[Biojava-l] FW: Location Problems

[Forsch, Dan]

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.

Dan Forsch, Principal Software Engineer
NetGenics, Inc.
1717 East 9th Street, #1600
Cleveland, OH  44114
phone: 206.374.4541


> -----Original Message-----
> From: Cox, Greg [mailto:gcox@netgenics.com]
> Sent: Tuesday, October 23, 2001 10:13 AM
> To: 'biojava-l@biojava.org'
> Subject: [Biojava-l] FW: Location Problems
> 
> 
> There's a architectural problem with how locations are 
> represented.  The
> problem is that strandedness is applied at the feature level, 
> but in some
> genbank files applies at the sub-location level.  For 
> example, MUSPRCON01
> has the feature:
> 
>      gene            join(complement(244..1502),L21211.1:1..105,
>                      L21222.1:1..141,L21212.1:1..89,L21213.1:1..101,
>                      L21214.1:1..185,L21215.1:1..225,L21216.1:1..113,
>                      L21217.1:1..116,L21218.1:1..130,L21219.1:1..198,
>                      L21223.1:1..137,L21220.1:1..141,L21221.1:1..664)
>                      /gene="PC4"
> 
> 	This highlights two things; first, remote feature 
> probably has to be
> re-worked.  It has no concept of strand, and should.  The 
> other is that
> there's at least one case where some component parts of a 
> compound location
> are on different strands.
> 
> 	I'm not making any proposals right now, just highlighting the
> problem.  Let me know if you have brilliant thoughts.
> 
> Greg
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