| Class Specialization Index_QGram An index based on an array of sorted q-grams.
Index
Index_QGram
Index<TText, Index_QGram<> > Parameters
TText | The text type. Types: String
Specialization of Index 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)
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.
indexCounts | Shortcut for getFibre(.., QGram_Counts).
indexCountsDir | Shortcut for getFibre(.., QGram_CountsDir).
indexCreate | Creates a specific Fibre. (Index)
indexDir | Shortcut for getFibre(.., QGram_Dir).
indexRequire | On-demand creation of a specific Fibre. (Index)
indexShape | Shortcut for getFibre(.., QGram_Shape).
indexSupplied | Returns whether a specific Fibre is present. (Index)
length | The number of items/characters. (Index)
setHaystack | Sets the haystack of a Finder object. (Index)
Remarks The fibres (see Index and Fibre) of this index are a suffix array sorted by the first q characters (see QGram_SA) and a q-gram directory (see QGram_Dir). Example Programs Index Finder, Index Finder StringSet, Maximal Repeats, Maximal Unique Matches, Mummy, Supermaximal Repeats See Also Index Find Algorithm, QGram Index Fibres SeqAn - Sequence Analysis Library - www.seqan.de