[Biojava-l] BlastLikeSearchBuilder and queryIDs

[Frank Vernaillen]

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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