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

Index

IndexQGram

OpenAddressing

Index<TText, IndexQGram<TShapeSpec, OpenAddressing> >
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 uses a non-trivial hashing for mapping q-gram hash values to buckets. This reduces the sizes of bucket directories (QGramDir, QGramCountsDir fibres) from |Σ|^q to min(α*n,|Σ|^q), for a load factor α>1. A bucket still stores occurrences (or counts) of the same q-gram, but in contrast to the IndexQGram index, buckets are in random order due to the hashing.
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)

Data Members

alpha | Load factor. Controls space/time-tradeoff and must be greater 1. Default value is 1.6.

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)
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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