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libdivsufsort as a project module
2013-11-29 16:19:49 +01:00
libdivsufsort - A lightweight suffix-sorting library.
-----------------------------------------------------
Introduction:
-------------
The libdivsufsort project provides a fast, lightweight, and robust
C API library to construct the suffix array and the Burrows-Wheeler
transformed string for any input string of a constant-size alphabet.
The suffix-sorting algorithm runs in O(n log n) worst-case time
using only 5n+O(1) bytes of memory space, where n is the length of
the input string.
The latest version of libdivsufsort is available at:
http://libdivsufsort.googlecode.com/
License:
--------
libdivsufsort is released under the MIT/X11 license. See the file
COPYING for more details.
APIs:
-----
* Data types
typedef int32_t saint_t;
typedef int32_t saidx_t;
typedef uint8_t sauchar_t;
* Constructs the suffix array of a given string.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The output array or suffixes.
* @param n The length of the given string.
* @return 0 if no error occurred, -1 or -2 otherwise.
saint_t
divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n);
* Constructs the burrows-wheeler transformed string of a given string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @return The primary index if no error occurred, -1 or -2 otherwise.
saidx_t
divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n);
* Constructs the burrows-wheeler transformed string of a given string and suffix array.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param SA[0..n-1] The suffix array. (can be NULL)
* @param n The length of the given string.
* @param idx The output primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
saint_t
bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
saidx_t n, saidx_t *idx);
* Inverse BW-transforms a given BWTed string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @param idx The primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
saint_t
inverse_bw_transform(const sauchar_t *T, sauchar_t *U,
saidx_t *A, saidx_t n, saidx_t idx);
* Checks the correctness of a given suffix array.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The input suffix array.
* @param n The length of the given string.
* @param verbose The verbose mode.
* @return 0 if no error occurred.
saint_t
sufcheck(const sauchar_t *T, const saidx_t *SA,
saidx_t n, saint_t verbose);
* Search for the pattern P in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param P[0..Psize-1] The input pattern string.
* @param Psize The length of the given pattern string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
saidx_t
sa_search(const sauchar_t *T, saidx_t Tsize,
const sauchar_t *P, saidx_t Psize,
const saidx_t *SA, saidx_t SAsize,
saidx_t *idx);
* Search for the character c in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param c The input character.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
saidx_t
sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
const saidx_t *SA, saidx_t SAsize,
saint_t c, saidx_t *idx);
* Returns the version string of libdivsufsort.
* @return the version string.
const char *
divsufsort_version(void);
Benchmark:
------------------
= Specifications =
Processor: 2.66 GHz Intel Core 2 Duo E6750
L1 Cache: (32 Kb + 32 Kb) x 2
L2 Cache: 4 Mb
RAM: 2 Gb main memory
Operating system: Windows XP Home SP 3 (with Cygwin)
Compiler: GCC version 4.3.1
= Programs =
Archon4r0 kvark's sorting algorithm http://forum.compression.ru/viewtopic.php?t=352
BPR Bucket-Pointer Refinement algorithm http://bibiserv.techfak.uni-bielefeld.de/bpr/
DC Difference-Cover algorithm (v = 32) http://www.cs.helsinki.fi/juha.karkkainen/publications/cpm03.tar.gz
DS Deep-Shallow sorting algorithm http://www.mfn.unipmn.it/~manzini/lightweight/
divsufsort1 libdivsufsort version 1.2.3 http://libdivsufsort.googlecode.com/
divsufsort2 libdivsufsort version 2.0.0 http://libdivsufsort.googlecode.com/
KA Ko-Aluru algorithm http://ko.pang.cn.googlepages.com/software2
KS Kärkkäinen-Sanders algorithm http://www.mpi-inf.mpg.de/~sanders/programs/suffix/
MSufSort3 MSufSort version 3.1.1 beta http://www.michael-maniscalco.com/msufsort.htm
qsufsort Larsson-Sadakane algorithm http://www.larsson.dogma.net/research.html
sais Induced Sorting algorithm http://yuta.256.googlepages.com/sais
All programs were compiled with gcc/g++ using '-O3 -fomit-frame-pointer -DNDEBUG'
optimization options. The times are the average of five runs, in seconds, and were
measured using the standard Unix/Cygwin 'time' command. (user + system) The spaces
were measured using the 'memusage' command.
