| Class Shape Stores hash value and shape for an ungapped or gapped q-gram.
Shape
FixedGappedShape | FixedShape | GappedShape | SimpleShape
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
FixedGappedShape | A fixed gapped shape.
FixedShape | A fixed length ungapped shape (also called q-gram or k-mer).
GappedShape | A variable gapped shape.
SimpleShape | A variable length ungapped shape (also called q-gram or k-mer).
Metafunctions
LENGTH | Number of elements in a fixed-size container.
Size | Type of an object that is suitable to hold size information.
Value | Type of the items in the container.
ValueSize | Number of different values a value type object can have.
WEIGHT | Number of relevant positions in a shape.
Member Functions
Shape | Constructor
Functions
createCountArray | Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
createQGramIndex | Builds a q-gram index on a sequence.
createQGramIndexDirOnly | Builds the directory of a q-gram index on a sequence.
createQGramIndexSAOnly | Builds the suffix array of a q-gram index on a sequence.
hash | Computes a (lower) hash value for a shape applied to a sequence.
hash2 | Computes a unique hash value of a shape, even if it is shorter than its span.
hash2Next | Computes a unique hash value for the adjacent shape, even if it is shorter than q.
hashNext | Computes the hash value for the adjacent shape.
hashUpper | Computes an upper hash value for a shape applied to a sequence.
indexShape | Shortcut for getFibre(.., QGram_Shape).
length | The number of items/characters.
value | Reference to the value.
weight | Number 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