[Biojava-l] Genbank parsing problem

Schreiber, Mark mark.schreiber@agresearch.co.nz
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.

- 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.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> 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.