Manual V1.02

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New Features of Structator v1.02
Benjamin Albrecht
January 2012
Structator v1.02 allows the user to perform a search without an index containing the
aflk tables. The advantage of omitting these tables is that there is less file traffic and,
thus, the system produces less page faults during a search after a particular sequencestructure pattern. However, omitting these tables each affix link has to be computed via
a certain search method (see Sec. 2) which take some extra time. In general, one can
say that a search with an index containing the aflk tables provides the better runtime
if its size does not exceed the system’s memory.

1 afconstruct
There are two new options for the index construction:
• -lcpTree
Constructs a table of 1 Byte per entry for the forward sequences.
• -lcprTree
Constructs a table of 1 Byte per entry for the reverse sequences.
These two options allow the user to generate a table of 1 Byte per entry which accelerates the search after an affix link. Providing the tables aflk an affix link is computed
in constant time. Omitting these tables an affix link has to be located somewhere in the
suffix array. Therefore, Structator v1.02 now offers two kind of search methods which
are described in the following section.

2 afsearch
There are two new possibilities to perform a search after a particular sequence-structure
pattern:
• A search with the precomputed tables suf and lcp.
With only 10 Bytes per entry, this search method requires the smallest precomputed index of all other methods. A mapping of the tables suf and lcp can be
achieved by applying the options -lcp and -lcpr.
• A search with the precomputed tables suf, lcp, and lcpTree.
With 12 Bytes per entry this search method requires a larger precomputed index
than the first method. With the help of the table lcpTree, however, a search can
be performed a bit faster and the index is still smaller than a search with the
table aflk (18 per entry). The mapping of the tables suf, lcp, and lcpTree can be
achieved by applying the options -lcpTree and -lcprTree.
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