[Biojava-l] FramedFeature interface

[Eric Blossom]

It might help to keep separate the notion of internal models and external
formats. Parsers and exporters can be the liason between internal models
and external formats. This includes GUI visualization. One possibility
might be to use 0 based numbering internally and the appropriate numbering
for external formats as well as letting a user choose a numbering style in
a GUI.

This might allow some flexibility and promote the reuse of packages that
are not bio-oriented. Many of these use 0 based numbering.

cheers,
Eric Blossom

On Wed, 5 Sep 2001, Mark Schreiber wrote:

> On Tue, 4 Sep 2001, Ewan Birney wrote:
> 
> > On Tue, 4 Sep 2001, Emig, Robin wrote:
> > 
> > > 	So what your saying is that if you have the sequence ATGGAC, that
> > > the first A is position 1 in the sequence/symbol list, but position 0 in the
> > > frame/phase. I realize that 0,1,2 may be the most common convention, but
> > > does anyone else see how that can get confusing?
> > 
> > That's the way it is...
> > 
> > We didn't make this world - we just have to live in it ;)
> >
> 
> 
> I didn't mean to start a holy Jihad but the reason I have come out in
> favour of the 0..2 idea is because it is compatible with gff and xff (i
> think) and my main goal was to retain the frame info from GFF when parsing
> these files.
> 
> Further to the GFF parsing I have made an implementation of the
> FramedFeature and modified my local copy of GFFEntrySet so that its
> annonymous Annotator class produces FramedFeatures. Probably better to
> make each GFF entry hold a FramedFeature but this may break existing code.
> I'll send in the code for inspection once i transfer it between computers.
> 
> Mark
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Mark Schreiber			Ph: 64 3 4797875
> Rm 218				email mark_s@sanger.otago.ac.nz
> Department of Biochemistry	email m.schreiber@clear.net.nz
> University of Otago		
> PO Box 56
> Dunedin
> New Zealand
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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