[SOSlib-devel] Re: Parameters with undefined values in odeSolver

[Ben B. <ben...@jp...>]

Hi Rainer, Mike,

Parameters are stored as C doubles so they need to store *some* value  
even when they're not set.  This value is set to NaN if you call  
unsetValue(), but when an SBML Parameter structure is first created /  
initialized, it's apparently zero.  Sorry, this is an implementation  
inconsistency on my part.

That said, the value returned by getValue() should *not* be used /  
trusted if isSetValue() returns false (zero).  LibSBML can't stop a  
programmer from calling getValue() (unless it throws an exception,  
but this wouldn't work for the C API).

This error should be caught by XML Schema validation, which is one  
reason why we never added a check to libSBML 2.  LibSBML 3 performs  
the check, since one of its design goals is to subsume all XML Schema  
checks.

Thanks.

Ben


On May 29, 2006, at 2:37 AM, Rainer Machne wrote:

> The non-constant parameters a and b in the example file have no  
> initial value, but are interpreted as 0 by SOSlib.
>
> I have attached a simple example program, which I compiled with  
> libsbml 2.3.4, probably from a version that was updated from CVS on  
> Feb 14 this year.
>
> It shows that Parameter_getValue returns 0 for both parameters even  
> though Parameter_isSetValue correctly returns "no" for both  
> parameters.
> No errors are reported by the consistency check.
>
>
> It is quite some bug in SOSlib.
> Unfortunately, we didn't think earlier of this problem.
>
> So I'd have some questions to start repairing SOSlib:
>
> Does this happen on purpose, i.e. is 0 the default value to return,  
> if no value is set?
>
> For which other values (species, compartments) does this happen?
>
> and:
>
> Should there be a test in the consistency check?