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Posts: 273
Registered:
June 2006
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Re: [jsbml-development] Our repository
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07 Oct '09 02:19
 
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Hi Nico and Marine,
The forgotten files are now committed. Originally, I didn't intend to
upload our reader/writer classes because we basically copy the libSBML
objects into these in memory constructs. However, maybe this can be
interesting for other people, too.
Regarding Nico's comments: I agree. For the start of the project, I
simply copied everything from SBMLsqueezer's repository. However, I
think there is just the first line that we have to change in each header.
The license of the trunk should be LGPL as Sara pointed out. For my
branch I would like to stick with GPL. This shouldn't be a problem.
One comment to the class Symbol: It is a convenient interface and the
SBML specification states at some places that fields should be of type
Variable or of type Symbol where Symbol means Variables that are allowed
to be constant. To have a common superclass for Parameters, Species and
Compartments is convenient for the following purposes:
1. We can create constructors that require an instance of Symbol and
therefore ensure not to get some other NamedSBase or what ever.
2. We can group the many common features of Species, Compartments, and
parameters, which is especially useful for applications that really use
our jsbml as an internal data structure and that perform computation on in.
But the problem is that the names of the arguments in SBML are sometimes
a bit different for these three entities, e.g., the value or unit
attribute in Species is called differently although it is basically the
equivalent.
Cheers
Andreas
--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany
Phone: +49-7071-29-70436
Fax: +49-7071-29-5091
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