[Bioperl-l] First commit of Bio::Structure objects

[Kris Boulez]

Quoting Chris Mungall (cjm@fruitfly.bdgp.berkeley.edu):
> Hi Kris
> 
> The object model design looks very sound. However, I noticed that there
> are cycles in the object graph (eg bidirectional links between Atom and
> Residue).
> 
I see your point :(
So it shows this is my first real set of objects I design.

> This causes problems for perl, as the garbage collector gets confused
> about reference counts and won't clean up properly. (IMHO this is part of
> a larger problem with object oriented design as a whole, as attributes
> aren't first class entities in their own right)
> 
> This won't be a problem for reading in a few PDB records, but, say,
> cycling through all of PDB will cause your memory usage to go up and up. I
> learned this lesson the hard way with my first perl object model, after
> doing java object models, it was a painful business going back and
> refactoring the code :@(
> 
> One way around this is to keep your own reference counts override the
> DESTROY method to make sure everything is cleared - this can be tricky.
> 
If the assumption is, that if an object is destroyed all its children
(everything underneath it) are destroyed, this should be doable.

> Another way would be to have everything go through a singleton
> ProteinData object which would hold all parent/child relationships. The
> Residue/Atom object would be unaware of their reciprocal links, the client
> code would have to ask the ProteinData object for this.
> 
> I notice you haven't checked in your StructureI object yet, so I can't run
> the tests - I may be missing something
> 
The StructureI object hasn't been checked in, as it doesn't exist yet.
This was one of my questions in my mail: should I go for one StructureI
or for seperate EntryI, ChainI,... files. Also: should every public
method have an Interface definition ?
I ran the tests as follows

  % cd bioperl-live/t
  % perl -I.. ./Structure.t

Kris,
-- 
Kris Boulez 				Tel: +32-9-241.11.00
AlgoNomics NV 				Fax: +32-9-241.11.02
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