[Biojava-dev] Extended ABIF Parser and SCF Writer

[Franklin Bristow]

Hi Everyone,
I've just spent the last few days putting together an extended ABIF parser
and and SCF writer.  The parser that I wrote extends the existing ABIFParser
but takes into account much of the information that was made available a few
years ago when ABI released the ABIF File Format specification (
http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf).
I've heavily based my code and methods on the perl implementation of the
ABIF parser Bio::Trace::ABIF by Nicola Vitacolonna.

I also wrote a writer for SCF formatted chromatograms.  I wrote this mostly
using the documentation found in the staden formats documentation (
http://staden.sourceforge.net/manual/formats_unix_2.html and
http://iubio.bio.indiana.edu/soft/molbio/molbio.old/staden/www_pages/scf-rfc.html
).

Finally, I have written a small utility class that will prepare an
ABIFChromatogram for writing out as an SCF formatted file.  This is the
entire reason that I wrote both of the above classes.  I will admit that
there is a pretty nasty hack in the SCFUtils class, but it was the quickest
way I could think of doing what I needed to do.  I use reflection in order
to make a protected method accessible so that I could set the value myself
without having to subclass ABIFChromatogram.  Of course, I would like to
change this but the circumstances under which I have had to write this code
forced me to do it this way for now.

All of this code is written for Java 5, but if it is necessary to change it
for inclusion into your source tree I will make the change.

So, I welcome comments and suggestions on how I can improve this to make it
appealing enough to have it included in biojava in the future.

Since the code is rather long, I've attached it as a zip file.  Andreas told
me that he would keep an eye on the filters for it and would let it through
when he saw it, so hopefully it makes it through okay.

Thanks everyone for your time!

-- 
Franklin
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ABIFParser.zip
Type: application/zip
Size: 19225 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-dev/attachments/20090618/44b13eb7/attachment-0002.zip>