[Biojava-l] sequence similarity searches - some code

[Matthew Pocock]

Gerald,

I have had a (quick) look through this code. I like the assertion stuff. I have a couple of queries.

a) I can't find any code that actualy builds the sub-hit alignments. Am I being blind? Oh - bonus
points for using the Alignment interface at all - esp as you define a usefull 'key' object
SeqSimilaritySearchSubHit.QUERY_LABEL - this is exactly how alignments are meant to be used.

b) do you think that it will be possible to build these objects from the xml blast output? This would
be a realy nice thing to get working as-and-when.

Matthew