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
See Also
Index Find Algorithm, QGram Index Fibres
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:51