| 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 Shape Metafunctions
Host | Type of the object a given object depends on. (Shape)
LENGTH | Number of elements in a fixed-size container. (Shape)
Size | Type of an object that is suitable to hold size information. (Shape)
Value | Type of the items in the container. (Shape)
ValueSize | Number of different values a value type object can have. (Shape)
WEIGHT | Number of relevant positions in a shape. (Shape)
Member Functions
Shape | Constructor
Functions
createCountArray | Builds an index on a StringSet storing how often a q-gram occurs in each sequence. (Shape)
createQGramIndex | Builds a q-gram index on a sequence. (Shape)
createQGramIndexDirOnly | Builds the directory of a q-gram index on a sequence. (Shape)
createQGramIndexSAOnly | Builds the suffix array of a q-gram index on a sequence. (Shape)
hash | Computes a (lower) hash value for a shape applied to a sequence. (Shape)
hash2 | Computes a unique hash value of a shape, even if it is shorter than its span. (Shape)
hash2Next | Computes a unique hash value for the adjacent shape, even if it is shorter than q. (Shape)
hashNext | Computes the hash value for the adjacent shape. (Shape)
hashUpper | Computes an upper hash value for a shape applied to a sequence. (Shape)
indexShape | Shortcut for getFibre(.., QGram_Shape). (Shape)
length | The number of items/characters. (Shape)
resize | Changes the length.
value | Reference to the value. (Shape)
weight | Number 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 UngappedShape SeqAn - Sequence Analysis Library - www.seqan.de