Spec AminoAcid
IUPAC code for amino acids.

Extends SimpleType
All Extended SimpleType
All Impl'd AlphabetConcept, AssignableConcept, ComparableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, EqualityComparableConcept, FiniteOrderedAlphabetConcept, LessThanComparableConcept, OrderedAlphabetConcept
Defined in <seqan/basic.h>
Signature typedef SingleType<unsigned char, AminoAcid_> AminoAcid;

Member Function Overview

Member Functions Inherited From SimpleType

Member Functions Inherited From AssignableConcept

Member Functions Inherited From ComparableConcept

Member Functions Inherited From EqualityComparableConcept

Member Functions Inherited From LessThanComparableConcept

Member Functions Inherited From OrderedAlphabetConcept

Interface Function Overview

Interface Functions Inherited From AssignableConcept

Interface Functions Inherited From ComparableConcept

Interface Functions Inherited From FiniteOrderedAlphabetConcept

Interface Functions Inherited From OrderedAlphabetConcept

Interface Metafunction Overview

Interface Metafunctions Inherited From AlphabetConcept

Interface Metafunctions Inherited From FiniteOrderedAlphabetConcept

Interface Metafunctions Inherited From OrderedAlphabetConcept

Member Variable Overview

Member Variables Inherited From SimpleType

Detailed Description

The ValueSize of AminoAcid is 27.

The amino acid symbols are as follows, i.e. they are sorted alphabetically up until the last two symbols:

'A' = 0, 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y', 'Z', 'X'. '*'

Of these 'B' is a wildcard for (Aspartic Acid, Asparagine), 'J' for (Leucine, Isoleucine), 'Z' for (Glutamic Acid, Glutamine) and 'X' for "any amino acid".

'O' refers to the rare Pyrrolysine, 'U' refers to the rare Selenocysteine and '*' to the terminator tRNA.

Objects of type AminoAcid can be converted to char and vice versa. Unknown values are converted to 'X'.

See Also