[Biojava-dev] Extended ABIF Parser and SCF Writer

[Franklin Bristow]

Hi Richard,
I've written a very small private class that extends ABIFChromatogram.  This
class has a method that basically copies what you have done in
ABIFChromatogram when you load a file as an ABIFChromatogram, specifically:

>         /**
>          * Create an instance of an ExtendedABIFChromatogram using the
> supplied
>          * file. This is meant to be called in lieu of the static create
> method
>          * that is found in {@link ABIFChromatogram}.
>          *
>          * @param f
>          *            the ABIF formatted file
>          * @return an instance of ExtendedABIFChromatogram
>          * @throws UnsupportedChromatogramFormatException
>          *             the file supplied is not an ABIF formatted
> chromatogram
>          * @throws IOException
>          *             if an I/O error occurs
>          */
>         public ExtendedABIFChromatogram createExtended(File f)
>                 throws UnsupportedChromatogramFormatException, IOException
> {
>             new Parser(f);
>             return this;
>         }
>
This removes the need for using reflection to alter the accessibility of the
methods.

I've attached the updated code to this message, I hope that you will allow
it through your filters again.  Thanks again for having a look at my code!

Thanks,
Franklin

On Fri, Jun 19, 2009 at 12:23 AM, <mark.schreiber at novartis.com> wrote:

>
> 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]
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
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-- 
Franklin
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