For our purposes, it's important to be able to reconstruct the Genbank record from a BioJava sequence. I wish Genbank didn't allow this construction, but since it does we have to deal with it. Even though this isn't a BioJava-type feature, I'd rather see BioJava's definition changed to fit Genbank/EMBL rather than vice-versa.
Looking at the docs, I'd rather have this mapped to a fuzzy point location, and relax the restriction on where features can be constructed. Greg Cox > -----Original Message----- > From: Schreiber, Mark [mailto:[EMAIL PROTECTED]] > Sent: Tuesday, April 30, 2002 5:33 PM > To: Thomas Down; Simon Foote > Cc: [EMAIL PROTECTED] > Subject: RE: [Biojava-l] Genbank parsing problem > > > To my mind a wholey remote feature is not really a Feature in the > biojava sense and might be best handled as an Annotation. Perhaps a > special kind of value (with a nice toString() method) could be > constructed for it. > > - Mark > > > > -----Original Message----- > > From: Thomas Down [mailto:[EMAIL PROTECTED]] > > Sent: Wednesday, 1 May 2002 3:26 a.m. > > To: Simon Foote > > Cc: [EMAIL PROTECTED] > > Subject: Re: [Biojava-l] Genbank parsing problem > > > > > > On Tue, Apr 30, 2002 at 09:12:59AM -0400, Simon Foote wrote: > > > I've recently run across a problem with parsing of Genbank files > > > containing unbounded locations. > > > Anyone have any idea what's causing it. I tried to trace it back > > > through but got lost. But I think it has to do with the > > single <1 for > > > the -35_signal as shown in the example. > > > > > > -35_signal <1 > > > /gene="entD" > > > > The default Feature implementations in the BioJava > > development tree explicitly forbid construction of Features > > with locations which aren't contained by the sequence to > > which they're attached. As a quick fix, you can just remove > > the check from the constructor of > > org.biojava.bio.seq.impl.SimpleFeature (lines 281--283 in my copy). > > > > I'm not sure what the proper solution for this problem is. > > Normally, features which extend beyond the sequence can be > > transformed into RemoteFeatures. However, this particular > > feature is nasty in that it doesn't even partially overlap > > the sequence. To my mind, it's actually pretty much > > meaningless, and the best thing to do would be to drop it. > > But some people like to be able to represent the whole of Genbank. > > > > Does anyone know how many more `wholly remote' features there > > are in the databases? And any great ideas about how they > > could be usefully represented? > > > > Thomas. > > > > _______________________________________________ > > Biojava-l mailing list - [EMAIL PROTECTED] > > http://biojava.org/mailman/listinfo/biojava-l > > > ============================================================== > ========= > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other > use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ============================================================== > ========= > _______________________________________________ > 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
