/karkkainen-sanders

Karkkainen Sanders Suffix Array construction in O(n) in C#, python, java, perl and octave

Primary LanguageJavaGNU General Public License v2.0GPL-2.0

code - contains the source code implementations in various languages

tests - contains tests of different sizes and formats

Running examples:
====================

Assmuption: running from current directory where this file is located

Java:
java -jar code/java/Bioinformatika.jar tests/test1.txt out.txt

Octave:
octave -q --path code/octave/ --eval "suffixArrayFromFile('tests/test1.txt', 'out.txt')"

C#:
code/c#/Bioinf-labos.exe tests/test1.txt out.txt

Python:
python code/python/projekt_v4.py tests/test1.txt out.txt

Perl:
perl code/perl/SuffixArrayAgain.pl tests/test1.txt out.txt


About tests:
-----------

testsBigXYZ.txt
- are tests of XYZ uniformly sampled random characters.
- They are used for testing the speeds and memory usages of the various
  implementations (time(1) and the script memusg were used to do so)

test1.txt and test2.txt
- They test the algorithms for correct output given a FASTA input
- The output of the programs shell be compared to output1.txt or
  output2.txt accordingly.