[Bioperl-l] Use of Bio namespace

Keith James kdj@sanger.ac.uk
13 Oct 2000 14:51:42 +0100

>>>>> "David" == David Block <dblock@gene.pbi.nrc.ca> writes:

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

I'll vaguely remembered seeing something like that in there. I'll
chase it up if I can lay my hands on a copy.

    >>  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.

    David> We'd love to see that!  We are mulling over displaying
    David> alignments right now.

It doesn't do much with the alignments themselves. It's more of a
coloured bars thing, like the NCBI Blast graphical overview. I was
going to put the text alignment in text widget underneath and use
callbacks from the overview to scroll the text widget to the right
place. I was thinking about making a sequence/alignment-aware text
widget for this, but this may be duplicating your stuff, which seems
pretty far advanced.

Unless there are any objections I'm going to use Ewan's suggestion of
Bio::PSU (Pathogen Sequencing Unit) to put my stuff in for now. Then
I'll see what I can do in terms of migrating functionality without
breaking anything.



-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA