Class Specialization
AminoAcid
Iupac code for amino acids.

Simple Type

SimpleType

AminoAcid

AminoAcid
Include Headers
seqan/basic.h
Remarks
The ValueSize of AminoAcid is 24.
The amino acids are enumerated from 0 to 15 in this order:
'A'=0, 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'=19.
The remaining 4 symbols are:
'B'=20 (Aspartic Acid, Asparagine), 'Z'=21 (Glutamic Acid, Glutamine), 'X'=22 (unknown), '*'=23 (terminator)
Objects of type AminoAcid can be converted to char and vice versa. Unkown values are converted to 'X'.
AminoAcid is typedef for SimpleType<char,AminoAcid_>, while AminoAcid_ is a helper specialization tag class.
Specialization of
SimpleType
Implements
Simple Type
Metafunctions

IsSimple | Tests type to be simple. (SimpleType)
Spec | The spec of a class. (SimpleType)
Value | Type of the items in the container. (SimpleType)

Functions

assign | Assigns one object to another object. (SimpleType)
assign | Assigns one object to another object. (SimpleType)
convertResidueToFrequencyDist | Coverts a residue to a frequency distribution (profile).
ordValue | Maps an alphabet 1-to-1 to the interval [0..ValueSize). (SimpleType)

Example Programs
Alphabets
See Also
ValueSize, Peptide, PeptideIterator
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:50