| 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 SeqAn - Sequence Analysis Library - www.seqan.de

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