[Bioperl-l] Re: should Bio::PrimarySeq be storage-independent after bioperl-db appear?

[Hilmar Lapp]

Why does it make it heavy? I don't quite understand that. The adaptor 
is a singleton, so there is only a single instance per application. I 
don't quite see why adding a pointer to a singleton makes an object 
heavier than it was before (like a SeqI is anyway, and most sequence 
objects you're dealing with is SeqIs, not PrimarySeqIs).

If you remove the adaptor, you are removing the persistence 
implementation by delegation. What is your proposal to maintain 
persistence instead? Through a naming context?

What exactly is the issue that concerns you? Do you have a memory 
footprint issue?

	-hilmar

On Friday, May 16, 2003, at 02:40  AM, Juguang Xiao wrote:

> Hi core guys, especially Hilmar.
>
> In my experience of using bioperl-db to store bioperl core object, 
> such as Bio::PrimarySeq, I found, Bio::PrimarySeq, at least it, stores 
> the bioperl-db adaptor in memory, which can be seen in perl debug 
> mood, and has a sub "adaptor" to access. Seriously, it makes the 
> bioperl business object relatively hugely heavy after it is either 
> fetched or stored as the adaptor is assigned.
>
> I think, to make the biological business object neat, we should remove 
> adaptor instance and reference from business objects.  I can see no 
> problem on that. How about you?
>
> I would like to work on that, if you are not free to make it, since I 
> have read the bioperl-db code for weeks.
>
> my 2 cents.
>
> Juguang
>
> ------------ATGCCGAGCTTNNNNCT--------------
> Juguang Xiao
> Temasek Life Sciences Laboratory, National University of Singapore
> 1 Research Link,  Singapore 117604
> juguang at tll.org.sg
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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