[Biojava-l] sequence similarity searches - some code

[Gerald Loeffler]

Matthew Pocock wrote:
> 
> 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.

the code to parse the sub-hit alignments from the blast-output is not
there yet, that's what i meant in my original posting when i said "The
hard parsing part, namely parsing the alignments from the textual output
of BLASTP still needs to be done...". I'll have to fill in this missing
part very soon, though... Another issue that's open is creating
SequenceDB objects that are actually capable of fulfilling a
getSequence() request for a sequenceID that was extracted from a blast
hit.

> 
> 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.

should be possible - but i haven't looked at the XML-SAX-BLAST-parser
code yet. I'll try to do this next week. Of course i'd be happy if i
could use existing code to actually get at the alignments...

	cheers,
	gerald
> 
> Matthew

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