allenday at ucla.edu
Sat Nov 27 02:06:41 EST 2004
On Fri, 26 Nov 2004, Hilmar Lapp wrote:
> Well, if you return an object from source_tag() instead of a string
> your SeqFeatureI compliance goes out the window right there. Friendly
> stringification through overloading double quotes does not mitigate
> Same goes BTW for primary_tag(), seq_id() etc. Looking at the code,
> you're returning an object for these. Not SeqFeatureI
stringified reference ( e.g. REF(0x804d584) ) is a string in my book.
this is a backward compatible change. if you're worried that the user
will see the stringified reference if treating the returned value as a
string and not a data structure, that's what the overloading is for.
i don't see a problem here.
> As an aside, your get_Annotations() short-cut is brittle. If someone
> happens to add a second 'source' annotation (or any other tag for that
> matter), it will break and return the length of the array instead of
this is intentional and documented.
> the first element. Furthermore, I wouldn't test for IS-A
> Bio::Annotation::OntologyTerm - this is only an implementation class
> and one day there may be better ones. What you really care about is
> that the object IS-A Bio::AnnotationI (so that you can add it to the
> collection) and IS-A Bio::Ontology::TermI (so that you have your
> ontology-enforced typing).
what class are you referring to here?
> On Thursday, November 25, 2004, at 02:45 AM, Allen Day wrote:
> > i don't think it should do this, the whole point of using an AC is to
> > retain typing. if you want to have a friendly stringification of the
> > source attribute, use overloading in SimpleValue. there is an
> > as_text()
> > method already in there that is currently commented out.
> > -allen
> > On Thu, 25 Nov 2004, Steffen Grossman wrote:
> >> Update of /home/repository/bioperl/bioperl-live/Bio/SeqFeature
> >> In directory pub.open-bio.org:/tmp/cvs-serv22868
> >> Modified Files:
> >> Annotated.pm
> >> Log Message:
> >> 'source' now gives back its value instead of a
> >> Bio::Annotation::SimpleValue object. (This is consisitent with
> >> 'type').
> >> Index: Annotated.pm
> >> ===================================================================
> >> RCS file:
> >> /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Annotated.pm,v
> >> retrieving revision 1.17
> >> retrieving revision 1.18
> >> diff -C2 -d -r1.17 -r1.18
> >> *** Annotated.pm 24 Nov 2004 16:31:59 -0000 1.17
> >> --- Annotated.pm 25 Nov 2004 10:02:50 -0000 1.18
> >> ***************
> >> *** 181,185 ****
> >> }
> >> ! return $self->get_Annotations('source');
> >> }
> >> --- 181,188 ----
> >> }
> >> ! my $source_anno = $self->get_Annotations('source');
> >> !
> >> ! return $source_anno->value if ($source_anno);
> >> ! return undef;
> >> }
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