[Bioperl-l] Use of Bio namespace

David Block dblock@gene.pbi.nrc.ca
Wed, 11 Oct 2000 10:28:10 -0600 (CST)

Just a note on AUTOLOADing, in my experience:

On 11 Oct 2000, Keith James wrote:

> >>>>> "Ewan" == Ewan Birney <birney@ebi.ac.uk> writes:
> As we don't have to deal with splicing in a lot of our genomes, we
> don't suffer so much from the introns/exons/splice-sites as top-level
> features problem. This EMBL parser deals in generic features because
> the interpretation depends on what particular convention the
> originators of the sequences you want to parse were using that day. (a
> case of the beauty of standards being that there are so many to choose
> from). The assumptions are made at the script level at the moment
> e.g. building gene objects.

We're going to have to do the same, I guess, with our bioTk stuff.

>     >> Terse, but intuitive manipulation of feature qualifiers in
>     >> scripts
>     >> 
>     Ewan> I don't like this part of Bioperl 100% either. What is your
>     Ewan> suggestion?
> I've been using various equivalents to the bioperl 'tags' methods, but
> with the ability to regex tag names, plus AUTOLOADing a method for
> each tag/qualifier which returns the first value, or all values
> depending in scalar/list context (keeping a list of valid AUTOLOADable
> methods). These can get called a lot, so I need to fix it so that the
> methods get created and installed in the module's namespace the first
> time round, so subsequent calls will find a 'real' one and not go
> looking.

Damian Conway's Object Oriented Perl gives a fantastic example of
dynamically generated get/set methods produced by an AUTOLOAD.  We are
using it for our database/Bio::Seq integration code, with an additional
update_db routine that handles the sql.  I'd love to share it with you,
but the lawyers here are trying to figure out how to get money out of you
people (fat chance :), so we're in waiting mode.

> One thing that I can put in pretty soon is a Tk Blast/Fasta search
> viewer widget because that relies on a pretty simple adapter to accept
> Hit/HSP objects and a callback to activate on clicking.

We'd love to see that!  We are mulling over displaying alignments right

> cheers,
and to you!

Dave "Stupid Middle Names" Block