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

[Smithies, Russell]

Porting an optimized application like blast+ to Java makes about as much sense as making an engine for your car out of Lego.
Sure you can copy all the individual components and eventually create a complete copy and it may even work but it will never be as powerful as the original.
Another option if you really want to integrate blast+ might be JNI?

--Russell

> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
> bounces at lists.open-bio.org] On Behalf Of Dragos-Bogdan Sima
> Sent: Wednesday, 4 April 2012 11:23 a.m.
> To: biojava-dev at lists.open-bio.org
> Subject: [Biojava-dev] Fwd: [Biojava-l] Port an Algorithm to Java
> 
> ---------- Forwarded message ----------
> From: Dragos-Bogdan Sima <simadragosbogdan at gmail.com>
> Date: Wed, Apr 4, 2012 at 2:21 AM
> Subject: Re: [Biojava-l] [Biojava-dev] Port an Algorithm to Java
> To: Amr AL-Hossary <amr_alhossary at hotmail.com>, Scooter Willis <
> HWillis at scripps.edu>, Andreas Prlic <andreas at sdsc.edu>
> 
> 
> Hello everyone,
> 
> As I went depth to the algorithms of Blast+ trying to figure out what whould
> be the best way to aproach the porting to Java, I came up with a new idea.
> 
> What if I first search for a source .cpp that does not have any dependencies
> (it does not need for another source .cpp for its processing)
> - "terminal source". For that source I could easily found out what is its input
> (print it in a file) and what is its output (print it in another file). Then in a java
> environment I would port that source to java and test manually (not
> necessary if I implement a test function) for the saved input, if its output is
> the same with the saved one. If true then the porting should be correct.
> 
> After processing with all the "terminal sources" I would advance with another
> level (directory) for each "terminal source" until all the porting is done.
> 
> Please tell me if I am thinking correctly and this approach is practical.
> 
> Have a nice day,
> Dragos.
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