Class Specialization
GappedShape
A fixed gapped shape.
Shape
GappedShape
Shape<TValue, GappedShape<TSpec> >
Include Headers
seqan/index.h
Parameters
TValue
The Value type of the string the shape is applied to (e.g. Dna).
TSpec
A structure to store the shape at compile-time.
Remarks
There are predefined shapes in index/shape_predefined.h. You can simply use them with Shape<TValue, ShapePatternHunter> for example.
Specialization of
Metafunctions
HostType of the object a given object depends on. (Shape)
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)
WEIGHTNumber of relevant positions in a shape. (Shape)
Member Functions
ShapeConstructor (Shape)
Functions
countOccurrencesReturns the number of occurences of representative substring or a q-gram in the index text. (Shape)
countOccurrencesMultipleReturns the number of occurences of a q-gram for every sequence of a StringSet . (Shape)
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)
getOccurrenceReturns an occurence of the representative substring or a q-gram in the index text. (Shape)
getOccurrencesReturns all occurences of the representative substring or a q-gram in the index text. (Shape)
hashComputes a (lower) hash value for a shape applied to a sequence. (Shape)
hash2Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span (Shape)
hash2NextComputes a unique hash value for the adjacent shape, even if it is shorter than q. (Shape)
hash2UpperComputes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span. (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(.., QGramShape). (Shape)
lengthThe number of items/characters. (Shape)
lengthThe number of items/characters. (Shape)
rangeReturns the suffix array interval borders of occurences of representative substring or a q-gram in the index text. (Shape)
shapeToStringConverts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). (Shape)
valueReference to the value. (Shape)
weightNumber of relevant positions in a shape. (Shape)
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