[Biojava-dev] GSoC - Final question about code exercise

[David Felty]

The directions for task 2 state:
> Write two FASTA output files one with sequences which contains ambiguous characters and another one without.

How should the input and output files be chosen? I currently have them
hard-coded into a main method, but this is obviously not very useful.
So should they be input on the command line, like:

java -jar runme.jar input.fa ambiuous.fa unambiguous.fa

Or should I just make a method, like:

public static void task2(File in, File ambiguous, File unambiguous) { ... }

Or would you prefer some other way?

Thanks,
David