Forums

>
> If we want a common base that is fine with me byt I

I would prefer one ...

>> would then like it to be:
>>
>> Assignment
>> == Rule
>> ==== AssignmentRule
>> ==== AlgebraicRule
>> ==== RateRule
>> == InitialAssignment
>> == EventAssignment
>
> You cannot do that because the AlgebraicRule does not have a variable. So
> you do not inherit anything.
>

Well ... then we need two abstract classes, in that case we won't loose what we have now (a concise way of talking about all rules).

|---- AlgebraicRule
Rule ------ |---- AssignmentRule --- |
|---- RateRule --- |
|---- Assignment
InitialAssignment --- |
EventAssignment --- |


Frank


>> This is only because end users really could work only with the 'rule'
>> objects. On the other hand I have no attachments to 'AlgebraicRule' either.
>>
>> Cheers
>> Frank
>>
>>> -----Original Message-----
>>> From: sbml-discuss-bounces@caltech.edu [mailto:sbml-discuss-
>>> bounces@caltech.edu] On Behalf Of Nicolas Le novère
>>> Sent: Tuesday, April 27, 2010 6:40 AM
>>> To: SBML Discussion List
>>> Subject: [sbml-discuss] assignments
>>>
>>> Hello,
>>>
>>> I would like to bring an issue for specification developers. That will
>>> not
>>> affect SBML support or usage. So everyone not concerned with spec
>>> writting,
>>> you can leave :-)
>>>
>>> At the moment, there is an abstract class in SBML definition, called
>>> Rule.
>>> This class is a functional one (a semantic one), and is used to create
>>> the
>>> concrete classes AssignmentRule, RateRule and AlgebraicRule.
>>>
>>> At the same time, there are in the SBML core four classes with the same
>>> syntax, that are used for a similar purpose:
>>>
>>> InitialAssignment
>>> AssignmentRule
>>> RateRule
>>> EventAssignment
>>>
>>> Those construct share the same goal, to assign a value to something, or
>>> the
>>> evolution of something. Although the attribute used to point to the
>>> something varies, symbol or variable, the something is the same, that
>>> is a
>>> species, a speciesReference, a compartment or a parameter.
>>>
>>> The abstract classes are not seen by the end users, and are mostly
>>> constructs used to reduce redundancy in the specification of the
>>> language.
>>> Therefore, I think a good alternative to the current:
>>>
>>> Rule
>>> == AssignmentRule
>>> == RateRule
>>> == AlgebraicRule
>>> InitialAssignment
>>> EventAssignment
>>>
>>> Would be:
>>>
>>> AlgebraicRule
>>> Assignment
>>> == AssignmentRule
>>> == RateRule
>>> == InitialAssignment
>>> == EventAssignment
>>>
>>> The effect is mild on the core, but propagate on the various packages.
>>>
>>> For instance, writing the package multi, we're now multiplicating the
>>> sections, UML diagrams and examples because the four assignments can
>>> affect
>>> subpools (SpeciesTypeInstances) in addition of regular species.
>>>
>>> (Whether we want to keep AlgebraicRule in SBML core is another story
>>> ...)
>>>
>>> --
>>> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
>>> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
>>> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nlenovere@hotmail.com(NOT
>>> email)
>>> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere
>>>
>>>
>>> ____________________________________________________________
>>> To manage your sbml-discuss list subscription, visit
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>>>
>>> For a web interface to the sbml-discuss mailing list, visit
>>> http://sbml.org/Forums/
>>>
>>> For questions or feedback about the sbml-discuss list,
>>> contact sbml-team@caltech.edu
>>
>> ____________________________________________________________
>> To manage your sbml-discuss list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss
>>
>> For a web interface to the sbml-discuss mailing list, visit
>> http://sbml.org/Forums/
>>
>> For questions or feedback about the sbml-discuss list,
>> contact sbml-team@caltech.edu
>
>
> --
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nlenovere@hotmail.com(NOT email)
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere
>
>
> ____________________________________________________________
> To manage your sbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss
>
> For a web interface to the sbml-discuss mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the sbml-discuss list,
> contact sbml-team@caltech.edu

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