Bioperl-guts: Seq rewrite

Kate katel@worldpath.net
Thu, 5 Aug 1999 22:00:54 -0700


----- Original Message -----
From: Matthew Pocock <mrp@sanger.ac.uk>
To: bioperl guts <vsns-bcd-perl-guts@lists.uni-bielefeld.de>
Sent: Tuesday, August 03, 1999 8:24 AM
Subject: Bioperl-guts: Seq rewrite


> Dear guts,
>
> I won't see you on the 5th. The last seq mail I sent was a bit of a
> mess. Sorry. I have tried to put my ideas down more clearly this time.
> Look at:
>
> http://www.sanger.ac.uk/Users/mrp/bioSeq.txt

   Thank you for your contribution.  Since I'm unable to attend the
conference( I'm camping on an island in a lake ) , I took a look at your
interface.My first impressions are

1.  I like the idea of a Seq abstract class.  But I prefer not to have the I
at the end.  I'm biased towards pronounceable names.  I've been hanging
around the wiki site too much :)

http://c2.com/cgi-bin/wiki

2.  I'd like the idea of DNASeq, RNASeq and protein sequence subclasses.  We
can use a type, but I think it will cause a lot of if then elses and cases,
that clutter the code.  I think we should aim for maintainable  and
self-documenting code,  even for sophisticated users.  They should be free
to focus their brain cells on the DNA code not our perl code :).  And then
we won't need a vanilla implementation.

3. What about making the annotation object a component, so you won't have to
carry the extra baggage unless you need it.

4.  I feel the translate modules should be based on tables, with optional
parameters to select for nonstandard codes.

$seq->translate()
$seq->translate( "mollusc" )

  Lets see what the others say when they get back!



                                                  Kate

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