Class Specialization
OpenAddressing
An index based on an array of sorted q-grams.
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Include Headers
seqan/index.h
Parameters
The text type. Types: String | |
The Shape specialization type. Note: This can be either a |
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
| Type of a specific container member (fibre). (Index) | |
| 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
| Load factor. Controls space/time-tradeoff and must be greater 1. Default value is 1.6. |
Functions
| Resets an object. (Index) | |
| Returns the number of occurrences of representative substring or a q-gram in the index text. (IndexQGram) | |
| Returns the number of occurrences of a q-gram for every sequence of a StringSet . (IndexQGram) | |
| Return the number of sequences in an index' underlying text. (Index) | |
| Builds a q-gram index on a sequence. (IndexQGram) | |
| Shortcut for | |
| The end of a container. (Index) | |
| Returns a specific fibre of a container. (Index) | |
| Creates a matrix storing the number of common q-grams between all pairs of sequences. (IndexQGram) | |
| Returns an occurrence of the representative substring or a q-gram in the index text. (IndexQGram) | |
| Returns all occurrences of the representative substring or a q-gram in the index text. (IndexQGram) | |
| Return the q-gram step size used for index creation. (IndexQGram) | |
| Shortcut for | |
| Shortcut for | |
| Shortcut for | |
| Creates a specific Fibre. (Index) | |
| Shortcut for | |
| On-demand creation of a specific Fibre. (Index) | |
| Shortcut for | |
| Shortcut for | |
| Returns whether a specific Fibre is present. (Index) | |
| Shortcut for | |
| The number of characters in the underlying text of the index is returned. (Index) | |
| This functions opens an index from disk. (Index) | |
| Returns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text. (IndexQGram) | |
| This functions saves an index to disk. (Index) | |
| Sets the haystack of a Finder object. (Index) | |
| Change the q-gram step size used for index creation. (IndexQGram) |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de