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:[EMAIL PROTECTED]] > Sent: Tuesday, October 23, 2001 10:13 AM > To: '[EMAIL PROTECTED]' > 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 > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
