Minimal effort performance improvements

[mcamagna]

Several performance critical steps are run on a single CPU instead of multi-threaded, which could be alleviated with minimal effort (less than 10 min work).

For example changing the static methods in the Methods class to non-static and call them in parallel. In the case of the --calculateThreshold step, calling Methods.rankVector() in parallel from the ExpressionMatrix class vastly improves the performance.
Also, performance could be improved by reading the data using Java's NIO BufferedReader.

I'd be willing to contribute these improvements to your program, but as I understand it, your licence seems to prohibit this, is this correct?