[Biojava-l] Genbank parsing problem

[Schreiber, Mark]

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:td2@sanger.ac.uk] 
> Sent: Wednesday, 1 May 2002 3:26 a.m.
> To: Simon Foote
> Cc: biojava-l@biojava.org
> 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.
> 
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> 
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