libSBML C++ API  5.18.0
Model Class Reference
Inheritance diagram for Model:
[legend]

Detailed Description

An SBML model.

In an SBML model definition, a single object of class Model serves as the overall container for the lists of the various model components. All of the lists are optional, but if a given list container is present within the model, the list must not be empty; that is, it must have length one or more. The following are the components and lists permitted in different Levels and Versions of SBML in version 5.18.0 of libSBML:

Although all the lists are optional, there are dependencies between SBML components such that defining some components requires defining others. An example is that defining a species requires defining a compartment, and defining a reaction requires defining a species. The dependencies are explained in more detail in the SBML specifications.

In addition to the above lists and attributes, the Model class in both SBML Level 2 and Level 3 has the usual two attributes of "id" and "name", and both are optional. As is the case for other SBML components with "id" and "name" attributes, they must be used according to the guidelines described in the SBML specifications. (Within the frameworks of SBML Level 2 and Level 3, a Model object identifier has no assigned meaning, but extension packages planned for SBML Level 3 are likely to make use of this identifier.)

Finally, SBML Level 3 has introduced a number of additional Model attributes. They are discussed in a separate section below.

Approaches to creating objects using the libSBML API

LibSBML provides two main mechanisms for creating objects: class constructors (e.g., Species::Species() ), and createObject() methods (such as Model::createSpecies()) provided by certain Object classes such as Model. These multiple mechanisms are provided by libSBML for flexibility and to support different use-cases, but they also have different implications for the overall model structure.

In general, the recommended approach is to use the createObject() methods. These methods both create an object and link it to the parent in one step. Here is an example:

// Create an SBMLDocument object in Level 3 Version 1 format:
SBMLDocument* sbmlDoc = new SBMLDocument(3, 1);
// Create a Model object inside the SBMLDocument object and set
// its identifier. The call returns a pointer to the Model object
// created, and methods called on that object affect the attributes
// of the object attached to the model (as expected).
Model* model = sbmlDoc->createModel();
model->setId("BestModelEver");
// Create a Species object inside the Model and set its identifier.
// Similar to the lines above, this call returns a pointer to the Species
// object created, and methods called on that object affect the attributes
// of the object attached to the model (as expected).
Species *sp = model->createSpecies();
sp->setId("MySpecies");

The createObject() methods return a pointer to the object created, but they also add the object to the relevant list of object instances contained in the parent. (These lists become the <listOfObjects> elements in the finished XML rendition of SBML.) In the example above, Model::createSpecies() adds the created species directly to the <listOfSpecies> list in the model. Subsequently, methods called on the species change the species in the model (which is what is expected in most situations).

Consistency and adherence to SBML specifications

To make it easier for applications to do whatever they need, libSBML version 5.18.0 is relatively lax when it comes to enforcing correctness and completeness of models during model construction and editing. Essentially, libSBML will not in most cases check automatically that a model's components have valid attribute values, or that the overall model is consistent and free of errors—even obvious errors such as duplication of identifiers. This allows applications great leeway in how they build their models, but it means that software authors must take deliberate steps to ensure that the model will be, in the end, valid SBML. These steps include such things as keeping track of the identifiers used in a model, manually performing updates in certain situations where an entity is referenced in more than one place (e.g., a species that is referenced by multiple SpeciesReference objects), and so on.

That said, libSBML does provide powerful features for deliberately performing validation of SBML when an application decides it is time to do so. The interfaces to these facilities are on the SBMLDocument class, in the form of SBMLDocument::checkInternalConsistency() and SBMLDocument::checkConsistency(). Please refer to the documentation for SBMLDocument for more information about this.

While applications may play fast and loose and live like free spirits during the construction and editing of SBML models, they should always make sure to call SBMLDocument::checkInternalConsistency() and/or SBMLDocument::checkConsistency() before writing out the final version of an SBML model.

Model attributes introduced in SBML Level 3

As mentioned above, the Model class has a number of optional attributes in SBML Level 3. These are "substanceUnits", "timeUnits", "volumeUnits", "areaUnits", "lengthUnits", "extentUnits", and "conversionFactor. The following provide more information about them.

The "substanceUnits" attribute

The "substanceUnits" attribute is used to specify the unit of measurement associated with substance quantities of Species objects that do not specify units explicitly. If a given Species object definition does not specify its unit of substance quantity via the "substanceUnits" attribute on the Species object instance, then that species inherits the value of the Model "substanceUnits" attribute. If the Model does not define a value for this attribute, then there is no unit to inherit, and all species that do not specify individual "substanceUnits" attribute values then have no declared units for their quantities. The SBML Level 3 specifications provide more details.

Note that when the identifier of a species appears in a model's mathematical expressions, the unit of measurement associated with that identifier is not solely determined by setting "substanceUnits" on Model or Species. Please see the discussion about units given in the documentation for the Species class.

The "timeUnits" attribute

The "timeUnits" attribute on SBML Level 3's Model object is used to specify the unit in which time is measured in the model. This attribute on Model is the only way to specify a unit for time in a model. It is a global attribute; time is measured in the model everywhere in the same way. This is particularly relevant to Reaction and RateRule objects in a model: all Reaction and RateRule objects in SBML define per-time values, and the unit of time is given by the "timeUnits" attribute on the Model object instance. If the Model "timeUnits" attribute has no value, it means that the unit of time is not defined for the model's reactions and rate rules. Leaving it unspecified in an SBML model does not result in an invalid model in SBML Level 3; however, as a matter of best practice, we strongly recommend that all models specify units of measurement for time.

The "volumeUnits", "areaUnits", and "lengthUnits" attributes

The attributes "volumeUnits", "areaUnits" and "lengthUnits" together are used to set the units of measurements for the sizes of Compartment objects in an SBML Level 3 model when those objects do not otherwise specify units. The three attributes correspond to the most common cases of compartment dimensions: "volumeUnits" for compartments having a "spatialDimensions" attribute value of "3", "areaUnits" for compartments having a "spatialDimensions" attribute value of "2", and "lengthUnits" for compartments having a "spatialDimensions" attribute value of "1". The attributes are not applicable to compartments whose "spatialDimensions" attribute values are not one of "1", "2" or "3".

If a given Compartment object instance does not provide a value for its "units" attribute, then the unit of measurement of that compartment's size is inherited from the value specified by the Model "volumeUnits", "areaUnits" or "lengthUnits" attribute, as appropriate based on the Compartment object's "spatialDimensions" attribute value. If the Model object does not define the relevant attribute, then there are no units to inherit, and all Compartment objects that do not set a value for their "units" attribute then have no units associated with their compartment sizes.

The use of three separate attributes is a carry-over from SBML Level 2. Note that it is entirely possible for a model to define a value for two or more of the attributes "volumeUnits", "areaUnits" and "lengthUnits" simultaneously, because SBML models may contain compartments with different numbers of dimensions.

The "extentUnits" attribute

Reactions are processes that occur over time. These processes involve events of some sort, where a single ``reaction event'' is one in which some set of entities (known as reactants, products and modifiers in SBML) interact, once. The extent of a reaction is a measure of how many times the reaction has occurred, while the time derivative of the extent gives the instantaneous rate at which the reaction is occurring. Thus, what is colloquially referred to as the "rate of the reaction" is in fact equal to the rate of change of reaction extent.

In SBML Level 3, the combination of "extentUnits" and "timeUnits" defines the units of kinetic laws in SBML and establishes how the numerical value of each KineticLaw object's mathematical formula is meant to be interpreted in a model. The units of the kinetic laws are taken to be "extentUnits" divided by "timeUnits".

Note that this embodies an important principle in SBML Level 3 models: all reactions in an SBML model must have the same units for the rate of change of extent. In other words, the units of all reaction rates in the model must be the same. There is only one global value for "extentUnits" and one global value for "timeUnits".

The "conversionFactor" attribute

The attribute "conversionFactor" in SBML Level 3's Model object defines a global value inherited by all Species object instances that do not define separate values for their "conversionFactor" attributes. The value of this attribute must refer to a Parameter object instance defined in the model. The Parameter object in question must be a constant; ie it must have its "constant" attribute value set to "true".

If a given Species object definition does not specify a conversion factor via the "conversionFactor" attribute on Species, then the species inherits the conversion factor specified by the Model "conversionFactor" attribute. If the Model does not define a value for this attribute, then there is no conversion factor to inherit. More information about conversion factors is provided in the SBML Level 3 specifications.

Examples:
addLayout.cpp, createExampleSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, qual_example1.cpp, SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, spec_example4.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.

Public Member Functions

int addCompartment (const Compartment *c)
 Adds a copy of the given Compartment object to this Model. More...
 
int addCompartmentType (const CompartmentType *ct)
 Adds a copy of the given CompartmentType object to this Model. More...
 
int addConstraint (const Constraint *c)
 Adds a copy of the given Constraint object to this Model. More...
 
int addCVTerm (CVTerm *term, bool newBag=false)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addEvent (const Event *e)
 Adds a copy of the given Event object to this Model. More...
 
int addFunctionDefinition (const FunctionDefinition *fd)
 Adds a copy of the given FunctionDefinition object to this Model. More...
 
int addInitialAssignment (const InitialAssignment *ia)
 Adds a copy of the given InitialAssignment object to this Model. More...
 
int addParameter (const Parameter *p)
 Adds a copy of the given Parameter object to this Model. More...
 
int addReaction (const Reaction *r)
 Adds a copy of the given Reaction object to this Model. More...
 
int addRule (const Rule *r)
 Adds a copy of the given Rule object to this Model. More...
 
int addSpecies (const Species *s)
 Adds a copy of the given Species object to this Model. More...
 
int addSpeciesType (const SpeciesType *st)
 Adds a copy of the given SpeciesType object to this Model. More...
 
int addUnitDefinition (const UnitDefinition *ud)
 Adds a copy of the given UnitDefinition object to this Model. More...
 
virtual int appendAnnotation (const XMLNode *annotation)
 Appends annotation content to any existing content in the "annotation" subelement of this object. More...
 
virtual int appendAnnotation (const std::string &annotation)
 Appends annotation content to any existing content in the "annotation" subelement of this object. More...
 
virtual int appendFrom (const Model *model)
 Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model. More...
 
int appendNotes (const XMLNode *notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
int appendNotes (const std::string &notes)
 Appends the given notes to the "notes" subelement of this object. More...
 
void clearAllElementIdList ()
 Clears the internal list of the identifiers of all elements within this Model object. More...
 
void clearAllElementMetaIdList ()
 Clears the internal list of the metaids of all elements within this Model object. More...
 
virtual Modelclone () const
 Creates and returns a deep copy of this Model object. More...
 
AlgebraicRulecreateAlgebraicRule ()
 Creates a new AlgebraicRule inside this Model and returns it. More...
 
AssignmentRulecreateAssignmentRule ()
 Creates a new AssignmentRule inside this Model and returns it. More...
 
CompartmentcreateCompartment ()
 Creates a new Compartment inside this Model and returns it. More...
 
CompartmentTypecreateCompartmentType ()
 Creates a new CompartmentType inside this Model and returns it. More...
 
ConstraintcreateConstraint ()
 Creates a new Constraint inside this Model and returns it. More...
 
DelaycreateDelay ()
 Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it. More...
 
EventcreateEvent ()
 Creates a new Event inside this Model and returns it. More...
 
EventAssignmentcreateEventAssignment ()
 Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it. More...
 
FunctionDefinitioncreateFunctionDefinition ()
 Creates a new FunctionDefinition inside this Model and returns it. More...
 
InitialAssignmentcreateInitialAssignment ()
 Creates a new InitialAssignment inside this Model and returns it. More...
 
KineticLawcreateKineticLaw ()
 Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it. More...
 
LocalParametercreateKineticLawLocalParameter ()
 Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More...
 
ParametercreateKineticLawParameter ()
 Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More...
 
ModifierSpeciesReferencecreateModifier ()
 Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it. More...
 
ParametercreateParameter ()
 Creates a new Parameter inside this Model and returns it. More...
 
SpeciesReferencecreateProduct ()
 Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it. More...
 
RateRulecreateRateRule ()
 Creates a new RateRule inside this Model and returns it. More...
 
SpeciesReferencecreateReactant ()
 Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it. More...
 
ReactioncreateReaction ()
 Creates a new Reaction inside this Model and returns it. More...
 
SpeciescreateSpecies ()
 Creates a new Species inside this Model and returns it. More...
 
SpeciesTypecreateSpeciesType ()
 Creates a new SpeciesType inside this Model and returns it. More...
 
TriggercreateTrigger ()
 Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it. More...
 
UnitcreateUnit ()
 Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it. More...
 
UnitDefinitioncreateUnitDefinition ()
 Creates a new UnitDefinition inside this Model and returns it. More...
 
void deleteDisabledPlugins (bool recursive=true)
 Deletes all information stored in disabled plugins. More...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package on this object. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package on this object. More...
 
IdList getAllElementIdList () const
 Returns the internal list of the identifiers of all elements within this Model object. More...
 
IdList getAllElementMetaIdList () const
 Returns the internal list of the metaids of all elements within this Model object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child objects. More...
 
virtual ListgetAllElementsFromPlugins (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects contained in SBML package plug-ins. More...
 
SBasegetAncestorOfType (int type, const std::string &pkgName="core")
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
XMLNodegetAnnotation ()
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetAnnotation () const
 Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More...
 
std::string getAnnotationString ()
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
std::string getAnnotationString () const
 Returns the content of the "annotation" subelement of this object as a character string. More...
 
const std::string & getAreaUnits () const
 Returns the value of the "areaUnits" attribute of this Model. More...
 
const AssignmentRulegetAssignmentRule (const std::string &variable) const
 Get a Rule object based on the variable to which it assigns a value. More...
 
AssignmentRulegetAssignmentRule (const std::string &variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
const AssignmentRulegetAssignmentRuleByVariable (const std::string &variable) const
 Get a Rule object based on the variable to which it assigns a value. More...
 
AssignmentRulegetAssignmentRuleByVariable (const std::string &variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
unsigned int getColumn () const
 Returns the column number where this object first appears in the XML representation of the SBML document. More...
 
const CompartmentgetCompartment (unsigned int n) const
 Get the nth Compartment object in this Model. More...
 
CompartmentgetCompartment (unsigned int n)
 Get the nth Compartment object in this Model. More...
 
const CompartmentgetCompartment (const std::string &sid) const
 Get a Compartment object based on its identifier. More...
 
CompartmentgetCompartment (const std::string &sid)
 Get a Compartment object based on its identifier. More...
 
const CompartmentTypegetCompartmentType (unsigned int n) const
 Get the nth CompartmentType object in this Model. More...
 
CompartmentTypegetCompartmentType (unsigned int n)
 Get the nth CompartmentType object in this Model. More...
 
const CompartmentTypegetCompartmentType (const std::string &sid) const
 Get a CompartmentType object based on its identifier. More...
 
CompartmentTypegetCompartmentType (const std::string &sid)
 Get a CompartmentType object based on its identifier. More...
 
const ConstraintgetConstraint (unsigned int n) const
 Get the nth Constraint object in this Model. More...
 
ConstraintgetConstraint (unsigned int n)
 Get the nth Constraint object in this Model. More...
 
const std::string & getConversionFactor () const
 Returns the value of the "conversionFactor" attribute of this Model. More...
 
CVTermgetCVTerm (unsigned int n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
ListgetCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
ListgetCVTerms () const
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
SBasePlugingetDisabledPlugin (unsigned int n)
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetDisabledPlugin (unsigned int n) const
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasegetElementByMetaId (const std::string &metaid) const
 Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element it can find with the given metaid. More...
 
const SBasegetElementBySId (const std::string &id) const
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element found that has the given id. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this object, which for Model, is always "model". More...
 
const EventgetEvent (unsigned int n) const
 Get the nth Event object in this Model. More...
 
EventgetEvent (unsigned int n)
 Get the nth Event object in this Model. More...
 
const EventgetEvent (const std::string &sid) const
 Get an Event object based on its identifier. More...
 
EventgetEvent (const std::string &sid)
 Get an Event object based on its identifier. More...
 
const std::string & getExtentUnits () const
 Returns the value of the "extentUnits" attribute of this Model. More...
 
const FunctionDefinitiongetFunctionDefinition (unsigned int n) const
 Get the nth FunctionDefinitions object in this Model. More...
 
FunctionDefinitiongetFunctionDefinition (unsigned int n)
 Get the nth FunctionDefinitions object in this Model. More...
 
const FunctionDefinitiongetFunctionDefinition (const std::string &sid) const
 Get a FunctionDefinition object based on its identifier. More...
 
FunctionDefinitiongetFunctionDefinition (const std::string &sid)
 Get a FunctionDefinition object based on its identifier. More...
 
virtual const std::string & getId () const
 Returns the value of the "id" attribute of this Model. More...
 
const std::string & getIdAttribute () const
 Returns the value of the "id" attribute of this SBML object. More...
 
const InitialAssignmentgetInitialAssignment (unsigned int n) const
 Get the nth InitialAssignment object in this Model. More...
 
InitialAssignmentgetInitialAssignment (unsigned int n)
 Get the nth InitialAssignment object in this Model. More...
 
const InitialAssignmentgetInitialAssignment (const std::string &symbol) const
 Get an InitialAssignment object based on the symbol to which it assigns a value. More...
 
InitialAssignmentgetInitialAssignment (const std::string &symbol)
 Get an InitialAssignment object based on the symbol to which it assigns a value. More...
 
const InitialAssignmentgetInitialAssignmentBySymbol (const std::string &symbol) const
 Get an InitialAssignment object based on the symbol to which it assigns a value. More...
 
InitialAssignmentgetInitialAssignmentBySymbol (const std::string &symbol)
 Get an InitialAssignment object based on the symbol to which it assigns a value. More...
 
const std::string & getLengthUnits () const
 Returns the value of the "lengthUnits" attribute of this Model. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
unsigned int getLine () const
 Returns the line number where this object first appears in the XML representation of the SBML document. More...
 
const ListOfCompartmentsgetListOfCompartments () const
 Get the ListOfCompartments object in this Model. More...
 
ListOfCompartmentsgetListOfCompartments ()
 Get the ListOfCompartments object in this Model. More...
 
const ListOfCompartmentTypesgetListOfCompartmentTypes () const
 Get the ListOfCompartmentTypes object in this Model. More...
 
ListOfCompartmentTypesgetListOfCompartmentTypes ()
 Get the ListOfCompartmentTypes object in this Model. More...
 
const ListOfConstraintsgetListOfConstraints () const
 Get the ListOfConstraints object in this Model. More...
 
ListOfConstraintsgetListOfConstraints ()
 Get the ListOfConstraints object in this Model. More...
 
const ListOfEventsgetListOfEvents () const
 Get the ListOfEvents object in this Model. More...
 
ListOfEventsgetListOfEvents ()
 Get the ListOfEvents object in this Model. More...
 
const ListOfFunctionDefinitionsgetListOfFunctionDefinitions () const
 Get the ListOfFunctionDefinitions object in this Model. More...
 
ListOfFunctionDefinitionsgetListOfFunctionDefinitions ()
 Get the ListOfFunctionDefinitions object in this Model. More...
 
const ListOfInitialAssignmentsgetListOfInitialAssignments () const
 Get the ListOfInitialAssignments object in this Model. More...
 
ListOfInitialAssignmentsgetListOfInitialAssignments ()
 Get the ListOfInitialAssignments object in this Model. More...
 
const ListOfParametersgetListOfParameters () const
 Get the ListOfParameters object in this Model. More...
 
ListOfParametersgetListOfParameters ()
 Get the ListOfParameters object in this Model. More...
 
const ListOfReactionsgetListOfReactions () const
 Get the ListOfReactions object in this Model. More...
 
ListOfReactionsgetListOfReactions ()
 Get the ListOfReactions object in this Model. More...
 
const ListOfRulesgetListOfRules () const
 Get the ListOfRules object in this Model. More...
 
ListOfRulesgetListOfRules ()
 Get the ListOfRules object in this Model. More...
 
const ListOfSpeciesgetListOfSpecies () const
 Get the ListOfSpecies object in this Model. More...
 
ListOfSpeciesgetListOfSpecies ()
 Get the ListOfSpecies object in this Model. More...
 
const ListOfSpeciesTypesgetListOfSpeciesTypes () const
 Get the ListOfSpeciesTypes object in this Model. More...
 
ListOfSpeciesTypesgetListOfSpeciesTypes ()
 Get the ListOfSpeciesTypes object in this Model. More...
 
const ListOfUnitDefinitionsgetListOfUnitDefinitions () const
 Get the ListOfUnitDefinitions object in this Model. More...
 
ListOfUnitDefinitionsgetListOfUnitDefinitions ()
 Get the ListOfUnitDefinitions object in this Model. More...
 
const std::string & getMetaId () const
 Returns the value of the "metaid" attribute of this SBML object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this SBML object. More...
 
const ModelgetModel () const
 Returns the Model object for the SBML Document in which the current object is located. More...
 
ModelHistorygetModelHistory () const
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModelHistorygetModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
ModifierSpeciesReferencegetModifierSpeciesReference (const std::string &sid)
 Get a ModifierSpeciesReference object based on its identifier. More...
 
const ModifierSpeciesReferencegetModifierSpeciesReference (const std::string &sid) const
 Get a ModifierSpeciesReference object based on its identifier. More...
 
virtual const std::string & getName () const
 Returns the value of the "name" attribute of this Model object. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of the XML Namespaces declared on the SBML document owning this object. More...
 
XMLNodegetNotes ()
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
XMLNodegetNotes () const
 Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More...
 
std::string getNotesString ()
 Returns the content of the "notes" subelement of this object as a string. More...
 
std::string getNotesString () const
 Returns the content of the "notes" subelement of this object as a string. More...
 
unsigned int getNumCompartments () const
 Get the number of Compartment objects in this Model. More...
 
unsigned int getNumCompartmentTypes () const
 Get the number of CompartmentType objects in this Model. More...
 
unsigned int getNumConstraints () const
 Get the number of Constraint objects in this Model. More...
 
unsigned int getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
unsigned int getNumDisabledPlugins () const
 Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getNumEvents () const
 Get the number of Event objects in this Model. More...
 
unsigned int getNumFunctionDefinitions () const
 Get the number of FunctionDefinition objects in this Model. More...
 
unsigned int getNumInitialAssignments () const
 Get the number of InitialAssignment objects in this Model. More...
 
unsigned int getNumParameters () const
 Get the number of Parameter objects in this Model. More...
 
unsigned int getNumPlugins () const
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
unsigned int getNumReactions () const
 Get the number of Reaction objects in this Model. More...
 
