[Biojava-l] FramedFeature interface

[Mark Schreiber]

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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