[Bioperl-l] Bio::Ontology::Term references quetsion

[Stefan Kirov]

Hilmar,
I traced it and you are right to say it is not Bio::Ontology::Term. It 
is because of the overload in Bio::Annotation::Reference. It returns 
undef if there is no title. This makes absolutely no sense to me. 
Actually both 1.4 and bioperl-live docs say:

 Args    : a hash with *optional* title, authors, location, medline, start and end
           attributes

And it acts like that. Surprisingly, when you call something like:
if ($ref) {
....blah blah
}
else {
    die;
}
surprisingly your script dies. And it is really hard to find out why. So 
there should be either a check for a title before creating the object or 
this overloading should go away.
Stefan

Hilmar Lapp wrote:

> What makes you think it does? I can't see anything in the code that 
> would enforce this. Do you get receive an error if you add a reference 
> without a title? If so, what is the stack trace?
>
>     -hilmar
>
> On Wednesday, April 27, 2005, at 11:59  AM, Stefan Kirov wrote:
>
>> Is it true that Bio::Ontology::Term add_references method checks for 
>> title? If so there is a discrepancy with Bio::Annotation::Reference, 
>> as this object does not require a title upon creation. I don't think 
>> this should be such requirement in Bio::Ontology::Term unless I am 
>> missing something. Also the documentation does not say there is such 
>> requirement...
>> Stefan
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