| Class Shape Stores hash value and shape for an ungapped or gapped q-gram.
Shape
GappedShape | GenericShape | OneGappedShape | 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.
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. Specializations
GappedShape | A fixed gapped shape.
GenericShape | A variable gapped shape.
OneGappedShape | A variable shape with one optional gap.
SimpleShape | A variable length ungapped shape (also called q-gram or k-mer).
UngappedShape | A fixed length ungapped shape (also called q-gram or k-mer).
Metafunctions
Host | Type of the object a given object depends on.
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.
WEIGHT | Number of relevant positions in a shape.
Member Functions
Shape | Constructor
Functions
countOccurrences | Returns the number of occurences of representative substring or a q-gram in the index text.
countOccurrencesMultiple | Returns the number of occurences of a q-gram for every sequence of a StringSet .
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.
getOccurrence | Returns an occurence of the representative substring or a q-gram in the index text.
getOccurrences | Returns all occurences of the representative substring or a q-gram in the index text.
hash | Computes a (lower) hash value for a shape applied to a sequence.
hash2 | Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span
hash2Next | Computes a unique hash value for the adjacent shape, even if it is shorter than q.
hash2Upper | Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span.
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(.., QGramShape).
length | The number of items/characters.
length | The number of items/characters.
range | Returns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
shapeToString | Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
value | Reference to the value.
weight | Number of relevant positions in a shape.
SeqAn - Sequence Analysis Library - www.seqan.de

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