Calculate rates of change for dependent species

[hsauro]

Add the following new methods (I assume getRatesOfChange is deprecated) to the C API (rrc_api.cpp)

vector getFloatingSpeciesRatesOfChange (RoadRunner* rr, bool amounts);
vector getIndFloatingSpeciesRatesOfChange (RoadRunner* rr, bool amounts);
vector getDepFloatingSpeciesRatesOfChange (RoadRunner* rr, bool amounts);

The methods should include some kind of flag (bool or int?) to set whether the rate of amounts or concentrations are to be returned.

Obviously, we also need to add the corresponding C interface methods, eg:

RRVectorPtr rrcCallConv getFloatingSpeciesRatesOfChange (RRHandle handle, bool amounts);

[luciansmith]

Currently, all dependent species have no rates of change because when conserved moiety analysis is on, they are set by assignment rules. In this particular case, we can back-calculate the rate of change and provide it if asked. If we do, it would also be possible to add it to the list of all floating species rates of change, and the dependent floating species rates of change.

Note that there's not a way to easily calculate the rate of change for anything else set by an assignment rule, only those species whos values are set by an assignment rule due to turning on conserved moiety analysis.

[luciansmith]

Once we have the calculated values, we can provide new API routines, for both C and C++

getIndependentRatesOfChangeIds --> currently implemented by getRatesofChangeIds.
getDependentRatesOfChangeIds