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Am 6/8/12 8:02 PM, schrieb mvaniersel:
> SBML-Qual has a method for defining the default result of a transition called defaultTerm. See for example this snippet:
>
>
> <listOfFunctionTerms>
> <functionTerm resultLevel="1">
> <math> < !−− A>= 1−−>
> <apply>
> <geq/>
> <c i>A</ c i>
> <c i>theta B A</ c i>
> </apply>
> </math>
> </functionTerm>
> <defaultTerm resultLevel="0" />
> </listOfFunctionTerms>
>
>
> See also the current specs: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
>
> defaultTerm is not currently implemented in JSBML. The problem is that this is a sub-element of a ListOf<FunctionTerm>, which we can not add additional members to. Or can we?
>
>


Hi Marijn and all others,

What I actually not understand in this definition is the following
question - I hope you can explain why it is as it is in the qual
specification:

The DefaultTerm is stored in the ListOfFunctionTerms. The Transition has
at most one such list. Why is the DefaultTerm not directly stored within
the Transition? The list is directly associated with precisely one
Transition. Hence, no other Transition has the identical list. Hence,
the DefaultTerm is also uniquely defined for one particular Transition.
From my perspective it is not clear why the actual list contains this
element besides its list members (i.e., instances of FunctionTerm).
Wouldn't it make sense to define that the Transition has a DefaultTerm
and optionally a ListOfFunctionTerms?

By the way, just now I see that all the classes in the UML diagrams of
the qual specification are spelled in upper case, whereas most SBML
elements (i.e., the things that are written in XML) are spelled in lower
case, e.g., <species.../> or <reaction.../>. Should maybe the UML
diagrams also be labeled with lower case names?

Best
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

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