= Testfiles =
Manzini's Large Corpus http://www.mfn.unipmn.it/~manzini/lightweight/corpus/
The Gauntlet http://www.michael-maniscalco.com/testset/gauntlet/
= Running times =
== Manzini's Corpus ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
chr22.dna 34553758 6.030 6.196 22.694 7.514 5.404 5.362 16.980 50.006 7.132 10.642 10.796
etext99 105277340 22.160 32.582 79.872 34.264 18.758 18.064 73.236 202.684 24.106 56.612 38.748
gcc-3.0.tar 86630400 13.856 20.692 61.690 35.822 10.382 10.084 40.908 135.174 14.952 40.766 20.990
howto 39422105 5.806 8.326 25.432 8.288 5.472 5.320 20.694 64.834 5.672 16.366 11.388
jdk13c 69728899 18.106 22.252 61.234 32.182 9.260 9.010 34.172 101.096 11.314 39.792 16.396
linux-2.4.5.tar 116254720 18.174 26.226 82.830 25.912 14.672 14.290 58.586 194.412 19.890 54.054 29.614
rctail96 114711151 32.490 55.826 119.026 62.502 18.500 17.914 70.072 190.562 21.060 70.456 33.248
rfc 116421901 20.736 35.404 91.284 29.666 16.116 15.658 64.390 196.500 17.936 61.436 32.224
sprot34.dat 109617186 22.832 36.720 93.122 32.096 17.894 17.404 68.084 187.594 23.352 56.946 34.092
w3c2 104201579 27.264 29.384 89.352 54.682 13.866 13.486 52.660 162.582 17.090 77.804 25.498
totals 896819039 187.454 273.608 726.536 322.928 130.324 126.592 499.782 1485.444 162.504 484.874 252.994
== The Gauntlet ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
abac 200000 0.044 0.064 0.104 27.914 0.042 0.036 0.058 0.048 0.050 0.062 0.044
abba 10500600 3.270 5.124 10.766 30.702 1.714 1.602 2.570 7.952 3.514 15.272 1.460
book1x20 15375420 4.392 3.530 13.872 97.468 2.312 2.154 7.442 15.756 3.542 22.376 3.912
fib_s14930352 14930352 12.728 10.830 18.524 179.040 3.638 3.588 3.544 10.232 6.700 18.224 2.542
fss10 12078908 11.390 8.974 15.130 85.328 2.828 2.824 3.344 8.646 4.618 14.754 2.076
fss9 2851443 1.002 1.210 1.644 5.256 0.410 0.416 0.618 1.290 0.554 2.836 0.336
houston 3840000 0.344 0.708 2.226 118.960 0.118 0.128 0.520 0.744 0.242 1.230 0.238
paper5x80 981924 0.110 0.154 0.454 0.806 0.092 0.090 0.210 0.256 0.144 0.448 0.110
test1 2097152 0.332 2.132 1.108 8.680 0.268 0.280 0.376 1.066 1.302 2.762 0.202
test2 2097152 0.710 0.616 1.110 8.682 0.180 0.176 0.374 1.076 3.354 2.768 0.206
test3 2097152 0.488 213.154 1.164 1.772 0.220 0.226 0.388 1.082 0.922 3.246 0.212
totals 67050103 34.810 246.496 66.102 564.608 11.822 11.520 19.444 48.148 24.942 83.978 11.338
= Space (in MiBytes) =
== Manzini's Corpus ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
chr22.dna 34553758 174.66 296.88 193.60 165.18 165.02 165.02 289.97 428.39 199.72 263.62 164.77
etext99 105277340 531.13 915.48 589.85 503.23 502.25 502.25 907.34 1305.20 604.45 803.20 502.00
gcc-3.0.tar 86630400 437.14 756.43 485.38 415.87 413.34 413.34 709.50 1074.01 497.79 660.94 413.09
howto 39422105 199.20 367.53 220.88 188.45 188.23 188.23 331.54 488.75 227.67 300.77 187.98
jdk13c 69728899 351.96 603.99 390.68 333.40 332.74 332.74 609.71 864.48 401.04 531.99 332.49
linux-2.4.5.tar 116254720 586.46 1061.83 651.36 555.76 554.60 554.60 977.81 1441.30 667.39 886.95 554.35
