Re: [jsbml-team] Extensions of extensions
10 May '12 07:10
On 10/05/12 06:20, Andreas Dräger wrote:
> Dear all,
> In contrast to all other SBML extensions implemented so far, the
> render extension does not extend the SBML core, but the layout
> extension. This is why, I would like to start the discussion how we
> can deal with this in the Java implementation.
> If we would strictly follow the specification of the render extension,
> it would have to be embedded within the annotation of the
> listOfLayouts inside of the layout extension. Currently, the
> SBasePlugin cannot be extended with additional plugins. And the
> annotation is very difficult to use based on XMLnode datastructures.
You need to have a look at how it has been implemented in libSBML as the
specification update are lacking. Interact with the render mailing list
(https://lists.sourceforge.net/lists/listinfo/sbml-render, just saw that
you posted a question there already) as well so that the decisions are
at least posted and discussed there.
Please don't speak about annotations, the whole point of doing an L3
package is to take it out of the annotations.
> I would therefore like to propose to implement the render extension
> also as a regular extension of the model, i.e., there would be a class
> such as ExtendedRenderModel that would be similar to the existing
> ExtendedLayoutModel. Virtually, all data structures beloning to the
> render extension would be linked as children to this element.
Again, I want to stress to check what decisions Franck and the libsbml
team have taken already to see if we store it as a child of the model
element or some layout elements.
> On the other hand, however, it would also make sense to implement this
> "plugin" as a plugin for the ExtendedLayoutModel, because the render
> extension makes only sense in combination with the layout extension.
> Should we introduce a mechanism to extend (Abstract)SBasePlugin with
> further plugins?
Yes, we just have to add the HashMap<String, SBasePlugin> with the
associated methods to SBasePlugin.
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