAcid::AA_Z = 22 [static]

const AminoAcid seq::AminoAcid::B [static]

const AminoAcid seq::AminoAcid::C [static]

const AminoAcid seq::AminoAcid::D [static]

const AminoAcid seq::AminoAcid::E [static]

const AminoAcid seq::AminoAcid::F [static]

const AminoAcid seq::AminoAcid::G [static]

const AminoAcid seq::AminoAcid::GAP [static]

const AminoAcid seq::AminoAcid::H [static]

const AminoAcid seq::AminoAcid::I [static]

const AminoAcid seq::AminoAcid::K [static]

const AminoAcid seq::AminoAcid::L [static]

const AminoAcid seq::AminoAcid::M [static]

const AminoAcid seq::AminoAcid::N [static]

const AminoAcid seq::AminoAcid::P [static]

const AminoAcid seq::AminoAcid::Q [static]

const AminoAcid seq::AminoAcid::R [static]

const AminoAcid seq::AminoAcid::S [static]

const AminoAcid seq::AminoAcid::STP [static]

const AminoAcid seq::AminoAcid::T [static]

const AminoAcid seq::AminoAcid::U [static]

const AminoAcid seq::AminoAcid::V [static]

const AminoAcid seq::AminoAcid::W [static]

const AminoAcid seq::AminoAcid::X [static]

const AminoAcid seq::AminoAcid::Y [static]

const AminoAcid seq::AminoAcid::Z [static]

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

• src/sequence/AminoAcid.h
• src/sequence/AminoAcid.C

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