[Biojava-l] CircularUpdates

[Mark Schreiber]

Hi -

I have tested and checked in modifications to the Circular API. Notable
changes:

1) It works with the new location schema
2) LocationTools can deal with CircularLocations
3) A new hidden class CircularLocationTools deals with most of the
ugliness
4) CicularSequence is deprecated in favour of the CircularView wrapper
5) Circular view can contain locations where the min is greater than the
max as long as the location is circular. (This allows overlaps of the
origin).
6) LocationTools has a static method for generating CircularLocations
7) CircLocTest has been updated and gives sensible results
8) Locations that overlap the origin are implented as a CompoundLocation
wrapped in a CircularLocation. This allows LocationTools to efficiently
handle Boolean operations. The only downside is that a location that
overlaps the origin is nonContiguous. I think this is a minor issue, you
could even argue that it is non-contiguous! A small price to pay for the
ease of boolean operations.

Ps this was my first adventure in CVS commits so let me know if I broke
anything.


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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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