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

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)
indexSA	Shortcut for getFibre(.., FibreSA). (Index)
indexShape	Shortcut for getFibre(.., QGramShape). (IndexQGram)
indexSupplied	Returns whether a specific Fibre is present. (Index)
indexText	Shortcut for getFibre(index, FibreText()). (Index)
length	The number of characters in the underlying text of the index is returned. (Index)
open	This functions opens an index from disk. (Index)
range	Returns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text. (IndexQGram)
save	This functions saves an index to disk. (Index)
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

SeqAn - Sequence Analysis Library - www.seqan.de