[Bioperl-l] Re: [Bioperl-guts-l] bioperl commit

[Allen Day]

Scott,

You can't handle Ontology_term as a SimpleValue, that's why I didn't
implement it that way.  You need to rather create a
Bio::Annotation::OntologyTerm.

-Allen

On Sat, 25 Sep 2004, Scott Cain wrote:

> 
> scain
> Sat Sep 25 07:41:29 EDT 2004
> Update of /home/repository/bioperl/bioperl-live/Bio/FeatureIO
> In directory pub.open-bio.org:/tmp/cvs-serv2444/Bio/FeatureIO
> 
> Modified Files:
> 	gff.pm 
> Log Message:
> two things:
>   * adding SOFA as an available ontology to DocumentRegistry.pm
>   * modifying FeatureIO::gff to use SOFA to validate, and to parse Ontology_term
> 
> bioperl-live/Bio/FeatureIO gff.pm,1.9,1.10
> ===================================================================
> RCS file: /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm,v
> retrieving revision 1.9
> retrieving revision 1.10
> diff -u -r1.9 -r1.10
> --- /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm	2004/09/21 23:15:22	1.9
> +++ /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm	2004/09/25 11:41:29	1.10
> @@ -91,8 +91,9 @@
>    }
>    $self->_pushback($directive);
>  
> +  #need to validate against SOFA, no SO
>    $self->so(
> -            Bio::Ontology::OntologyStore->get_ontology('Sequence Ontology')
> +            Bio::Ontology::OntologyStore->get_ontology('Sequence Ontology Feature Annotation')
>             );
>  }
>  
> @@ -315,9 +316,9 @@
>    }
>  
>    #Handle Ontology_term attributes
> -  if($attr{Ontology_term}){
> -    $self->warn("Warning for line:\n$feature_string\nOntology_term attribute handling not yet implemented, skipping it");
> -  }
> +#  if($attr{Ontology_term}){
> +#    $self->warn("Warning for line:\n$feature_string\nOntology_term attribute handling not yet implemented, skipping it");
> +#  }
>  
>    #Handle Gap attributes
>    if($attr{Gap}){
> @@ -351,7 +352,7 @@
>      $ac->add_Annotation('Name',$a);
>    }
>  
> -  foreach my $other_canonical (qw(Alias Parent Note)){
> +  foreach my $other_canonical (qw(Alias Parent Note Ontology_term)){
>      if($attr{$other_canonical}){
>        foreach my $value (@{ $attr{$other_canonical} }){
>          my $a = Bio::Annotation::SimpleValue->new();
> 
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