[Biocorba-l] Going forward with BioCorba-0.2.0

[Alan Robinson]

Hello all,

For the most part, I believe BioCorba-0.2.0 can deal with >95% of the
common cases in (EMBL) sequences and their features, and it is fantastic
that bioperl, biojava and biopython should be trying to include it at this
time, as this is the only way it is going to evolve and improve.


However, having been playing with it a bit, there are some issues with it
that I think can be discussed and acted upon quickly (and moved into
BioCorba-0.2.1), and there are some other issues that are more fundamental
and we should discuss at length, i.e. include in BioCorba-0.3.0 *AFTER*
bioperl-0.7.0 is released and others start to test the BioCorba-0.2 IDL
too.


1) In the 'Seq' interface, the method 'all_SeqFeatures(...)' be named
   'get_SeqFeatures(...)' for consistency with the other methods of the
   interface. [For BioCorba-0.2.1?]

2) At the moment, you cannot attach general annotations to a sequence,
   only SeqFeature's that are tied to a particular location. [For
   BioCorba-0.2.1?]

3) I think we need to re-visit the SeqFeature / sub_SeqFeature design as
   in the current model it's very easy to get confused. [For
   BioCorba-0.3.0?]

4) I think we need to re-visit the SeqFeatureLocation design as it's
   currently limited to 'join' operations only.  [For BioCorba-0.3.0?]


In the next four e-mails, I'll go through my thoughts on points 2-4, plus
a conclusion and an IDL file with UML.
 

My thoughts are obviously influenced by what has happened previously with
BioCorba, OMG's BSA, the EMBL IDL, biojava and bioperl.

I'd especially like comments on aspects of the object design and the
relationships between objects: In a nutshell, I model:

 - Sequence features using a 'composite' design pattern. 

 - A SeqFeature 'has-a' location tree.

 - A location tree is composed of 'location' objects and 'operator'
   objects that describe how 'locations' are combined (e.g. 'join' or
   'order').


Thanks,
Alan.


--
============================================================
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/
============================================================