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Posts: 273
Registered:
June 2006
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Re: jsbml/parsing errors
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31 Mar '11 02:05
 
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Dear all,
There is currently a discussion going on in the JSBML mailing list that
requires the opinion of some people from the SBML community.
The question is:
Should we or should we not keep the information constant=true in local
parameters with SBML Level < 3 when writing an SBML file given that this
was written in an original file?
>>> One question is, do we want to write back the constant attribute to keep
>>> the file as it was ?? If yes, we probably need to add a class attribute
>>> to tell us if the constantAttribute was set and then add it in the
>>> writeAttribute method.
>>>
>>
>> It does not really make sense to write "constant=true" in a local
>> parameter with Level < 3, because by default this is always the case. No
>> matter what was written in an original file, I would remove this in any
>> case.
>>
>>
> There is nothing wrong to put the attribute to true, like this, you are
> sure that other software that use your SBML file
> will set the attribute to true even if they do not know the default
> value that is written in the SBML specs.
>
> But also, it is nice to give back the model as it was written by the
> user or the tool that created it. This is why we are doing that for all
> the other
> attributes in all the other classes that have a default value in the
> specs. If the user set it in the original file, we are writing it back
> even if it is the default value.
>
> Not sure why we should make an exception for the constant attribute in
> the class parameter.
Cheers
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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