Class Specialization
SimpleShape
A variable length ungapped shape (also called q-gram or k-mer).
Shape
SimpleShape
Shape<TValue, SimpleShape>
Parameters
TValue
The Value type of the string the shape is applied to (e.g. Dna).
Specialization of
Metafunctions
LENGTHNumber of elements in a fixed-size container. (Shape)
SizeType of an object that is suitable to hold size information. (Shape)
ValueType of the items in the container. (Shape)
ValueSizeNumber of different values a value type object can have. (Shape)
WEIGHTNumber of relevant positions in a shape. (Shape)
Member Functions
ShapeConstructor
Functions
createCountArrayBuilds an index on a StringSet storing how often a q-gram occurs in each sequence. (Shape)
createQGramIndexBuilds a q-gram index on a sequence. (Shape)
createQGramIndexDirOnlyBuilds the directory of a q-gram index on a sequence. (Shape)
createQGramIndexSAOnlyBuilds the suffix array of a q-gram index on a sequence. (Shape)
hashComputes a (lower) hash value for a shape applied to a sequence. (Shape)
hash2Computes a unique hash value of a shape, even if it is shorter than its span. (Shape)
hash2NextComputes a unique hash value for the adjacent shape, even if it is shorter than q. (Shape)
hashNextComputes the hash value for the adjacent shape. (Shape)
hashUpperComputes an upper hash value for a shape applied to a sequence. (Shape)
indexShapeShortcut for getFibre(.., QGram_Shape). (Shape)
lengthThe number of items/characters. (Shape)
resizeChanges the length.
valueReference to the value. (Shape)
weightNumber of relevant positions in a shape. (Shape)
Remarks
A SimpleShape must be resized first to a valid length. To do so, call resize.
See Also
SeqAn - Sequence Analysis Library - www.seqan.de