Class Specialization
IndexQGram
An index based on an array of sorted q-grams.
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.
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
Specializations
OpenAddressingAn index based on an array of sorted q-grams.
Metafunctions
FibreType of a specific index 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)
Functions
beginThe begin of a container. (Index)
clearResets an object. (Index)
countOccurrencesReturns the number of occurences of representative substring or a q-gram in the index text.
countOccurrencesMultipleReturns the number of occurences of a q-gram for every sequence of a StringSet .
createQGramIndexBuilds a q-gram index on a sequence.
dirAtShortcut for value(indexDir(..), ..).
endThe end of a container. (Index)
getFibreReturns a specific Fibre of an Index object. (Index)
getKmerSimilarityMatrixCreates a matrix storing the number of common q-grams between all pairs of sequences.
getOccurrenceReturns an occurence of the representative substring or a q-gram in the index text.
getOccurrencesReturns all occurences of the representative substring or a q-gram in the index text.
getStepSizeReturn the q-gram step size used for index creation.
indexBucketMapShortcut for getFibre(.., QGramBucketMap).
indexCountsShortcut for getFibre(.., QGramCounts).
indexCountsDirShortcut for getFibre(.., QGramCountsDir).
indexCreateCreates a specific Fibre. (Index)
indexDirShortcut for getFibre(.., QGramDir).
indexRequireOn-demand creation of a specific Fibre. (Index)
indexShapeShortcut for getFibre(.., QGramShape).
indexSuppliedReturns whether a specific Fibre is present. (Index)
lengthThe number of items/characters. (Index)
rangeReturns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
setHaystackSets the haystack of a Finder object. (Index)
setStepSizeChange the q-gram step size used for index creation.
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