Re: [sbml-render] Ids and names on elements
14 May '12 23:29
Am 5/11/12 8:27 PM, schrieb Michael Hucka:
> On Thu, 10 May 2012 07:31:26 +0200, Andreas Dräger wrote:
>> My question is therefore, first, why it was actually decided not to have
>> a name attribute in addition to the id for several elements in
>> SBML-render, and second, if you have some proposal what we can do for
>> our implementation?
> I don't remember the precise reasons, but layout& render are the two oldest packages, predating even the final L3 specification. It probably has more than one oddity as a result of the fact that many principles were never fully worked out at the time they were first developed.
> These specifications are not 100% final, and small details like this could probably be adjusted.
In this case, I propose to let all classes from SBML-Render that have
just an ID but no name in the specification extend AbstractNamedSBase,
which gives the possibility to also set a name. The important point of
this will be that then the model will be able to register links to these
elements and take care to avoid duplicate identifiers. Otherwise, we
would have to split the interface NamdeSBase (and AbstractNamedSBase as
well) from JSBML's core into two distinct classes, one caring about the
ID and a derived class that also has a name tag. This would make JSBML
again a bit more complicated and would also cause additional effort. The
easier way seems to be to introduce an optional name attribute on some
Render elements. By making this optional, all existing render files
would still be valid, no real change.
Dr. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
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