[Biojava-dev] biojava3-ws alternate NCBIQBlastService implementation

[Gediminas Rimša]

Hello,
I have just uploaded an alternate implementation for NCBIQBlastService 
to biojava-live (available in org.biojava3.ws.alignment.qblast2 package).

The main difference is that this service accepts any Blast URL-API 
(http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html) parameters set using 
corresponding setAlignmentOption/setOutputOption methods.
For example, you could specify Entrez query by calling 
setAlignementOption("ENTREZ_QUERY", "query string") for 
NCBIQBlastAlignmentProperties2 object and it, along with any other 
alignment options, would be transformed to Blast URL parameters.

I think it should either be merged with the current implementation or 
kept as an alternate to maintain backwards-compatibility for current 
service users. Any thoughts on that?

Gediminas