Forums

F.A.Q. F.A.Q.    Register Register    Login Login    Home Home
Search Search
SBML Discussions » jsbml-development » create compartment is missing id
Show: Today's Posts  :: Message Navigator
| Subscribe to topic 
Return to the default flat view Create a new topic Submit Reply
AuthorTopic
Andreas Dräger


Posts: 273
Registered:
June 2006
Re: create compartment is missing id 18 Apr '11 20:17 Go to previous messageGo to previous message

> I would suggest that either creation of SBML objects without any arguments
> be illegal, or that they default to the *latest* level and version, not
> the first.

Hi Lucian,

Actually, there is no default Level/Version combination in JSBML at
the moment. If it is unspecified, [l, v] will be [-1, -1], i.e., kind
of invalid, just like in libSBML. The problem in this example was that
when writing SBML it was checked if the level attribute is greater
than one. If this was the case, the id was written. Locally, I changed
the check to if level != 1 write the id. In this way, the id will also
be written if the level attribute is undefined. I'm going to commit
this later on.

However, there is still the question
* if we should have a static field, maybe in SBMLDocument, for the
latest Level/Version combination and set this as default when creating
an element without specifying the Level/Version combination or

* if we should stick with setting L/V to -1, -1 in this case?

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
____________________________________________________________
To manage your jsbml-development list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/jsbml-development

For a web interface to the jsbml-development mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the jsbml-development list,
contact sbml-team@caltech.edu

      

SubjectPosterDate
Read Message   create compartment is missing id spike18 Apr '11 02:57
Read Message   Re: create compartment is missing id Mike Hucka18 Apr '11 09:00
Read Message   Re: create compartment is missing id Lucian Smith18 Apr '11 19:49
Read Message   Re: create compartment is missing id Mike Hucka18 Apr '11 20:16
Read Message   Re: create compartment is missing id Andreas Dräger18 Apr '11 09:28
Read Message   Re: create compartment is missing id Andreas Dräger18 Apr '11 09:56
Read Message   Re: create compartment is missing id Clemens Wrzodek18 Apr '11 09:59
Read Message   Re: create compartment is missing id rodrigue18 Apr '11 10:42
Read Message   Re: create compartment is missing id Lucian Smith18 Apr '11 19:50
Read Message   Re: create compartment is missing id  Andreas Dräger18 Apr '11 20:17
Read Message   Re: create compartment is missing id spike19 Apr '11 01:34
Previous Topic:how to represent a family of proteins
Next Topic:Write to SBML
Go to forum:
-=] Back to Top [=-

Powered by FUDforum. (Copyright Advanced Internet Designs Inc.)

Please use our issue tracking system for any questions or suggestions about this website.