[Bioperl-l] Bio::SeqFeature::Annotated API change, problem with Genewise.t

[Sendu Bala]

Sendu Bala wrote:
> Following Chris's changes to SF::Annotated et al., lots of existing user 
> code breaks. Also, at least some Bioperl code breaks, notably 
> Bio::DB::SeqFeature::Store, which in mysql mode calls 
> _get_location_and_bin() which calls $feature->seq_id which ends up 
> storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
> the database, instead of an actual sequence id (which completely breaks 
> searching by seq_id).
> 
> I propose its API be changed to be more consistent with 
> Bio::SeqFeatureI, eg. instead of:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> we have:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> This would apply to seq_id(), name(), type(), source(), phase() and 
> frame(). Internally the implementation could store the string value in a 
> SimpleValue object.

I've now done this except for type() and source(), since these aren't in 
Generic. Instead we have source_tag() and primary_tag() accepting and 
returning strings.

source() and type() return objects as before, but now only accept 
objects when setting for consistency.


One test that pops up with an error is t/Genewise.t
I don't understand what's causing the problem. Can anyone help?