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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
