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Hi Neil,

Thanks for the reply. Yes, this is the sort of program I should have tried
first before emailing the group, but thanks for doing it and showing the
output. This is what I had suspected was happening.

The example below shows the behaviour if you try to update a species in Java
(it isn't linked to the model you got it from), or add an "updated" species
with the same id (it gets added as a duplicate rather than updating the
original). So, then, I wonder what the best way is to update a species? All
I want to do is add more annotation. I have gotten as far as making a new
version (locally) of the original species + new annotation, and now don't
know how to get it back in without breaking things.

I'll have a think :)

2009/1/21 Neil Swainston <neil.swainston@manchester.ac.uk>

> Hi Allyson,
>
> Try running the following program:
>
> import org.sbml.libsbml.*;
>
> /**
> *
> * @author Neil Swainston
> */
> public class SbmlSpeciesIdTest
> {
> /**
> *
> */
> static
> {
> System.loadLibrary( "sbmlj" ); //$NON-NLS-1$
> }
>
> /**
> *
> */
> public void test()
> {
> final Species species = new Species( "Newcastle" );
> final SBMLDocument document = new SBMLDocument();
> document.createModel();
>
> document.getModel().addSpecies( species );
>
> // Print out original:
> System.out.println( document.toSBML() );
>
> // Attempt to update species and print out:
> species.setId( "Manchester" );
> System.out.println( document.toSBML() );
>
> // Add a duplicate species and print out:
> document.getModel().addSpecies( new Species( "Newcastle" )
> );
> System.out.println( document.toSBML() );
> }
>
> /**
> *
> * @param args
> */
> public static void main( String[] args )
> {
> new SbmlSpeciesIdTest().test();
> }
> }
>
> The output that I received was as follows:
>
> <sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
> version="3">
> <model>
> <listOfSpecies>
> <species id="Newcastle"/>
> </listOfSpecies>
> </model>
> </sbml>
>
> <sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
> version="3">
> <model>
> <listOfSpecies>
> <species id="Newcastle"/>
> </listOfSpecies>
> </model>
> </sbml>
>
> <sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
> version="3">
> <model>
> <listOfSpecies>
> <species id="Newcastle"/>
> <species id="Newcastle"/>
> </listOfSpecies>
> </model>
> </sbml>
>
> The take-home messages seem to be that you can indeed add "duplicate"
> species to the model (two species with the same id).
>
> Also, updating the "local". Java species to give it the id of
> "Manchester" seems not to update the underlying species in the C++
> layer - presumably down to some JNI subtlety that I won't pretend to
> understand.
>
> Cheers,
>
> Neil.
>
> On 21 Jan 2009, at 11:49, Allyson Lister wrote:
>
> > Hi all,
> >
> > I'm using libSbml 3.2.0 in its Java incarnation.
> >
> > I would like to get a species from a model (model.getSpecies(myId),
> > modify
> > it, and then put it back in, essentially overwriting what was there
> > before.
> > However, it is unclear from the docs whether
> > model.addSpecies( mySpecies)
> > will overwrite any existing species with that same id, or if it will
> > not add
> > the new version of the species. Alternatively, should I remove the old
> > version first, and then add the new species (I'm guessing that's
> > not an
> > option, as it will mess up all existing links to that species within
> > the
> > model). Looking at the C++ code, it seems to run an append()
> > function over
> > the species set, but I don't know if that append function will allow
> > duplicates or not, or how duplicates are determined. I may be
> > overthinking
> > this, but the best way to do this would be great!
> >
> > thanks,
> > allyson
> >
> > --
> >
> > Allyson Lister
> > http://lurena.vox.com
> >
> > CISBAN, http://www.cisban.ac.uk
> > Newcastle University
> > ____________________________________________________________
> > To manage your sbml-interoperability list subscription, visit
> > https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
> >
> > For a web interface to the sbml-interoperability mailing list, visit
> > http://sbml.org/Forums/
> >
> > For questions or feedback about the sbml-interoperability list,
> > contact sbml-team@caltech.edu
>
>
> Neil Swainston
> Experimental Officer
>
> Manchester Centre for Integrative Systems Biology
> Manchester Interdisciplinary Biocentre
> University of Manchester
> Manchester M1 7DN
> United Kingdom
>
>
>
>
>
> ____________________________________________________________
> To manage your sbml-interoperability list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
>
> For a web interface to the sbml-interoperability mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the sbml-interoperability list,
> contact sbml-team@caltech.edu
>



--

Allyson Lister
http://lurena.vox.com

CISBAN, http://www.cisban.ac.uk
Newcastle University
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