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
Metafunctions
FibreType of a specific container member (fibre). (Index)
SAValueThe default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (Index)
Data Members
alphaLoad factor. Controls space/time-tradeoff and must be greater 1. Default value is 1.6.
Functions
beginThe begin of a container. (Index)
clearResets an object. (Index)
countOccurrencesReturns the number of occurrences of representative substring or a q-gram in the index text. (IndexQGram)
countOccurrencesMultipleReturns the number of occurrences of a q-gram for every sequence of a StringSet . (IndexQGram)
countSequencesReturn the number of sequences in an index' underlying text. (Index)
createQGramIndexBuilds a q-gram index on a sequence. (IndexQGram)
dirAtShortcut for value(indexDir(..), ..). (IndexQGram)
endThe end of a container. (Index)
getFibreReturns a specific fibre of a container. (Index)
getKmerSimilarityMatrixCreates a matrix storing the number of common q-grams between all pairs of sequences. (IndexQGram)
getOccurrenceReturns an occurrence of the representative substring or a q-gram in the index text. (IndexQGram)
getOccurrencesReturns all occurrences of the representative substring or a q-gram in the index text. (IndexQGram)
getStepSizeReturn the q-gram step size used for index creation. (IndexQGram)
indexBucketMapShortcut for getFibre(.., QGramBucketMap). (IndexQGram)
indexCountsShortcut for getFibre(.., QGramCounts). (IndexQGram)
indexCountsDirShortcut for getFibre(.., QGramCountsDir). (IndexQGram)
indexCreateCreates a specific Fibre. (Index)
indexDirShortcut for getFibre(.., QGramDir). (IndexQGram)
indexRequireOn-demand creation of a specific Fibre. (Index)
indexShapeShortcut for getFibre(.., QGramShape). (IndexQGram)
indexSuppliedReturns whether a specific Fibre is present. (Index)
lengthThe number of items/characters. (Index)
rangeReturns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text. (IndexQGram)
setHaystackSets the haystack of a Finder object. (Index)
setStepSizeChange the q-gram step size used for index creation. (IndexQGram)
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