[Bioperl-l] Hilmar and Ewan debate SeqFeatures some more...

Hilmar Lapp lapp@gnf.org
Fri, 19 Jan 2001 12:53:00 -0800

Thomas Down wrote:
> Actually, my understanding is that the per-object overhead in
> perl is pretty high, especially for objects implemented as
> hashes.  If you ever want to hold millions of SeqFeatures in
> memory (a not unreasonable requirement, I'd suggest), a few
> hundred bytes per location might come back with a vengence.

Hmm. I guess I can't make a sensible comment on this. Anyone else out
there who has experienced a performance drawback imposed by Perl's
object handling (well, I know in fact it's not objects Perl handles

If this problem is real, any chances this will be mitigated in
upcoming Perl releases (5.6? 6.0?)? In general I hate having to adapt
an object model to the limitations of a language ... :(

> Of course, this can probably be mitigated by implementing the
> locations as C structs.  Is this approach currently being
> used in BioPerl?

Well, given the users on Win32 and Mac this is probably not an option
for any module that is somewhat part of the core.

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757