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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

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).

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:

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:

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

Get the internal representation.

See also:

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:

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

Get the uppercase character representation for this amino acid.

See also:

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]

The documentation for this class was generated from the following files:
Generated on Fri Jul 14 15:30:43 2006 for libseq by  doxygen 1.4.4