| Class Specialization IndexEsa The enhanced suffix array index is very fast index, requiring more memory than other indices. In addition to the suffix array an lcp (longest common prefix) table and a child table (containing structural information of the suffix tree) are provided.
Index
IndexEsa
Index<TText, IndexEsa<> > Parameters
TText | The text type. Types: String, StringSet
Remarks The main fibres (see Index and Fibre) of this index are a suffix array (see EsaSA), a lcp table (see EsaLcp) and a child table (see EsaChildtab). This index can be accessed as a Suffix Tree using the VSTree Iterator classes. ..include:seqan/index.h Specialization of Index 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)
VertexDescriptor | Type of an object that represents a vertex descriptor.
Functions
begin | Returns an iterator pointing to the root node of the virtual string tree/trie of an index. The only exception are Postorder iterators, where begin returns an iterator pointing to the leftmost node in the tree/trie.
bwtAt | Shortcut for value(indexBwt(..), ..).
childAt | Shortcut for value(indexChildtab(..), ..).
clear | Resets an object. (Index)
countSequences | Return the number of sequences in an index' underlying text. (Index)
end | The end of a container. (Index)
getFibre | Returns a specific fibre of a container. (Index)
indexBwt | Shortcut for getFibre(.., EsaBwt).
indexChildtab | Shortcut for getFibre(.., EsaChildtab).
indexCreate | Creates a specific Fibre. (Index)
indexLcp | Shortcut for getFibre(.., EsaLcp).
indexLcpe | Shortcut for getFibre(.., EsaLcpe).
indexRawSA | Shortcut for getFibre(.., EsaRawSA).
indexRawText | Shortcut for getFibre(.., EsaRawText).
indexRequire | On-demand creation of a specific Fibre. (Index)
indexSA | Shortcut for getFibre(.., FibreSA). (Index)
indexSupplied | Returns whether a specific Fibre is present. (Index)
indexText | Shortcut for getFibre(index, FibreText()). (Index)
lcpAt | Shortcut for value(indexLcp(..), ..).
lcpeAt | Shortcut for value(indexLcpe(..), ..).
length | The number of characters in the underlying text of the index is returned. (Index)
open | This functions opens an index from disk. (Index)
rawsaAt | Shortcut for value(indexRawSA(..), ..).
rawtextAt | Shortcut for value(indexRawText(..), ..).
resizeVertexMap | Initializes a vertex map.
saAt | Shortcut for value(indexSA(..), ..).
save | This functions saves an index to disk. (Index)
textAt | Shortcut for value(indexText(..), ..).
Example Programs Maximal Repeats, Index Finder StringSet, Mummy, Maximal Unique Matches, Index lcpAt, saAt, Index Finder, Index countOccurrencesMultiple, Supermaximal Repeats, Index countChildren See Also ESA Index Fibres SeqAn - Sequence Analysis Library - www.seqan.de

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