[Biojava-l] circular sequences

[Thomas Down]

On Fri, Jan 26, 2001 at 09:35:30AM -0800, Emig, Robin wrote:
> 
> > Circular Sequence objects are slightly more of a pain, since I
> > might want a Feature running from, say, 900 - 100.  Not sure
> > what the best way to handle this is -- it's not a case recognized
> > by out current Location objects.
> > 
> 	Maybe we should have a direction value for a feature?

We already have directional features (well, StrandedFeature).
The problem is that, right now, our locations can only cope
with cases like 100-900 (which has the same meaning on both
linear and circular sequences).  On a circular sequence, 900-100
(spanning the `join' in the circle) has a completely different
meaning.

Matthew has suggested a scheme of special CircularLocations
which should solve this problem.  The only slight inelegance
is that CircularLocations will need to know about the length of
sequence they are referring to, while all the current  Location
implementations are context-independant.

This is probably the way to go, though...

   Thomas.