BucketRefinement

Class Specialization

BucketRefinement

An index based on a refined array of sorted q-grams.



Index

IndexQGram

BucketRefinement

Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >

Include Headers

seqan/index.h

Parameters

TText	The text type. Types: String
TShapeSpec	The Shape specialization type. Note: This can be either a TSpec argument (e.g. SimpleShape) or a complete Shape class (e.g. Shape<Dna, SimpleShape>).

Remarks

This index refines q-gram buckets by sorting and uses binary search to locate them.

Specialization of

IndexQGram

Metafunctions

Fibre	Type of a specific container member (fibre). (Index)
SAValue	The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (Index)

Functions

begin	The begin of a container. (Index)
clear	Resets an object. (Index)
countOccurrences	Returns the number of occurrences of representative substring or a q-gram in the index text. (IndexQGram)
countOccurrencesMultiple	Returns the number of occurrences of a q-gram for every sequence of a StringSet . (IndexQGram)
countSequences	Return the number of sequences in an index' underlying text. (Index)
createQGramIndex	Builds a q-gram index on a sequence. (IndexQGram)
dirAt	Shortcut for value(indexDir(..), ..). (IndexQGram)
end	The end of a container. (Index)
getFibre	Returns a specific fibre of a container. (Index)
getKmerSimilarityMatrix	Creates a matrix storing the number of common q-grams between all pairs of sequences. (IndexQGram)
getOccurrence	Returns an occurrence of the representative substring or a q-gram in the index text. (IndexQGram)
getOccurrences	Returns all occurrences of the representative substring or a q-gram in the index text. (IndexQGram)
getStepSize	Return the q-gram step size used for index creation. (IndexQGram)
indexBucketMap	Shortcut for getFibre(.., QGramBucketMap). (IndexQGram)
indexCounts	Shortcut for getFibre(.., QGramCounts). (IndexQGram)
indexCountsDir	Shortcut for getFibre(.., QGramCountsDir). (IndexQGram)
indexCreate	Creates a specific Fibre. (Index)
indexDir	Shortcut for getFibre(.., QGramDir). (IndexQGram)
indexRequire	On-demand creation of a specific Fibre. (Index)
indexShape	Shortcut for getFibre(.., QGramShape). (IndexQGram)
indexSupplied	Returns whether a specific Fibre is present. (Index)
length	The number of items/characters. (Index)
range	Returns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text. (IndexQGram)
setHaystack	Sets the haystack of a Finder object. (Index)
setStepSize	Change the q-gram step size used for index creation. (IndexQGram)

Example Programs

Maximal Repeats, Index Finder StringSet, Mummy, Maximal Unique Matches, Index lcpAt, saAt, Index Finder, Index countOccurrencesMultiple, Supermaximal Repeats, Index countChildren

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