Bioperl-guts: Seq rewrite
Thu, 5 Aug 1999 22:00:54 -0700
----- Original Message -----
From: Matthew Pocock <email@example.com>
To: bioperl guts <firstname.lastname@example.org>
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:
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 :)
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( "mollusc" )
Lets see what the others say when they get back!
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