[Biojava-l] implementing writeSequence for EMBL/Genbank

Cox, Greg gcox@netgenics.com
Wed, 21 Feb 2001 14:30:18 -0500

	Before you spend time on FuzzyLocations, be aware that they are
being redesigned as we speak.  

	My two cents on the writing format issue:  If EMBLLikeFormat is
limited to SwissProt and EMBL, you can switch on the type of the sequence.
AA sequences turn into SwissProt and Nucleotides go to EMBL.  Are there
other formats that are EMBL-like?


> -----Original Message-----
> From: Keith James [mailto:kdj@sanger.ac.uk]
> Sent: Wednesday, February 21, 2001 11:45 AM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] implementing writeSequence for EMBL/Genbank
> I'm about to start on writeSequence for EMBL format (and other
> EMBL-like formats). All these will probably have a bunch of utility
> methods in common e.g. writing/wrapping lines with variable leader
> strings, formatting sequence blocks and other tiresome stuff. Perhaps
> a utility class with static methods for these?
> At the moment the EmblLikeFormat class has a writeSequence method
> which explicitly throws a RuntimeException, as does
> GenbankFormat. Only FastaFormat is not "faking it".
> As EmblLikeFormat is generic how is writeSequence to know whether (and
> how) to write EMBL or SwissProt etc? The writeSequence method is not
> parameterized to accept a formatting object. If this were done at the
> constructor it would impinge on sequence reading, which does just fine
> without help from other classes. Anyway, a formatting object for a
> format object doesn't seem very elegant.
> Matt has suggested splitting the SequenceFormat interface into two;
> one for reading, one for writing. I don't know enough about design to
> judge the merits of this in the long term. As a naive user of BioJava
> I quite like the one-stop SequenceFormat which knows all about
> reading/writing its own data; "it does exactly what it says on the
> tin". But maybe I'm wrong...
> I'd like to get some opinions before I start hacking.
> cheers,
> -- 
> -= Keith James - kdj@sanger.ac.uk - 
http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
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