[Bioperl-l] Bio::BioEntry

[Hilmar Lapp]

On Sunday, September 8, 2002, at 06:38  AM, Ewan Birney wrote:

> On Fri, 6 Sep 2002, Hilmar Lapp wrote:
>
>>
>> BioEntry would be different from PrimarySeq in not having a 
>> sequence associated with it.
>>
>> 	Bio::BioEntry is-a Bio::IdentifiableI
>> 	Bio::BioEntry is-a Bio::DescribableI
>>
>> and that's about it.
>
> [...]
> Is there any better solution. What do you have as BioEntries and not as
> Bio::Seq's?
>
>

All objects that are to end up as Bioentries in biosql, but aren't 
sequences. E.g. OMIM entries, or clusters (Unigene). Of course, 
those would have additional annotation that needed to be stored too.

The advantage could rather be that you can inherit off a base class 
that gives you IdentifiableI and DescribableI implemented via @ISA. 
Not a big deal OTOH.

I needed it already in one place in bioperl-db to store a namespace 
in some object, so I did implement it. Right now it's in 
Bio::BioEntry in bioperl-db. It can stay there as it may indeed only 
be relevant in bioperl-db, or I can move it over to the bioperl-live 
trunk. Whatever people vote (also, I'm open to renaming 
suggestions) ... :-)

	-hilmar
--
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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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