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Hi all,

Here's an update.

I did a little more digging into this with a unit test, and discovered you
could change the underlying species if you first get it with getSpecies().
Below is a modified unit test based on Neil's, but using thoughts I came up
with after pondering a little more on Frank's email - looks like the Java
behavior is the same as C++ in this instance:

Thanks all! :) allyson p.s. unit test and it's output follows:

unit test (passes):
@Test
public void testDuplicateSpecies() {
final String id = "Newcastle";
final String modifiedId = "Manchester";
final String name = "Sunderland";
final String modifiedName = "Tyne";

Species species = new Species( id );
species.setName( name );
SBMLDocument document = new SBMLDocument();
document.createModel();

document.getModel().addSpecies( species );
species = document.getModel().getSpecies( id ); // re-set species to
the result of getSpecies! if you don't do this, then the changes aren't
propogated back to the model. Comment out this line and see how the behavior
changes.

assertEquals( name, species.getName() );

// Print out original:
System.out.println( document.toSBML() );
System.out.println( "----------" );

// Attempt to update species and print out:
species.setId( modifiedId );

System.out.println( document.toSBML() );
System.out.println( "----------" );

// prove that the Species within the model can be updated via
reference:
assertNull( document.getModel().getSpecies( id ) );
assertNotNull( document.getModel().getSpecies( modifiedId ) );

// set the species back to the original Id, and modify the name
species.setId( id );
species.setName( modifiedName );

assertNotNull( document.getModel().getSpecies( id ) );
assertNull( document.getModel().getSpecies( modifiedId ) );

System.out.println( document.toSBML() );
}


output:

<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
version="3">
<model>
<listOfSpecies>
<species id="Newcastle" name="Sunderland"/>
</listOfSpecies>
</model>
</sbml>
----------
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
version="3">
<model>
<listOfSpecies>
<species id="Manchester" name="Sunderland"/>
</listOfSpecies>
</model>
</sbml>
----------
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
version="3">
<model>
<listOfSpecies>
<species id="Newcastle" name="Tyne"/>
</listOfSpecies>
</model>
</sbml>

2009/1/22 Allyson Lister <allyson.lurena@googlemail.com>

> Hi Frank,
>
> This sounds and looks very much like C++ code ;) While I used to use that
> back in a previous job, here I'm using the Java version of libSBML, and as
> Neil pointed out, when we run getSpecies() in Java, I don't think we get
> back a reference/pointer - I think it's a copy. I even tried removing the
> "final" parts of Neil's code above, to make sure that wasn't the problem,
> but I get the same results as he does.
>
> Very good idea, but not sure it will work for us Java-ites.
>
> thanks very much! :)
>
> 2009/1/21 Frank Bergmann <fbergman@u.washington.edu>
>
> Actually it is easier than all that, all you need to do, is to get
>> your species
>>
>> Species *species = model->getSpecies("sbmlId" or unsigned int index);
>>
>> now you check whether the species was there, by testing for NULL, and
>> if all is well you do your modification:
>>
>> if (species != NULL) species->setInitialAmount(newValue);
>>
>> as you only received a reference to the actual species, all changes
>> will be there the next time you write this model out.
>>
>> As to your question when does the validation happen, the next
>> validation happens upon a call to checkConsinstency ... which will
>> fill your error log ...
>>
>> i hope this helps,
>> best
>> Frank
>>
>> On Jan 21, 2009, at 3:49 AM, 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
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>> >
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>> > http://sbml.org/Forums/
>> >
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>> > contact sbml-team@caltech.edu
>>
>> ____________________________________________________________
>> To manage your sbml-interoperability list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
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>
>
>
> --
>
> Allyson Lister
> http://lurena.vox.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University
>



--

Allyson Lister
http://lurena.vox.com

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