Forums

Hi all,

I take on board the complications surrounding platform independence
and the hassles therein.

As far as the second issue goes, I agree that it would be nice to
exploit Java features such as this (and equals() and comparable
methods etc.) but personally don't think that it would be a huge
amount of hassle to put together a few helper classes for us Javans to
do things like this:

/**
*
* @param model
* @return List<Species>
*/
public static List<Species> getListOfSpecies( final Model model )
{
final List<Species> list = new ArrayList<Species>();
final ListOfSpecies listOfSpecies = model.getListOfSpecies();

for( long l = 0; l < listOfSpecies.size(); l++ )
{
list.add( listOfSpecies.get( l ) );
}

return list;
}

I'm not sure that it's Mike et al.'s responsibility to do things that
we could be doing and sharing between ourselves. I've got a library of
libsbml-related Java classes that I recently shared up at http://sbml.org/Community/Programs/libAnnotationSBML
. I'm sure other Java-ites have the odd class that would be of
interest to the community as a whole. I reckon if we're more active in
sharing them, then I'd imagine that the requests for a pure Java
implementation would diminish.

Cheers,

Neil.

Neil Swainston
Experimental Officer

Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
England

On 18 May 2009, at 23:08, Michael Hucka wrote:

>>>>>> On 18 May 2009, Neil Swainston
>>>>>> <neil.swainston@manchester.ac.uk> wrote:
> NS> Hi Mike, Did you get convincing reasons as to why the
> NS> current JNI approach is unsatisfactory?
>
> Hi Neil,
>
> It's mostly the expected reasons -- portability, deployment,
> and Java-ishness of the API.
>
> Since the survey is anonymous, I think it's ok to report the
> specific comments about this issue here. Here they are (in
> no particular order):
>
> "The Java binding currently leads to plattform dependence
> of libSBML and therefore the great advantage of the
> plattform independence of Java gets lost. It would be
> beneficial to have a Java implementation."
>
> "The java API could make use of java generics instead of
> having a ListOfX for every type X. For example,
> List<Species> instead of ListOfSpecies."
>
> "I know it isn't really practical at all, but I really
> dislike having to install the C++ libs everywhere I want to
> use the jars :)"
>
> "Having a pure java libSBML."
>
> MH
>
> ____________________________________________________________
> To manage your libsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>
> For a web interface to the libsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the libsbml-development list,
> contact sbml-team@caltech.edu
>

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

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

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