[Biojava-l] FramedFeature interface

[Simon Brocklehurst]

"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?

Robin,

In general, I think there are no right or wrongs with this kind of thing.  For
example, in regard of *sequences* starting at zero or one, it can obviously be
sensibly argued that index positions should start at zero, to mirror the way
programming languages tend to work.

In regard of reading frames, I'm unclear about the point of referring to the
frame directly by the *value* of an integer.  Rather, I would have it that the
*name* of a public static final int constant be used e.g.
FramedFeature.FORWARD_1 or FramedFeature.PLUS_1. That is, a name with a clear
meaning.  In this case, the actual *value* of the constant itself is irrelevant.

Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com