[Biojava-l] pair-wise alignment demo

[Matthew Pocock]

Dear all,

I have been poking around in the pair-wise dp code, trying to make it
cope with ambiguity symbols & gaps. I don't think that I am all the way
there yet, and performace could be improved a lot (as soon as I can
profile it).

I have added a demo - dp.PairiseAlignment - that alignms all the
sequences in one fasta file to all of the sequences in another file. It
runs like a dog, but I think it is doing something sensible. I will add
prety-printing of the alignments when I get the time.

If any of you want to try to profile the demo, I would be keen to hear
where the CPU bottle-necks are.

All the best,

Matthew