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

[Andreas Prlic]

Hi Dragos,

many years of research have been put into both Blast and Hmmer and it
will be highly unlikely that you will be able to come up with
something better in a summer. As such best to focus on getting a plain
port. If you get ideas how to make the algorithms perform better
during that time, probably best to feed back that information to the
original developers.

> Secondly, converting C/C++ source code into Java would be a very interesting
> and challenging task for me. At least for the C++ part I am thinkig to
> approach the use oh JNI, but is it possible to occur problems with
> portability, building, or JVM's stability? I have also read about NestedVM
> which provides binary translation for Java Bycode, and this approach could
> be useful.

Scooter, do you want to answer this one?

Thanks,

Andreas