libSBML Python API
5.20.2
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This has the following consequence. If an application queries for the presence of Layout in an SBML Level 2 document by testing only for the existence of the plugin object, it will always get a positive result; in other words, the presence of a Layout extension object is not an indication of whether a read-in Level 2 document does or does not use SBML Layout. Instead, callers have to query explicitly for the existence of layout information. An example of such a query is the following code:
The special, always-available Level 2 Layout behavior was motivated by a desire to support legacy applications. In SBML Level 3, the Layout package uses the normal SBML Level 3 scheme of requiring declarations on the SBML document element. This means that upon reading a model, libSBML knows right away whether it contains layout information. In SBML Level 2, there is no top-level declaration because layout is stored as annotations in the body of the model. Detecting the presence of layout information when reading a Level 2 model requires parsing the annotations. For efficiency reasons, libSBML normally does not parse annotations automatically when reading a model. However, applications that predated the introduction of Level 3 Layout and the updated version of libSBML never had to do anything special to enable parsing layout; the facilities were always available for every Level 2 model as long as libSBML was compiled with Layout support. To avoid burdening developers of legacy applications with the need to modify their software, libSBML provides backward compatibility by always preloading the Layout package extension when reading Level 2 models. The same applies to the creation of Level 2 models: with the plugin-oriented libSBML, applications normally would have to take deliberate steps to activate package code, instantiate objects, manage namespaces, and so on. LibSBML again loads the Layout package plugin automatically when creating a Level 2 model, thereby making the APIs available to legacy applications without further work on their part.