cloning and Storable Re: [Bioperl-l] bugs on branch; tests on main trunk

[Heikki Lehvaslaiho]

I've removed the dependency for Storable. Storable is still used if it
is installed. Local code can clone everything except circular
references. If someone knows how to do it, I'd be happy to receive help.
Not having it here does not really matter because the the main use of
the clone method is to allow in-memory creation of a new enzyme based on
an existing one.

The clone code is written in very general way and should be able to deep
copy any in-memory objects. If you need to add a clone method your own
classes, copy from there. Ewan feels strongly that deep cloning is too
prone to errors to be a general property of bioperl objects, so better
not add this into Bio::Root::Root, although it would be handy.

	-Heikki 

On Mon, 2003-09-01 at 10:48, Heikki Lehvaslaiho wrote:
> On Fri, 2003-08-29 at 17:56, Ewan Birney wrote:
> > Heikki or Rob --- does RestrictionEnzyme *really* need Storeable?
> > Storeable doesn't come by default on systems, so if it didn't need
> > it then it would be more useful not to use it. Any chance of this?
> 
> Storable is used to do deep cloning of Enzyme objects. Storable is also
> used by Bio::DB::FileCache and Bio::SeqFeature::Collection (or is the
> documentation for Collection outdated?). 
> 
> Storable is part of 5.8.1 distribution. There is Clone in CPAN which is
> faster but less systems are bound to have is.
> 
> If you think is is critical to get rid of this dependency I can rewrite
> the cloning method.
> 
> 	-Heikki
> 
> > 
> > I put a require eval() in tutorial around the restriction enzyme stuff.
> > 
> > 
> > 
> > 
> > Chris (and the unflattening crew...) the Unflattener is issueing alot of
> > warnings with -w --- any chance of one of you looking at it?
> > 
> > 
> > However, I now have on the main trunk:
> > 
> > 
> > All tests successful, 33 subtests skipped.
> > Files=168, Tests=7643, 383 wallclock secs (287.31 cusr + 25.46 csys = 312.77 CPU)
> > 
> > 
> > 
> > 
> > 
> > 
> > Pretty darn impressive.
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
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