[Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Nov 26 13:38:31 EST 2008


------- Comment #11 from cjfields at bioperl.org  2008-11-26 13:38 EST -------
(In reply to comment #10)
> Thanks, Heikki-
> > 3. Using annotations to store the additional information is fine, cause that
> > allows you to use normal rich sequence formats, but accessing is not that
> > straightforward. Why do not you create a new sequence object that inherits from
> > Bio::Seq::RichSeqI (or Bio::Seq::RichSeq) and adds convenience methods for
> > accessing the additional information.
> I will look at this carefully. [The patches above remove the special
> annotations all together in favor of a more fluid and easier to use 'internal'
> solution.]

The more generic the solution, the less likely you'll run into odd issues (i.e.
the persistence issue I mentioned above).  However, at some point you can
certainly suggest changes/patches to allow certain behaviors or deal with some
types of data, particularly if they are widely applicable.

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