Forums

Problems found so far while trying to have the current libsbml test
files working and checking the current tracker items :

* Some of the unsetMethod are not working and return an exception all
the time.
for ex : species.unsetCompartment()

* getAnnotation() != null even is no annotation defined : We have to
check if people use a lot this test before reading an annotation.

* getDerivedUnitDefinition() is not working properly if there is not
unit defined.
see
http://sbml.svn.sourceforge.net/viewvc/sbml/trunk/libsbml/src/units/UnitFormulaFormatter.cpp?revision=12199&view=markup
see
http://sbml.svn.sourceforge.net/viewvc/sbml/trunk/libsbml/src/sbml/Model.cpp?revision=12199&view=markup

In Model.cpp, see the method populateListFormulaUnitsData
Seems to be a lot of work not going to be part of the first release
for sure and may be one of the functionality to get via webservices ?

* finish implementing the Notes related methods, people need to test
that the output of their files is fine. Any UTF-8 character allowed
character would still
be written in plain instead of using the html or xml code.

* fd1.setMath(ASTNode.parseFormula("lamda(2)")); does not work. an
ASTNode of type LAMBDA is expected and it is of type FUNCTION
* fd2.setMath(ASTNode.parseFormula("lamda(x, x+2)")); does not work
either, there is a ParserException

* UnitDefinition.createUnit() can not work at the moment.

* Model.findSymbol to update to support SpeciesReference (SBML level 3),
eventualy reaction (SBML level 2). And review the code that can
manipulate these beast, not sure which interface we decided to use at
the end

* just thinking about the use of initDefaults() for L3. In fact, people
might want to use this method or a similar method to set the default as
in L2, I don't think it is possible at the moment.

* add a method taking an XMLEventReader in the stax.SBMLReader

* add more libsbml tests files



Differences to document :

* we cannot add several times the same object to a list

* we cannot use the same ASTNode in several objects as it is not cloned.
In general, the values are not copied in java when passed to a method.


Documentation :

* more complete javadoc : remove as much as possible of the warning when
building the doc (currently 937 warnings)

* build the new web site on the sbml.org wiki

* complete the document about differences with libsbml (did not read the
existing document yet), may be have a developer documentation as well
for newcomers.

* update the Authors list to put all the contributors and may be alumni.



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