AminoAcid

Class Specialization

AminoAcid

Iupac code for amino acids.

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

Implements

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