[Bioperl-l] Priorities for a bioperl-1.6 release

[Sendu Bala]

aaron.j.mackey at gsk.com wrote:
> One GraphViz trick you could try would be to group Bio::X::* (nodes and 
> your collection groups sharing common Bio::X:: prefixes) together as 
> subgraphs; that should quickly show you which edges go outside of the 
> various "domains", and which are entirely self contained.

Not quite sure if I used the 'trick' you were thinking of, but I now 
'cluster' them as you describe. It's no longer quite as attractively 
proportioned, but I suppose it's more useful :)


> you could also try to distinguish "use base" relationships (i.e. 
> inheritance) vs. "use Bio::X" (delegation, composition, etc.) vs. "require 
> Bio::X" wrapped in an eval (optional use if available) by various edge 
> colorings -- this might help to further break things up if we can guess at 
> the intended "use" of any Bio::X by Bio::Y.

I haven't distinguished the eval require cases, but now edges are green 
for inheritance and blue for use/require.


I updated the jpeg:
*warning, may crash your browser; download it and view in a dedicated
  image viewer*
http://bix.sendu.me.uk/files/module_usage.jpeg


If someone wants to mess with the script so it will output a sane ps 
file for conversion to pdf, please do so. I can't figure out how to get 
it to work correctly.