[Biojava-dev] Fwd: [Biojava-l] Port an Algorithm to Java

[Russ Kepler]

On Wednesday, April 04, 2012 11:52:18 AM Smithies, Russell wrote:
> Another option
> if you really want to integrate blast+ might be JNI?

Back when I was doing a lot of that it worked out as well to integrate with 
the command line executable - the output files were generally transportable and 
often could be parsed from the standard output.  I don't think it would work 
as well with an application with fine granularity but those aren't very common 
in this line of work.