[Biocorba-l] SeqFeature and Id

[Juha Muilu]

Thanks Brad and Ewan,

Actually I reported bug in orbit-perl IDL parser, already couple of
months ago... Did not know that ORBit itself do not work either.

How about this kind of solution (if we really have to drop the
recursion):

    struct SeqLocation { 
      SeqFeaturePosition start; 
      SeqFeaturePosition end;
      StrandTypeDef strand;          
    };

    struct SeqFeatureLocation  {
      SeqLocation seq_location ;
      SeqFeatureLocOpDef region_operator;
      sequence <SeqLocation> sub_seq_locations;
      Identifier id;
    };


Then we can use the SeqFeatureLocation as before, except we have only
one level of sub locations. 

It is also possible to flatten the tree into a array (as done in the
EMBL corba-server) , but that is tricky to use.


Ewan Birney wrote:
> 
> Thanks Brad for this. I'll take a look at the IDL and start rolling this
> into bioperl...
> 
> Juha - I am going to push hard for making the struct's non-recursive so we
> can bind Perl with default ORBit. I think binding Perl is a much, much
> bigger win than being "correct". Obviously the best case is both, but
> let's be serious here --- we are not going to get a bug-fix patch release
> on ORBit distributed widely enough to make that work.
> 
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