IndexQGram

Class Specialization

IndexQGram

An index based on an array of sorted q-grams.



Index

IndexQGram

OpenAddressing

Index<TText, IndexQGram<TShapeSpec[, TSpec]> >

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>).
TSpec	The specializing type. Types: OpenAddressing Default: Default

Remarks

The fibres (see Index and Fibre) of this index are a suffix array sorted by the first q characters (see QGramSA) and a q-gram directory (see QGramDir).

Specialization of

Index

Specializations

OpenAddressing

An index based on an array of sorted q-grams.

Metafunctions

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

Example Programs

Maximal Repeats, Index Finder StringSet, Mummy, Maximal Unique Matches, Index Finder, Supermaximal Repeats