sbml-render — The SBML L3 Rendering package discussion list

Re: [sbml-render] Ids and names on elements

[Michael H. <mh...@ca...>]

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.

MH

Re: [sbml-render] Ids and names on elements

[Lucian S. <lp...@sp...>]

* Andreas Drger <and...@un...> [2012-05-10 06:35] writes:
> Dear all,
> 
> I am new to the render extension for SBML and would like to ask a few 
> questions. Currently, we are starting to implement it in JSBML, which 
> requires to find a good way for a convenient in-memory representation of 
> all objects.
> 
> I noticed that the render extension contains several elements that have 
> an identifier, but no name. In all other classes in SBML that have an ID 
> there is also the possibility to define a name in addition to the id 
> (since Level 2). Therefore, JSBML has an abstract class 
> AbstractNamedSBase that contains methods for manipulating name and id 
> fields. There is even a mechanism to register things within the model 
> based on the id if certain interfaces are implemented. Then it is 
> possible to query the model for an element with given id in logarithmic 
> time.
> 
> Now, we encounter things with id but without name, so it doesn't nicely 
> fit into the framework described before. If we would let these things 
> extend AbstractNamedSBase, it would be possible to set a name that 
> cannot be written to SBML later on.
> 
> 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 can't speak for render specifically, but I do know that for two other 
packages (comp and I believe qual) when it was pointed out that a proposed 
new element had an 'id' but no 'name' attribute, a 'name' attribute was 
then added, for exactly the same reason we have 'name' in core.

I would vote we add 'name' to id'ed elements in render, too.

-Lucian

[sbml-render] Ids and names on elements

[Andreas D. <and...@un...>]

Dear all,

I am new to the render extension for SBML and would like to ask a few 
questions. Currently, we are starting to implement it in JSBML, which 
requires to find a good way for a convenient in-memory representation of 
all objects.

I noticed that the render extension contains several elements that have 
an identifier, but no name. In all other classes in SBML that have an ID 
there is also the possibility to define a name in addition to the id 
(since Level 2). Therefore, JSBML has an abstract class 
AbstractNamedSBase that contains methods for manipulating name and id 
fields. There is even a mechanism to register things within the model 
based on the id if certain interfaces are implemented. Then it is 
possible to query the model for an element with given id in logarithmic 
time.

Now, we encounter things with id but without name, so it doesn't nicely 
fit into the framework described before. If we would let these things 
extend AbstractNamedSBase, it would be possible to set a name that 
cannot be written to SBML later on.

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?

Thanks
Andreas

-- 
Dr. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-78982
Fax:   +49-7071-29-5091