Release notes for bpr2 (bucket-pointer refinement,  version 2.0.0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Copyright (C) 2005 Klaus-Bernd Schürmann

  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., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA


This package contains the implementation of the bucket-pointer refinement algorithm version 2.0.0 (bpr2)
to construct suffix arrays ('./src/SuffixArray/kbs_SuffixArrayConstDStepAndPre.c' resp.
'./src/SuffixArray/kbs_SuffixArrayConstDStepAndPreNumbers.c').

This is a faster enhanced implementation of the algorithm described in the paper:
Klaus-Bernd Schürmann and Jens Stoye
An Incomplex Algorithm for Fast Suffix Array Construction
'Proceedings of the 7th Workshop on Algorithm Engineering and Experiments
and the 2nd Workshop on Analytic Algorithmics and Combinatorics ({ALENEX}/{ANALCO} 2005)'.
The current algorithm is presented in my PhD thesis.


The programs of this package are
	1. bprtime     - timing for the bpr algorithm
	2. fibstring   - generation of fibonacci string of certain length
	3. periodicstr - generation of periodic string with certain alphabet size, period length, and string length


To install the programs execute
	./bootstrap.sh
	./configure CC=<compiler-command> CFLAGS="<compiler-options>" bindir=<directory-to-install-binaries>
	make
	make install

The default options for ./configure are CC=gcc, CFLAGS="-O3 -fomit-frame-pointer -funroll-loops -fprefetch-loop-arrays -W -Winline -Wall", 
and the default bindir of the system.

The program is executed by: bprtime -q=<size of prefixes to which respect the suffixes are initially sorted> <File of Input String>,
where the -q Option can be omitted.


To see more documentation of the source code, execute
	doxygen doxyBpr.cfg
The documentation of the source code will be located in the directory ./docs

For more details on how to deal with automake read the file 'INSTALL'

The software in this archive should be considered an ALPHA version. I will be
glad to receive your comments and bug reports.

Klaus-Bernd Schürmann
([email protected])