[Bioperl-l] [Fwd: Bio::Graph::SimpleGraph]

Sendu Bala bix at sendu.me.uk
Mon Feb 26 06:46:39 EST 2007

Nat replied, but I messed up to To:s so his reply didn't make it to the
list. Here's what he said:

Nathan (Nat) Goodman wrote:
Hi Tels

I agree it's sad to reinvent the wheel, but I don't think that's what
happened here. Your module seems to be focused on rendering graphs while
my module is concerned with computations on graphs.

In any case, as Sendu notes, SimpleGraph is in the process of being
deprecated. I fully support this move. It was intended to be a stopgap
until the main Perl Graph module was fixed.  Since that has now
happened, it's time for SimpleGraph to retire.

For the benefit of anyone using Graph: last I checked (six months or
more ago), it had serious performance problems on large graphs (probably
not too much of a surprise), and also was inexplicably slow on graphs
with edge attributes.  I see that the latter bug is marked "resolved" in
CPAN, but there's no indication of when or how.  We've moved to Boost
for graphs as large as the human protein interaction network.


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