[Bioperl-l] Use of Bio namespace
13 Oct 2000 14:51:42 +0100
>>>>> "David" == David Block <email@example.com> 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
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
-= Keith James - firstname.lastname@example.org - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA