[Biojava-dev] Hello and support for FASTA34

[Richard Holland]

Hello! It's great that you are volunteering. We really appreciate all the
help we can get.

Does your new code support both the older 3.3 and the new 3.4 format, or
does it support only the newer one? It'd be nice if it could read both
even if it can only write the newer one (that's the way our newer parsers
in the BioJavaX extension packages work).

The best way to contribute small amounts of code is to do what you have
done and post a message to the list. Then, someone with CVS access will
offer to review it and commit it.

So, the next step is to email me the code you have written as an
attachment, to the email address I am sending this message from. I'll then
check it through and commit it.

We also ask that test cases be written for each new piece of code
submitted. I don't know if you've come across JUnit at all, but if you
have and you know how to write a JUnit test to test your new code then
that would be extremely useful to have.

Thanks again for your help and I'm looking forward to seeing your code.

cheers,
Richard


On Mon, July 9, 2007 8:31 pm, kdoshi at asuragen.com wrote:
> Hello Biojava.
>
> My name is Kishore Doshi. I have been programming in Java and C++ for 8+
> years now and I just completed my PhD in Molecular Biology at the
> University of Texas at Austin. For my PhD work, I developed a software
> toolkit in Java for RNA comparative sequence analysis at the Gutell Lab.
>
> As part of my new job, I have just come across the Biojava API and I am
> very impressed with the capabilities available. I wish I would have used
> it a few years ago when developing my RNA comparative sequence analysis
> toolkit.
>
> I would be interested in lending my time to help Biojava as it continues
> to evolve. One area I have noticed I could provide immediate help would
> be in support for parsing FASTA search results. The classes
> FastaSearchParser and FastaSearchSAXParser appear to support FASTA 3.3;
> however, they do not appear to support FASTA 3.4. I have modified
> FastaSearchParser and FastaSearchSAXParser to support the tag
> modifications in FASTA 3.4 output. I would be interested in contributing
> my changes back to the community if possible. Please advise on how I
> should move forward.
>
> Thanks
> Kishore Doshi, M.S.;Ph.D. | Bioinformatics
> Asuragen, Inc. -- A Spin-Off of Ambion
> 2150 Woodward, Suite 100, Austin TX USA 78744
> Tel: 1-512-681-5397 | Fax: 1-512-681-5201
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK