libSBML C++ API
libSBML 5.17.2 C++ API
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Prints the annotation strings for each element in a given model.
#include <iostream>
using namespace std;
void printAnnotation(
SBase *sb,
const string&
id =
"")
{
string pid = id;
{
}
<< ") annotation -----" << endl;
cout << endl;
}
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printAnnotation filename" << endl << endl;
return 1;
}
unsigned int i,j;
const char* filename = argv[1];
cout << endl;
cout << "filename: " << filename << endl;
cout << endl;
if(errors > 0)
{
delete document;
return errors;
}
printAnnotation(m);
{
printAnnotation(re);
{
}
{
}
{
}
{
printAnnotation(kl);
{
printAnnotation(pa);
}
}
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
{
printAnnotation(const_cast<Trigger*>(tg));
}
{
printAnnotation(const_cast<Delay*>(dl));
}
{
printAnnotation(ea);
}
}
{
printAnnotation(sp);
}
{
printAnnotation(sp);
}
delete document;
return errors;
}
const KineticLaw * getKineticLaw() const
Returns the KineticLaw object contained in this Reaction.
Definition: Reaction.cpp:391
A reference to an SBML species in a reaction.
Definition: SpeciesReference.h:271
unsigned int getNumInitialAssignments() const
Get the number of InitialAssignment objects in this Model.
Definition: Model.cpp:3266
unsigned int getNumParameters() const
Get the number of Parameter objects in this Model.
Definition: Model.cpp:3256
const FunctionDefinition * getFunctionDefinition(unsigned int n) const
Get the nth FunctionDefinitions object in this Model.
Definition: Model.cpp:2458
An SBML parameter: a named symbol with a value.
Definition: Parameter.h:192
const EventAssignment * getEventAssignment(unsigned int n) const
Return a specific EventAssignment object of this Event.
Definition: Event.cpp:1051
bool isSetTrigger() const
Predicate for testing whether the trigger for this Event is set.
Definition: Event.cpp:446
const Parameter * getParameter(unsigned int n) const
Get the nth Parameter object in this Model.
Definition: Model.cpp:2710
An SBML reaction between species in an SBML model.
Definition: Reaction.h:214
An SBML constraint, for stating validity assumptions.
Definition: Constraint.h:148
const Species * getSpecies(unsigned int n) const
Get the nth Species object in this Model.
Definition: Model.cpp:2668
const std::string & getSpecies() const
Get the value of the "species" attribute.
Definition: SimpleSpeciesReference.cpp:144
The rate expression for an SBML reaction.
Definition: KineticLaw.h:193
Include all SBML types in a single header file.
A definition of a unit used in an SBML model.
Definition: UnitDefinition.h:272
unsigned int getNumConstraints() const
Get the number of Constraint objects in this Model.
Definition: Model.cpp:3286
const Parameter * getParameter(unsigned int n) const
Returns the nth Parameter object in the list of parameters in this KineticLaw instance.
Definition: KineticLaw.cpp:728
unsigned int getNumSpeciesTypes() const
Get the number of SpeciesType objects in this Model.
Definition: Model.cpp:3207
bool isSetAnnotation() const
Predicate returning true if this object's "annotation" subelement exists and has content.
Definition: SBase.cpp:1183
const Delay * getDelay() const
Get the assignment delay portion of this Event, if there is one.
Definition: Event.cpp:357
virtual const std::string & getId() const
Returns the value of the "id" attribute of this SBML object, if it has one, or the "variable" attribu...
Definition: SBase.cpp:709
const Reaction * getReaction(unsigned int n) const
Get the nth Reaction object in this Model.
Definition: Model.cpp:3029
unsigned int getNumReactants() const
Returns the number of reactant species in this Reaction.
Definition: Reaction.cpp:1260
SBMLDocument * readSBML(const std::string &filename)
Definition: SBMLReader.cpp:103
bool isSetKineticLaw() const
Predicate returning true if this Reaction contains a kinetic law object.
Definition: Reaction.cpp:465
unsigned int getNumReactions() const
Get the number of Reaction objects in this Model.
Definition: Model.cpp:3296
std::string getAnnotationString()
Returns the content of the "annotation" subelement of this object as a character string.
Definition: SBase.cpp:803
const InitialAssignment * getInitialAssignment(unsigned int n) const
Get the nth InitialAssignment object in this Model.
Definition: Model.cpp:2752
A discontinuous SBML event.
Definition: Event.h:345
A user-defined function in an SBML model.
Definition: FunctionDefinition.h:140
unsigned int getNumModifiers() const
Returns the number of modifier species in this Reaction.
Definition: Reaction.cpp:1281
const Compartment * getCompartment(unsigned int n) const
Get the nth Compartment object in this Model.
Definition: Model.cpp:2626
File and text-string SBML reader.
Definition: SBMLReader.h:333
unsigned int getNumParameters() const
Returns the number of parameters in this KineticLaw instance.
Definition: KineticLaw.cpp:825
bool isSetDelay() const
Predicate for testing whether the delay for this Event is set.
Definition: Event.cpp:456
An SBML compartment, where species are located.
Definition: Compartment.h:480
unsigned int getNumEvents() const
Get the number of Event objects in this Model.
Definition: Model.cpp:3306
unsigned int getNumUnitDefinitions() const
Get the number of UnitDefinition objects in this Model.
Definition: Model.cpp:3187
The trigger expression for an SBML event.
Definition: Trigger.h:173
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1176
const Constraint * getConstraint(unsigned int n) const
Get the nth Constraint object in this Model.
Definition: Model.cpp:3009
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:353
An SBML initial assignment, evaluated once only.
Definition: InitialAssignment.h:279
An assignment to a variable by an SBML event.
Definition: EventAssignment.h:286
SBML's SBase class, base class of most SBML objects.
Definition: SBase.h:181
An SBML model.
Definition: Model.h:475
A species type in SBML Level 2.
Definition: SpeciesType.h:99
unsigned int getNumRules() const
Get the number of Rule objects in this Model.
Definition: Model.cpp:3276
unsigned int getNumProducts() const
Returns the number of product species in this Reaction.
Definition: Reaction.cpp:1270
const ModifierSpeciesReference * getModifier(unsigned int n) const
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of t...
Definition: Reaction.cpp:1212
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:1199
A delay on the time of execution of an SBML event.
Definition: Delay.h:222
const SpeciesType * getSpeciesType(unsigned int n) const
Get the nth SpeciesType object in this Model.
Definition: Model.cpp:2584
unsigned int getNumFunctionDefinitions() const
Get the number of FunctionDefinition objects in this Model.
Definition: Model.cpp:3177
const Trigger * getTrigger() const
Get the event trigger portion of this Event.
Definition: Event.cpp:337
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:1126
unsigned int getNumSpecies() const
Get the number of Species objects in this Model.
Definition: Model.cpp:3227
bool isSetSpecies() const
Predicate returning true if this SimpleSpeciesReference's "species" attribute is set.
Definition: SimpleSpeciesReference.cpp:178
const Event * getEvent(unsigned int n) const
Get the nth Event object in this Model.
Definition: Model.cpp:3135
Parent class for SBML rules in libSBML.
Definition: Rule.h:153
const UnitDefinition * getUnitDefinition(unsigned int n) const
Get the nth UnitDefinition object in this Model.
Definition: Model.cpp:2500
unsigned int getNumEventAssignments() const
Returns the number of EventAssignment objects attached to this Event.
Definition: Event.cpp:1093
virtual const std::string & getElementName() const
Returns the XML element name of this object.
Definition: SBase.cpp:3433
unsigned int getNumCompartments() const
Get the number of Compartment objects in this Model.
Definition: Model.cpp:3217
virtual bool isSetId() const
Predicate returning true if a call to getId() returns a non-empty string.
Definition: SBase.cpp:1141
An SBML species – a pool of entities.
Definition: Species.h:419
const Rule * getRule(unsigned int n) const
Get the nth Rule object in this Model.
Definition: Model.cpp:2818
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:63
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:1169
Overall SBML container object.
Definition: SBMLDocument.h:338
A reference to an SBML modifier species.
Definition: ModifierSpeciesReference.h:82