rctail96 114711151 578.68 987.64 642.71 548.32 547.24 547.24 1004.98 1422.16 658.43 875.18 546.99
rfc 116421901 587.30 1005.85 652.29 556.53 555.39 555.39 956.52 1443.37 668.26 888.23 555.14
sprot34.dat 109617186 553.01 941.95 614.17 524.03 522.95 522.95 930.06 1359.01 629.26 836.31 522.70
w3c2 104201579 525.71 958.37 583.82 498.09 497.12 497.12 912.00 1291.87 598.82 795.00 496.87
totals 896819039 4525.25 7895.95 5024.74 4288.86 4278.88 4278.88 7629.43 11118.54 5152.83 6842.19 4276.38
mean - 5.29 9.23 5.88 5.01 5.00 5.00 8.92 13.00 6.02 8.00 5.00
== The Gauntlet ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
abac 200000 1.51 1.73 1.12 0.98 1.21 1.20 1.75 2.48 3.15 1.53 0.95
abba 10500600 53.43 90.19 58.83 50.21 50.32 50.32 86.20 130.18 62.09 80.11 50.07
book1x20 15375420 78.00 134.00 86.15 73.52 73.57 73.57 132.42 190.62 89.99 117.31 73.32
fib_s14930352 14930352 75.75 128.15 83.65 71.71 71.44 71.44 117.16 185.10 87.43 113.91 71.19
fss10 12078908 61.38 103.68 67.68 58.05 57.85 57.85 107.05 149.75 71.12 92.16 57.60
fss9 2851443 14.87 24.48 15.98 13.71 13.85 13.85 25.27 35.35 18.32 21.76 13.60
houston 3840000 19.85 36.96 21.52 18.46 18.56 18.56 28.79 47.58 23.98 29.30 18.31
paper5x80 981924 5.45 11.40 5.50 4.72 4.93 4.93 8.59 12.17 7.63 7.49 4.68
test1 2097152 11.07 82.00 11.75 10.10 10.25 10.25 18.34 25.99 14.01 16.00 10.00
test2 2097152 11.07 82.00 11.75 10.10 10.25 10.25 18.34 25.99 14.01 16.00 10.00
test3 2097152 11.07 82.00 11.75 10.05 10.25 10.25 18.34 26.00 14.63 16.00 10.12
totals 67050103 343.45 776.59 375.68 321.61 322.48 322.47 562.25 831.21 406.36 511.57 319.84
mean - 5.37 12.14 5.88 5.03 5.04 5.04 8.79 13.00 6.35 8.00 5.00
Algorithm:
----------
libdivsufsort uses the following algorithms for suffix sorting.
- The improved version of Itho-Tanaka two-stage sorting algorithm. [2][6]
- A substring sorting/encoding technique. [1][3]
- Maniscalco's tandem repeat sorting algorithm. [5]
- Larsson-Sadakane sorting algorithm. [4]
References:
-----------
1. Stefan Burkhardt and Juha K"arkk"ainen. Fast lightweight suffix
array construction and checking. Proceedings of the 14th Annual
Symposium on Combinatorial Pattern Matching, LNCS 2676,
Springer, pp. 55-69, 2003.
2. Hideo Itoh and Hozumi Tanaka, An Efficient Method for in Memory
Construction of Suffix Arrays, Proceedings of the IEEE String
Processing and Information Retrieval Symposium, pp. 81-88, 1999.
3. Pang Ko and Srinivas Aluru, Space-efficient linear time
construction of suffix arrays, Proceedings of the 14th Annual
Symposium on Combinatorial Pattern Matching, pp. 200-210, 2003.
4. Jesper Larsson and Kunihiko Sadakane, Faster suffix sorting.
Technical report LU-CS-TR:99-214, Department of Computer
Science, Lund University, Sweden, 1999.
5. Michael Maniscalco, MSufSort.
http://www.michael-maniscalco.com/msufsort.htm
6. Yuta Mori, Short description of improved two-stage suffix sorting
algorithm, 2005.
http://homepage3.nifty.com/wpage/software/itssort.txt
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