[Biopython-dev] reusable code in Genbank

Cayte katel at worldpath.net
Wed Mar 14 03:47:53 EST 2001

----- Original Message -----
From: "Brad Chapman" <chapmanb at arches.uga.edu>
To: <biopython-dev at biopython.org>
Sent: Saturday, March 10, 2001 11:19 AM
Subject: Re: [Biopython-dev] reusable code in Genbank

> Cayte:
> > _EventGenerator in GenBank looks like generic glue code that
> > could be used in my Kabat parser.  I could cut and paste it but
> > code adds to the maintenance load.  Andrew, I suggest moving it to
> Jeff:
> > Looks more appropriate for Bio/ParserSupport.py.
> I'm glad this code can be of more general use. I just cleaned up
> _EventGenerator a bit (it had some ugly GenBank-specific stuff in it)
> and moved it into ParserSupport.py, as Jeff suggested. It's called
> EventGenerator(), and now GenBank uses it from ParserSupport.
> One thing I was worried about is that EventGenerator is an XML
> handler, so it derives from an XML handler class. I didn't want to
> make ParserSupport only be usable if the user had XML installed (since
> non-Martel-based parsers use ParserSupport) so EventGenerator will
> only be conditionally created if the XML import goes okay, otherwise
> an error message will be printed.
.   Since this post, I've noticed more opportunities to reuse code.  I think
the class Referennce.py in Genbank is close enough to the Kabat references
to use as a base class.

   All of us may be able to create more efficient code by exchanging ideas
and refactoring rather than just eaxh writing our own code


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