Class
Shape
Stores hash value and shape for an ungapped or gapped q-gram.
Shape
GappedShape
GenericShape
SimpleShape
UngappedShape
Shape<TValue, TSpec>
Parameters
TValue
The Value type of the string the shape is applied to (e.g. Dna).
TSpec
The specializing type.
Default: SimpleShape, for ungapped q-grams.
Specializations
GappedShapeA fixed gapped shape.
GenericShapeA variable gapped shape.
SimpleShapeA variable length ungapped shape (also called q-gram or k-mer).
UngappedShapeA fixed length ungapped shape (also called q-gram or k-mer).
Metafunctions
HostType of the object a given object depends on.
LENGTHNumber of elements in a fixed-size container.
SizeType of an object that is suitable to hold size information.
ValueType of the items in the container.
ValueSizeNumber of different values a value type object can have.
WEIGHTNumber of relevant positions in a shape.
Member Functions
ShapeConstructor
Functions
createCountArrayBuilds an index on a StringSet storing how often a q-gram occurs in each sequence.
createQGramIndexBuilds a q-gram index on a sequence.
createQGramIndexDirOnlyBuilds the directory of a q-gram index on a sequence.
createQGramIndexSAOnlyBuilds the suffix array of a q-gram index on a sequence.
hashComputes a (lower) hash value for a shape applied to a sequence.
hash2Computes a unique hash value of a shape, even if it is shorter than its span.
hash2NextComputes a unique hash value for the adjacent shape, even if it is shorter than q.
hashNextComputes the hash value for the adjacent shape.
hashUpperComputes an upper hash value for a shape applied to a sequence.
indexShapeShortcut for getFibre(.., QGram_Shape).
lengthThe number of items/characters.
valueReference to the value.
weightNumber of relevant positions in a shape.
Remarks
The ValueSize of Shape is the ValueSize of TValue which is the alphabet size.
To get the span or the weight of a shape call length or weight.
SeqAn - Sequence Analysis Library - www.seqan.de