[Biojava-l] BlastLikeSearchBuilder and queryIDs

Schreiber, Mark mark.schreiber at agresearch.co.nz
Tue May 13 11:32:37 EDT 2003

Hi -

There have been some very recent changes made to the CVS to allow the
recovery of things like the query ID that where previously not
supported. They will be in BioJava1.3 final and I will make an effort to
update the BioJava in anger site when they come out.

In the meantime hopefully Keith James can tell you how it all works...
Keith, are you there???

- Mark

> -----Original Message-----
> From: Frank Vernaillen [mailto:fr_ve at hotmail.com] 
> Sent: Tuesday, 13 May 2003 9:03 a.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] BlastLikeSearchBuilder and queryIDs
> Hello!
> I'm planning to use BioJava for parsing some relatively large 
> (multi-megabyte, flat-file) Blast result files. My idea was 
> to parse the 
> data somewhat along the lines of 
> http://bioconf.otago.ac.nz/biojava/BlastParser.htm and 
> http://bioconf.otago.ac.nz/biojava/ExtractSearchInformation.htm.
> This way I end up with a Vector of SeqSimilaritySearchResults. The 
> SeqSimilaritySearchResult interface offers a 
> getQuerySequence() method, but 
> it returns a SymbolList, not a Sequence. Now this is a 
> problem, because I 
> can't seem to obtain the *queryID* of the sequence anymore, only the 
> sequence symbols themselves. Was this a deliberate design choice?
> Any ideas on how to elegantly obtain the queryIDs from the 
> parsed Blast 
> output?
> I am using biojava-1.3pre2-jdk14.
> Cheers,
> Frank.
> --
> Frank Vernaillen
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