This is a program designed to sort through a text file with strings of characters to determine the distance and matching score of all elements in the file. The program will take in a file destination as the input, the file output destination as output, and the number of processing threads to use as cores (it is suggested to have it at 4).
java -jar MotifSearching <input> <output> <cores>
<Input> and <Output> is needed, but <cores> is an optional input. If no value is found for <cores> it will default to 4.
First clone the project or download as a zip.
Unpack the archived projects.
Import an existing project into eclipse.
Browse for the main project folder and only select MotifSearching for the project. Make sure you uncheck motif.mapreducer as that is not used. Not doing this will cause some file read conflicts unless you make some changes yourself in the MotifLauncher class.
You should have a structure looking like this.
Make sure you find the launcher class MotifLauncher to run the project from.
That's all there really is to it. Give it a run and look through the code to see how it all works!