Fmindex

This is a prototype of fmindex by herumi.

The original version is fmindex-plus-plus. (http://code.google.com/p/fmindex-plus-plus/)

This includes sais.hxx by Yuta Mori

Build

mkdir work
cd work
git clone git://github.com/herumi/cybozulib.git
git clone git://github.com/herumi/opti.git
git clone git://github.com/herumi/fmindex.git
(cd opti/comp && sh ./build-wavelet-sh)
cd fmindex
make -j

A tiny benchmark

input.txt is 203MB UTF-8 text file. query.txt is 10KB UTF-8 text file.

% dir input.txt
-rw-r--r-- 1 shigeo shigeo 213829088 Mar 21 16:14 input.txt
% wc query.txt
1431   442 10389 query.txt
; original fmindex
% time ./fmconstruct input.txt input.dat
start reading the input-file
alphabet size:219
build SA
calculate statistics
build BWT
build WaveletTree
build sampledSA
cpu time:61.690000
75.520u 1.712s 1:17.43 99.7%    0+0k 0+866456io 0pf+0w
% dir input.dat
-rw-r--r-- 1 shigeo shigeo 443623615 Mar 21 16:16 input.dat
% time ./fmsearch input.dat query.txt >a.txt
exact search mode:
cpu time: 160.560000
160.750u 0.704s 2:42.03 99.6%   0+0k 0+448816io 0pf+0w

; use wavelet-matrix-cpp
% time ./construct2 input.txt input.dat
start reading the input-file
alphabet size:219
build SA
calculate statistics
build BWT
build WaveletTree
build sampledSA
cpu time:64.540000
77.716u 1.824s 1:19.74 99.7%    0+0k 0+815496io 0pf+0w
% dir input.dat
-rw-r--r-- 1 shigeo shigeo 417532311 Mar 23 05:00 input.dat
% time ./search2 input.dat ../query.txt > b.txt
exact search mode:
cpu time: 71.930000
71.992u 0.720s 1:12.94 99.6%    0+0k 0+448768io 0pf+0w

; forked fmindex with cybozu/wavelet_matrix.hpp
% time ./construct input.txt input.dat
start reading the input-file
alphabet size:219
build SA
calculate statistics
build BWT
build WaveletTree
build sampledSA
cpu time:60.730000
74.536u 1.404s 1:16.13 99.7%    0+0k 0+923808io 0pf+0w
% dir input.dat
-rw-r--r-- 1 shigeo shigeo 472987963 Mar 21 16:16 input.dat
% time ./search input.dat ../query.txt >c.txt
exact search mode:
cpu time: 30.050000
29.869u 0.744s 0:30.72 99.6%    0+0k 0+448776io 0pf+0w

a.txt, b.txt and c.txt are all same.

License

fmindex-plus-plus

Copyright (c) 2010 Yasuo Tabei

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above Copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above Copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the authors nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

---

sais.hxx for sais-lite Copyright (c) 2008-2009 Yuta Mori All Rights Reserved.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.