Re: If there were a pure Java libSBML ...
19 May '09 02:25
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 ) );
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.
Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
On 18 May 2009, at 23:08, Michael Hucka wrote:
>>>>>> On 18 May 2009, Neil Swainston
>>>>>> <firstname.lastname@example.org> 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."
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