Dna5Q

Class Specialization

Dna5Q

Alphabet for DNA plus PHRED quality including 'N' character.



FiniteOrderedAlphabetConcept

SimpleType

AlphabetWithQualitiesConcept

Dna5Q

Remarks

The ValueSize of Dna5Q is 5. The nucleotides are enumerated this way: 'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3. The 'N' character ("unkown nucleotide") is encoded by 4.

Objects of type Dna5 can be converted to various other types and vice versa.

Dna5Q is typedef for SimpleType<char,Dna5Q_>, while Dna5Q_ is a helper specialization tag class.

Note that the default quality value is set to 60.

Specialization of

SimpleType

Implements

FiniteOrderedAlphabetConcept, AlphabetWithQualitiesConcept

Metafunctions

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

Functions

assign	Assigns one object to another object. (SimpleType)
assignQualityValue	Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence.
getQualityValue	Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with a specified element from a sequence.
ordValue	Maps an alphabet 1-to-1 to the interval [0..ValueSize). (SimpleType)