[Biojava-l] Genbank parsing problem
Wed, 1 May 2002 09:32:47 +1200
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.
> -----Original Message-----
> From: Thomas Down [mailto:firstname.lastname@example.org]
> Sent: Wednesday, 1 May 2002 3:26 a.m.
> To: Simon Foote
> Cc: email@example.com
> 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?
> Biojava-l mailing list - Biojavafirstname.lastname@example.org
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