[Biojava-l] circular sequences

[Mark Schreiber]

On Fri, 26 Jan 2001, Matthew Pocock wrote:

> 
> The circular-view option gets my vote. I think it is prety much as 
> simple as saying ((indx-1) % length) + 1 in apropreate places. Could we 
> make the circular view a Sequence implementor, and leave all SybmolLists 
> linear? We can automagicaly handle the Location issue during the process 
> of instantiating a Feature.Template as a Feature instance. I think the 
> Location objects will need wrapping in a CircularLocation object that 
> knows the sequence length, and makes the wrapped location appear to 
> repeat for ever - e.g. If we have a Range 20..30 and a sequence length 
> 100 then CircularLocation wraps this and makes it behave as if it 
> contains 20+n100..30+n100 (n is any integer, positive or negative).
> 
> Anybody keen to write this code?

I don't mind giving it a go, I'm pretty new to biojava but keen to
contribute. I think a will go for the circular veiw approach. Again the
circularlocation wrapper is probably a good idea. I think it should be a
wrapper on a StrandedFeature object as only DNA can be circular and
900..115 in the direct orientation is different to 900..115 in the reverse
orientation.


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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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