[Bioperl-l] bioperl-gui feedback

Ewan Birney birney@ebi.ac.uk
Mon, 30 Oct 2000 08:41:57 +0000 (GMT)

Mark and David -

as you might have heard we have successfully reused (or at least - got to
run -) the bioperl-gui front end off Ensembl as a back-end.

I'd like to say first off - respect to you guys for getting this working;
also respect to Greg helt and Nomi for the original Bio::Tk stuff.

This is also a real tribute to people writing to interfaces - because you
read off the Bio::SeqI interface and we @ Ensembl complied with the
Bio::SeqI interface the result was almost instant working of these two
pieces of code that were developed completely separately.

This is component reuse at its best!

Now of course we want to mess with it - I hope we can coordinate the
changes/fixes through you etc etc.

Now --- for the gripes ---

(a) On some systems the fonts you use aren't there (Arial etc). These
are hard coded in some places. 

As well as them being user-defined I think it would also be nice to have
one obvious place to set a single default font as the biggest problem in
me reusing the code was finding a font a had Tk installed with (helvetica
if you are interested!). 

Even better would be to auto-probe this in the Makefile.PL and set the
default font to a working font. Definitely a later thing

(b) I think a real life application in the package would be a real boon. 
Something like - loading up a sequence from a file etc. Code needs to
be in modules to be usefully reused but it is easier to hack something
that works than rebuild a script, in particular Perl Tk applications.

(c) How do you add/manipulate SeqFeatures? This is not obvious at the

Anyway. Respect. bioperl-gui is a great addition to bioperl.

Lorenz - I never got GTK bindings to perl to work out so I couldn't test
your stuff out. Apologies - your viewer I am sure is also great. (ewan
winces that Lorenz's stuff has been around for a while). I guess
bioperl-gui might be a more natural cvs module for your stuff. 

There is nothing wrong in my view in having a good set of different
viewers to play with...

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420