[Biojava-l] Can I modify a SeqSimilaritySearchSubHit?

[mark.schreiber at novartis.com]

Hello -

They are immutable because the Annotation object (and others) throw 
ChangeVetoExceptions when altered. This is probably a good thing.

The decision to not include the query ID is pretty contraversial and ran 
along the lines of ... you knew what it was when you did the search you 
should know it now. Probably not the best reason. I'm pretty sure the 
query is emmitted by the BLASTLikeSAXParser it's just not listened for by 
the subsequent SeqSimilarityAdapter or BlastLikeSearchBuilder  (see 
http://www.biojava.org/docs/bj_in_anger/BlastParser.htm for a description 
of the Blast parsing pipeline). To check if the Query is emitted, and what 
type of event it generates, you could use the example here 
(http://www.biojava.org/docs/bj_in_anger/blastecho.htm).

If the event is emitted then a simple modification to SeqSimilarityAdapter 
of BlastLikeSearchBuilder should allow it to be included in the Annotation 
object of the SeqSimilaritySearchHit.

- Mark





Douglas Hoen <douglas.hoen at mail.mcgill.ca>
Sent by: biojava-l-bounces at portal.open-bio.org
04/13/2005 01:34 AM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Can I modify a SeqSimilaritySearchSubHit?


Hi,

I want to modify the annotation of a SeqSimilaritySearchSubHit.
(Specifically, I want to add the query ID, since I can't find a way to
get at it from a SeqSimilaritySearchSubHit.) However, 
SeqSimilaritySearchSubHit appears to be immutable. Is there any way I
can make this class mutable, or do I have to write my own class (e.g. a
wrapper)?

Thanks,
Doug

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