[Biojava-l] FW: Location Problems

[Ewan Birney]

On Wed, 24 Oct 2001, Forsch, Dan wrote:

> I'm pretty sure this doesn't qualify as 'brilliant thought', but...
> 
> I'd like to see the solution to this problem move BioJava away from having
> StrandedFeature as a sub-interface of Feature, thereby eliminating those
> annoying (to me anyway) 'if instanceof StrandedFeature' checks in the code.
> A Strand could become an attribute of (and inner class within) something
> else, possibly of Locations.  If each Location has an associated Strand then
> the components of a CompoundLocation could differ.  I'm not sure if this
> fixes the issue with RemoteFeatures but I think the same principle would
> apply.

This is like the bioperl approach. (bioperl takes locations into a whole
tree-system to allow representation of FuzzyLocations)


I know that Thomas likes in BioJava strandness being a property of the
feature, not the location which I think it quite a good principled
stand: it just causes havoc wrt to EMBL/GenBank.



I think I made a similar stand against "complex" locations in Bioperl for
a while before I was overruled by people wanting, understandably, to parse
the *whole* of GenBank, and then round-trip it properely.



It is going to be interesting to see BioJava's approach to this. 


But - just to say - I don't think there is a 100% clean solution
here. Just different compromises.

ewan