[Bioperl-l] Errors on Annotaion

[Jason Stajich]

You're using the old API (Bio::Annotation).  Use the new API which is
for Bio::AnnotationCollectionI -> implemented by
Bio::Annotation::Collection.

if you call
my $ann = $seq->annotation();
print ref($ann), "\n";

You'll see that you are getting back a Bio::Annotation::Collection object.
Specifically you'll replace
    my $comm = $ann->get_Comment()
  with
    my $comm = $ann->get_Annotations('comment');

I'll add this to the FAQ.

-jason
On Tue, 11 Jun 2002, Aun Ja wrote:

> Hello,
>
> I try to use the Bio::Annotation object (version 1.0
> and 1.01, but I always get the following errors.
> ----------------------------------------------------
> each_Comment (old style Annotation) on new style
> Annotation::Collection
> STACK Bio::Annotation::Collection::each_Comment
> D:/Perl/site/lib/Bio/Annotation/
> Collection.pm:402
> STACK toplevel dbparse.pl:87
> each_DBLink (old style Annotation) on new style
> Annotation::Collection
> STACK Bio::Annotation::Collection::each_DBLink
> D:/Perl/site/lib/Bio/Annotation/C
> ollection.pm:445
> STACK toplevel dbparse.pl:90
> ------------------------------------------------
>
> Any thoughts?
> Aun Ja
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu