[Biojava-dev] Extended ABIF Parser and SCF Writer

[mark.schreiber at novartis.com]

Hi Franklin -

If there is a good argument for making the protected setBaseCallAlignment 
method public then we could look at changing this so you don't need to use 
reflection.  As you say in your code comments this reflection will not 
work unless the security policy allows it which will not be the case in 
many systems.

Another alternative would be to modify ABIFChromatogram and provide a 
public method that lets people safely call the setBaseCallAlignment 
(requires write access to the SVN). Finally you could extend 
ABIFChromatogram and add a public method that will call the protected 
method (of course this won't work if the method is private).

Nice to see well documented code!

- Mark

biojava-dev-bounces at lists.open-bio.org wrote on 06/19/2009 10:31:13 AM:

> 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
> [attachment "ABIFParser.zip" deleted by Mark Schreiber/GP/Novartis] 
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> http://lists.open-bio.org/mailman/listinfo/biojava-dev

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