A command-line program that prints information about the units of measurement used in a given SBML file.
A command-line program that prints information about the units of measurement used in a given SBML file.
#include <iostream>
#include <sbml/units/UnitFormulaFormatter.h>
#include <sbml/units/FormulaUnitsData.h>
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
int
main (int argc, char *argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printUnits filename" << endl << endl;
return 1;
}
const char* filename = argv[1];
{
cerr << "Encountered the following SBML errors:" << endl;
return 1;
}
if (model == 0)
{
cout << "No model present." << endl;
return 1;
}
unsigned int i,j;
for (i = 0; i < model->getNumSpecies(); i++)
{
cout << "Species " << i << ": "
}
for (i = 0; i < model->getNumCompartments(); i++)
{
cout << "Compartment " << i << ": "
<< endl;
}
for (i = 0; i < model->getNumParameters(); i++)
{
cout << "Parameter " << i << ": "
<< endl;
}
for (i = 0; i < model->getNumInitialAssignments(); i++)
{
cout << "InitialAssignment " << i << ": "
cout << " undeclared units: ";
}
for (i = 0; i < model->getNumEvents(); i++)
{
Event *e = model->getEvent(i);
cout << "Event " << i << ": " << endl;
{
cout << "Delay: "
cout << " undeclared units: ";
}
{
cout << "EventAssignment " << j << ": "
cout << " undeclared units: ";
}
}
for (i = 0; i < model->getNumReactions(); i++)
{
cout << "Reaction " << i << ": " << endl;
{
cout << "Kinetic Law: "
cout << " undeclared units: ";
}
{
{
cout << "Reactant stoichiometryMath" << j << ": "
cout << " undeclared units: ";
}
}
{
{
cout << "Product stoichiometryMath" << j << ": "
cout << " undeclared units: ";
}
}
}
for (i = 0; i < model->getNumRules(); i++)
{
Rule *r = model->getRule(i);
cout << "Rule " << i << ": "
cout << " undeclared units: ";
}
delete document;
return 0;
}
SBMLDocument_t * readSBML(const char *filename)
Include all SBML types in a single header file.
Definitions of UnitDefinition and ListOfUnitDefinitions.
@sbmlpackage{core}
Definition: Compartment.h:490
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment object's de...
Definition: Compartment.cpp:892
bool containsUndeclaredUnits()
Predicate returning true if the "math" expression in this Delay instance contains parameters with und...
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: Delay.cpp:219
@sbmlpackage{core}
Definition: EventAssignment.h:296
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this EventAssignment contains literal numbers or p...
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: EventAssignment.cpp:273
@sbmlpackage{core}
Definition: Event.h:355
const EventAssignment * getEventAssignment(unsigned int n) const
Return a specific EventAssignment object of this Event.
Definition: Event.cpp:1055
bool isSetDelay() const
Predicate for testing whether the delay for this Event is set.
Definition: Event.cpp:465
unsigned int getNumEventAssignments() const
Returns the number of EventAssignment objects attached to this Event.
Definition: Event.cpp:1097
const Delay * getDelay() const
Get the assignment delay portion of this Event, if there is one.
Definition: Event.cpp:366
@sbmlpackage{core}
Definition: InitialAssignment.h:289
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers...
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: InitialAssignment.cpp:277
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with u...
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: KineticLaw.cpp:859
@sbmlpackage{core}
Definition: Parameter.h:202
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Parameter's value.
Definition: Parameter.cpp:531
@sbmlpackage{core}
Definition: Reaction.h:224
unsigned int getNumReactants() const
Returns the number of reactant species in this Reaction.
Definition: Reaction.cpp:1267
const KineticLaw * getKineticLaw() const
Returns the KineticLaw object contained in this Reaction.
Definition: Reaction.cpp:396
const SpeciesReference * getProduct(unsigned int n) const
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reacti...
Definition: Reaction.cpp:1176
bool isSetKineticLaw() const
Predicate returning true if this Reaction contains a kinetic law object.
Definition: Reaction.cpp:470
unsigned int getNumProducts() const
Returns the number of product species in this Reaction.
Definition: Reaction.cpp:1277
const SpeciesReference * getReactant(unsigned int n) const
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reac...
Definition: Reaction.cpp:1133
@sbmlpackage{core}
Definition: Rule.h:163
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: Rule.cpp:478
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this Rule contains parameters/numbers with undecla...
@sbmlpackage{core}
Definition: SBMLDocument.h:349
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1153
void printErrors(std::ostream &stream=std::cerr) const
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document...
Definition: SBMLDocument.cpp:1176
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:346
@sbmlpackage{core}
Definition: Species.h:429
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or conc...
Definition: Species.cpp:1138
@sbmlpackage{core}
Definition: SpeciesReference.h:281
const StoichiometryMath * getStoichiometryMath() const
Get the content of the "stoichiometryMath" subelement as an ASTNode tree.
Definition: SpeciesReference.cpp:239
bool isSetStoichiometryMath() const
Predicate returning true if this SpeciesReference's "stoichiometryMath" subelement is set.
Definition: SpeciesReference.cpp:280
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this StoichiometryMath object contains literal num...
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition object that expresses the units returned by the math expressi...
Definition: StoichiometryMath.cpp:485
static std::string printUnits(const UnitDefinition *ud, bool compact=false)
Expresses the given definition in a plain-text form.
Definition: UnitDefinition.cpp:1506