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patflick / psac

Parallel Suffix Array, LCP Array, and Suffix Tree Construction
Apache License 2.0
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suffix tree construction #2

Open zhutongxue opened 5 years ago

zhutongxue commented 5 years ago

Thanks for the great work. I have a question here. Does the repo contains the code of constructing the suffix tree using SA and LCP? The suffix tree construction code is not found in the current repo.

Looking forward to the reply. Many thanks in advance.

patflick commented 5 years ago

The construction code for the ST construction is implemented in the files include/ansv.hpp (for the gANSV algorithm described in the paper) and include/suffix_tree.hpp (for constructing the ST from the SA & LCP using gANSV).

The main executable ./psac can be used for constructing the ST and timing the SA vs ST construction time for a given input file. This is a MPI executable, so it should be executed as follows:

mpirun -np $NP ./psac -t -f <input_file>

where the -t option designates construction of the ST.

The code to call the suffix tree construction given an input is implemented in the executable here: psac.cpp:98.