[Biojava-l] Parsing out identities from a blast file

[mark.schreiber at novartis.com]

Hi -

You need to use the SeqSimilaritySearchHit which is that parent of the 
SeqSimilaritySearchSubHit.  It has a method called getSubjectID() which 
gives you the ID of the hit subject.  All subhits with the same parent 
search hit will have the same subject ID so it makes more sense to store 
the information in this class.

- Mark


biojava-l-bounces at lists.open-bio.org wrote on 03/04/2009 11:36:21 PM:

> Hi there,
> 
> Does anyone know what methods I need to invoke to pull out the identity
> for a particular hit when parsing a blast output?
> 
> I can get the score, the start & end points etc using:
> SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)obj;
>                 LOGGER.debug("match:" + hit.getSubjectID() + ", score:"
> + hit.getScore() + ", e-value:" + hit.getEValue());
> 
> But I can't seem to find any method to pull out the identity of the hit,
> which I would have thought would be in the SeqSimilaritySearchSubHit
> interface.
> 
> Many thanks,
> 
> Ben
> 
> 
> 
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