[Biojava-l] beginners bug fileToBiojava problem with msf format

[Keith James]

I've checked in the changes.

Looking back at my notes I can see why I left out MSF and Clustal from
the auto-guessing method. By adding them we end up treating some
alignment formats differently to others i.e. MSF/Clustal
vs. fasta/raw. As fasta and raw can be either alignments or single
sequences, depending on the intention of the user I thought is better
never to allow guessing and always make the application programmer
specify explicitly themselves (using the method I mentioned in my
other post).

However, I think I was wrong as it's obviously given a nasty
surprise. So I've applied the fix and added the relevant tests.

Keith

-- 

- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -