libSBML C++ API
libSBML 5.18.0 C++ API
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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;
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;
{
cout << "Species " << i << ": "
}
{
cout << "Compartment " << i << ": "
<< endl;
}
{
cout << "Parameter " << i << ": "
<< endl;
}
{
cout << "InitialAssignment " << i << ": "
cout << " undeclared units: ";
}
{
cout << "Event " << i << ": " << endl;
{
cout << "Delay: "
cout << " undeclared units: ";
}
{
cout << "EventAssignment " << j << ": "
cout << " undeclared units: ";
}
}
{
cout << "Reaction " << i << ": " << endl;
{
cout << "Kinetic Law: "
cout << " undeclared units: ";
}
{
{
cout << "Reactant stoichiometryMath" << j << ": "
cout << " undeclared units: ";
}
}
{
{
cout << "Product stoichiometryMath" << j << ": "
cout << " undeclared units: ";
}
}
}
{
cout << "Rule " << i << ": "
cout << " undeclared units: ";
}
delete document;
return 0;
}
A reference to an SBML species in a reaction.
Definition: SpeciesReference.h:275
unsigned int getNumInitialAssignments() const
Get the number of InitialAssignment objects in this Model.
Definition: Model.cpp:3274
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: Rule.cpp:473
unsigned int getNumParameters() const
Get the number of Parameter objects in this Model.
Definition: Model.cpp:3264
An SBML parameter: a named symbol with a value.
Definition: Parameter.h:196
const EventAssignment * getEventAssignment(unsigned int n) const
Return a specific EventAssignment object of this Event.
Definition: Event.cpp:1055
const Parameter * getParameter(unsigned int n) const
Get the nth Parameter object in this Model.
Definition: Model.cpp:2718
An SBML reaction between species in an SBML model.
Definition: Reaction.h:218
const Species * getSpecies(unsigned int n) const
Get the nth Species object in this Model.
Definition: Model.cpp:2676
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:361
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition object that expresses the units returned by the math expressi...
Definition: StoichiometryMath.cpp:480
static std::string printUnits(const UnitDefinition *ud, bool compact=false)
Expresses the given definition in a plain-text form.
Definition: UnitDefinition.cpp:1540
Include all SBML types in a single header file.
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this Rule contains parameters/numbers with undecla...
const Reaction * getReaction(unsigned int n) const
Get the nth Reaction object in this Model.
Definition: Model.cpp:3037
unsigned int getNumReactants() const
Returns the number of reactant species in this Reaction.
Definition: Reaction.cpp:1264
const KineticLaw * getKineticLaw() const
Returns the KineticLaw object contained in this Reaction.
Definition: Reaction.cpp:395
bool isSetKineticLaw() const
Predicate returning true if this Reaction contains a kinetic law object.
Definition: Reaction.cpp:469
unsigned int getNumReactions() const
Get the number of Reaction objects in this Model.
Definition: Model.cpp:3304
SBMLDocument_t * readSBML(const char *filename)
const InitialAssignment * getInitialAssignment(unsigned int n) const
Get the nth InitialAssignment object in this Model.
Definition: Model.cpp:2760
A discontinuous SBML event.
Definition: Event.h:349
const Compartment * getCompartment(unsigned int n) const
Get the nth Compartment object in this Model.
Definition: Model.cpp:2634
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Parameter's value.
Definition: Parameter.cpp:535
bool isSetDelay() const
Predicate for testing whether the delay for this Event is set.
Definition: Event.cpp:460
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: KineticLaw.cpp:851
An SBML compartment, where species are located.
Definition: Compartment.h:484
unsigned int getNumEvents() const
Get the number of Event objects in this Model.
Definition: Model.cpp:3314
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1184
An SBML initial assignment, evaluated once only.
Definition: InitialAssignment.h:283
An assignment to a variable by an SBML event.
Definition: EventAssignment.h:290
const StoichiometryMath * getStoichiometryMath() const
Get the content of the "stoichiometryMath" subelement as an ASTNode tree.
Definition: SpeciesReference.cpp:234
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers...
An SBML model.
Definition: Model.h:479
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: Delay.cpp:214
unsigned int getNumRules() const
Get the number of Rule objects in this Model.
Definition: Model.cpp:3284
Definitions of UnitDefinition and ListOfUnitDefinitions.
const Delay * getDelay() const
Get the assignment delay portion of this Event, if there is one.
Definition: Event.cpp:361
unsigned int getNumProducts() const
Returns the number of product species in this Reaction.
Definition: Reaction.cpp:1274
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or conc...
Definition: Species.cpp:1142
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:1207
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with u...
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this EventAssignment contains literal numbers or p...
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:1130
unsigned int getNumSpecies() const
Get the number of Species objects in this Model.
Definition: Model.cpp:3235
bool containsUndeclaredUnits()
Predicate returning true if the "math" expression in this Delay instance contains parameters with und...
const Event * getEvent(unsigned int n) const
Get the nth Event object in this Model.
Definition: Model.cpp:3143
Parent class for SBML rules in libSBML.
Definition: Rule.h:157
unsigned int getNumEventAssignments() const
Returns the number of EventAssignment objects attached to this Event.
Definition: Event.cpp:1097
unsigned int getNumCompartments() const
Get the number of Compartment objects in this Model.
Definition: Model.cpp:3225
bool isSetStoichiometryMath() const
Predicate returning true if this SpeciesReference's "stoichiometryMath" subelement is set.
Definition: SpeciesReference.cpp:275
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: EventAssignment.cpp:268
An SBML species – a pool of entities.
Definition: Species.h:423
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment object's de...
Definition: Compartment.cpp:911
const Rule * getRule(unsigned int n) const
Get the nth Rule object in this Model.
Definition: Model.cpp:2826
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
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:1173
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: InitialAssignment.cpp:272
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this StoichiometryMath object contains literal num...
Overall SBML container object.
Definition: SBMLDocument.h:342