[Biocorba-l] Biocorba IDL - Clarifications

[Alan Robinson]

Hi all,

Could someone clarify the correct behaviour for the following situations
for me, please?

I have an EMBL sequence with the following feature and location:

  FT mRNA join(397..627,1194..1339,1596..1682,2294..2473,2608..3327)

What should be the SeqFeaure returned for this?

Currently, I simply generate and return:

	type = mRNA
	source = <none>
	seq_primary_id = X02158
*	start = 397
*	end = 3327
	strand = +1
	qualifiers = <none>
	PrimarySeq_is_available = true
	
It's the start and end values I'm concerned with. The current SeqFeature
is rather minimal (not necessarily a bad thing!). But, I cannot see any
way to specify the multiple locations of this feature cleanly in
SeqFeature.

If I were to define each location separately, I cannot see how to describe
their implicit relationship under the current IDL without some potentially
hairy naming convention or qualifiers that stresses the life of the client
writer.

Alternatively, one could return the location string via a new method, or 
in the qualifier.


Secondly, just to check - the 'source' variable of SeqFeature - Is this
just containing the value of an /evidence qualifier?


The sooner I get clarification on these - the sooner I can finish the
server! ;)


cheers,
al

--
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Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
European Bioinformatics Institute     Fax:+44-(0)1223 494468
EMBL Outstation - Hinxton             Email:  alan@ebi.ac.uk
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/
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