SuffixArray version 1.0
=======================
FULL NAME:
Suffix array computation tool
DESCRIPTION:
Suffix array is a data structure used commonly for full text indices,
data compression algorithms and in various matching algorithms in
bioinformatics and computational biology. It is an array of indices
each corresponding to a starting position of a suffix in a given string.
This software is a C++ encapsulation of sais-light-2.4.1 library written
by Yuta Mori [1] implementing the induced sorting [2] based suffix
array construction algorithm.
SYNOPSIS:
#include<vector>
#include<SuffixArray.hpp>
string text("This is my text");
/* Make SuffixArray */
/* Construction */
SuffixArray<int|long|unsigned|double> SA(text);
/* OR */
SuffixArray<int|long|unsigned|double> SA;
SA.make(text);
/* Get Array */
vector<int|long|unsigned|double>Array = SA.GetSuffixArray(); // [15 4 7 10 0 12 1 2 5 8 3 6 14 11 13 9]
CONSTRUCTION AND RUNTIME COMPLEXITY:
For:
|S| - input string size
The algorithm runs in O(|S|) worst-case time
ACKNOWLEDGMENTS:
1. Yuta Mori, 2010. https://sites.google.com/site/yuta256/sais
2. Ge Nong, Sen Zhang and Wai Hong Chan, Two Efficient Algorithms
for Linear Suffix Array Construction, 2008.
AUTHOR:
Robert Bakaric <rbakaric@irb.hr>, <bakaric@evolbio.mpg.de>
COPYRIGHT AND LICENSE:
* Copyright 2015 Robert Bakaric
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
* MA 02110-1301, USA.