While the ideal solution would be a clean port of the BLAST algorithm to Java, the complexity of such a mature and performance-optimized code might be a bit too much for a GSOC project.
The JNI solution, while not optimal, would be an acceptable fallback solution. If implemented properly, a base for using existing programs like BLAST, HMMER, … via JNI could be created. The project goal is: "Make BLAST work locally, without internet connection in addition to the existing NCBIQBlastService method" Hannes On Sun, Mar 18, 2012 at 08:42, Komal Sanjeev <[email protected]> wrote: > Hi Amr, > > The following has been mentioned in the project description: > "Converting C or C++ source code by hand is not a trivial undertaking and > it is recommended that a C/C++ to Java conversion tool be used to do as > much of the work as possible. It is also an option to consider a JNI > approach for integrating these applications into Java." > > I am a bit confused. Kindly tell me what exactly has to be done in the > project. > > Thanks, > Komal > > > > On Sun, Mar 18, 2012 at 9:35 AM, Amr AL-Hossary > <[email protected]>wrote: > >> Dear Komal, >> >> As far as I know, The project is about porting the code to Java, not using >> existing C code within JNI. >> That means you should be able to digest the algorithm first, Build it >> using Java from scratch, depending on C code as a reference Implementation. >> >> Regards >> >> Amr >> >> -----Original Message----- >> From: Komal Sanjeev >> Sent: Sunday, March 18, 2012 12:59 AM >> To: Andreas Prlic ; [email protected] >> Subject: Re: [Biojava-l] Interested in working with BioJava for GSoC 2012 >> >> Hi all, >> >> Introducing myself a bit more, I also work as a remote intern for >> DARNED<http://darned.ucc.ie/>. >> DARNED is a database of RNA Editing, and currently new features are being >> added into the project, one of which is incorporating the BLAST feature for >> sequence based search. Having worked on a similar project recently, I think >> I will be comfortable working with the 'Porting an Algorithm to Java' >> project. >> >> The following is what I understood about the project. Please correct me if >> I am wrong. >> This(link) <http://biojava.org/wiki/BioJava:CookBook3:NCBIQBlastService> >> is >> the current method used for BLAST, which accesses the NCBI website each >> time. The NCBIQBlastService class is currently used. The project aims at >> replacing this with code which will perform the search within Biojava. I >> downloaded the source codes of BLAST and HMMER. My job will be to convert >> these to Java. >> >> Regarding the C/C++ to Java converter, i found this on the internet: >> >> http://tangiblesoftwaresolutions.com/Product_Details/CPlusPlus_to_Java_Converter_Details.html >> >> but it is not free of cost. >> Apart from this, I saw that many people discourage the use of C/C++ to Java >> tools saying that they are not efficient. Does anyone know of any better >> tool which can do this? >> >> Regarding the JNI, would it not be better if the whole code was written in >> Java, rather than a part of it being in C/C++? I haven't used it before, >> but if it is better than converting the code, I don't have a problem >> working with it. >> >> Kindly clear my doubts. >> Thanks in advance, >> Komal >> >> >> >> On Thu, Mar 15, 2012 at 1:17 AM, Andreas Prlic <[email protected]> wrote: >> >> > Hi Komal, >> > >> > stay tuned to this list, we still don't know if we will get funded >> > from Google this year. >> > >> > Andreas >> > >> > >> > On Wed, Mar 14, 2012 at 12:27 PM, Komal Sanjeev >> > <[email protected]> wrote: >> > > Hi Everyone, >> > > >> > > I am Komal, an undergraduate student from IT-BHU, India. I'm interested >> > in >> > > working with BioJava for GSoC 2012. I am particularly interested in >> > working >> > > on the 'Porting an Algorithm to Java' project. >> > > Kindly help me about how I should proceed. >> > > >> > > Thanks, >> > > Komal >> > > _______________________________________________ >> > > Biojava-l mailing list - [email protected] >> > > http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
