[Biojava-l] BLAST Parser in Anger!

[staatsb]

I was successful in getting the BLAST parser to work outlined by the 
"BioJava in Anger" doc by changing the version number too 2.0.11 (thank 
you Mark Schreiber X2).  However, a few of the APIs dont seem to 
function i.e.  getSequenceID() is not recognized, but I dont think 
thats due to the version change.  Also, I have noticed many API calls 
to certain BLAST file features missing i.e. getQueryID, getGaps, 
getQuerySequence, getSubjectSequence, and more.  Are these really 
missing or does the programmer (me) need to define them from the APIs 
existing  structure?  Has anyone else been able to obtain these 
features with the missing APIs?  Can anyone offer any advise, 
suggestions, explanations, etc, to these issues?

Thanks

Brian Staats
Bioinformatics Programmer Analyst
NIH/NCI/Core Genotyping Facility
staatsb at mail.nih.gov