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
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)
VertexDescriptorType of an object that represents a vertex descriptor.
Functions
beginReturns 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.
bwtAtShortcut for value(indexBwt(..), ..).
childAtShortcut for value(indexChildtab(..), ..).
clearResets an object. (Index)
countSequencesReturn the number of sequences in an index' underlying text. (Index)
endThe end of a container. (Index)
getFibreReturns a specific fibre of a container. (Index)
indexBwtShortcut for getFibre(.., EsaBwt).
indexChildtabShortcut for getFibre(.., EsaChildtab).
indexCreateCreates a specific Fibre. (Index)
indexLcpShortcut for getFibre(.., EsaLcp).
indexLcpeShortcut for getFibre(.., EsaLcpe).
indexRawSAShortcut for getFibre(.., EsaRawSA).
indexRawTextShortcut for getFibre(.., EsaRawText).
indexRequireOn-demand creation of a specific Fibre. (Index)
indexSAShortcut for getFibre(.., FibreSA). (Index)
indexSuppliedReturns whether a specific Fibre is present. (Index)
indexTextShortcut for getFibre(index, FibreText()). (Index)
lcpAtShortcut for value(indexLcp(..), ..).
lcpeAtShortcut for value(indexLcpe(..), ..).
lengthThe number of characters in the underlying text of the index is returned. (Index)
openThis functions opens an index from disk. (Index)
rawsaAtShortcut for value(indexRawSA(..), ..).
rawtextAtShortcut for value(indexRawText(..), ..).
resizeVertexMapInitializes a vertex map.
saAtShortcut for value(indexSA(..), ..).
saveThis functions saves an index to disk. (Index)
setHaystackSets the haystack of a Finder object. (Index)
textAtShortcut for value(indexText(..), ..).
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