[Biojava-l] Blast xml parsing

[Jose Duarte]

I am a newbie to biojava so sorry if questions are too simple!

I am trying to use Biojava's blast xml parsing following the cookbook 
from biojava's web.

So far I managed to parse correctly the xml output from blast getting 
the SeqSimilaritySearchResult object and then the SeqSimilaritySearchHit 
and SeqSimilaritySearchSubHit. From those I could get bit scores, a 
SimpleAlignment object, sequences as SymbolList objects and all kinds of 
things. My question is how to get the percentage identity as well as all 
of those. That must be obvious but I've been looking around and couldn't 
find how.

Any pointers appreciated

Thanks

Jose


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Jose M. Duarte
Max Planck Institute for Molecular Genetics
Ihnestr. 63-73
14195 Berlin
Germany