unsigned int getNumRules () const
 Get the number of Rule objects in this Model. More...
 
unsigned int getNumSpecies () const
 Get the number of Species objects in this Model. More...
 
unsigned int getNumSpeciesTypes () const
 Get the number of SpeciesType objects in this Model. More...
 
unsigned int getNumSpeciesWithBoundaryCondition () const
 Get the number of Species in this Model having their "boundaryCondition" attribute value set to true. More...
 
unsigned int getNumUnitDefinitions () const
 Get the number of UnitDefinition objects in this Model. More...
 
unsigned int getPackageCoreVersion () const
 Returns the SBML Core Version within the SBML Level of the actual object. More...
 
const std::string & getPackageName () const
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
unsigned int getPackageVersion () const
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
const ParametergetParameter (unsigned int n) const
 Get the nth Parameter object in this Model. More...
 
ParametergetParameter (unsigned int n)
 Get the nth Parameter object in this Model. More...
 
const ParametergetParameter (const std::string &sid) const
 Get a Parameter object based on its identifier. More...
 
ParametergetParameter (const std::string &sid)
 Get a Parameter object based on its identifier. More...
 
SBasegetParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent SBML object containing this object. More...
 
SBasePlugingetPlugin (const std::string &package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
const SBasePlugingetPlugin (const std::string &package) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugingetPlugin (unsigned int n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
const SBasePlugingetPlugin (unsigned int n) const
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
std::string getPrefix () const
 Returns the XML namespace prefix of this element. More...
 
const RateRulegetRateRule (const std::string &variable) const
 Get a Rule object based on the variable to which it assigns a value. More...
 
RateRulegetRateRule (const std::string &variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
const RateRulegetRateRuleByVariable (const std::string &variable) const
 Get a Rule object based on the variable to which it assigns a value. More...
 
RateRulegetRateRuleByVariable (const std::string &variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
const ReactiongetReaction (unsigned int n) const
 Get the nth Reaction object in this Model. More...
 
ReactiongetReaction (unsigned int n)
 Get the nth Reaction object in this Model. More...
 
const ReactiongetReaction (const std::string &sid) const
 Get a Reaction object based on its identifier. More...
 
ReactiongetReaction (const std::string &sid)
 Get a Reaction object based on its identifier. More...
 
BiolQualifierType_t getResourceBiologicalQualifier (std::string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
ModelQualifierType_t getResourceModelQualifier (std::string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
const RulegetRule (unsigned int n) const
 Get the nth Rule object in this Model. More...
 
RulegetRule (unsigned int n)
 Get the nth Rule object in this Model. More...
 
const RulegetRule (const std::string &variable) const
 Get a Rule object based on the variable to which it assigns a value. More...
 
RulegetRule (const std::string &variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
const RulegetRuleByVariable (const std::string &variable) const
 Get a Rule object based on the variable to which it assigns a value. More...
 
RulegetRuleByVariable (const std::string &variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
int getSBOTerm () const
 Returns the integer portion of the value of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermAsURL () const
 Returns the URL representation of the "sboTerm" attribute of this object. More...
 
std::string getSBOTermID () const
 Returns the string representation of the "sboTerm" attribute of this object. More...
 
const SpeciesgetSpecies (unsigned int n) const
 Get the nth Species object in this Model. More...
 
SpeciesgetSpecies (unsigned int n)
 Get the nth Species object in this Model. More...
 
const SpeciesgetSpecies (const std::string &sid) const
 Get a Species object based on its identifier. More...
 
SpeciesgetSpecies (const std::string &sid)
 Get a Species object based on its identifier. More...
 
SpeciesReferencegetSpeciesReference (const std::string &sid)
 Get a SpeciesReference object based on its identifier. More...
 
const SpeciesReferencegetSpeciesReference (const std::string &sid) const
 Get a SpeciesReference object based on its identifier. More...
 
const SpeciesTypegetSpeciesType (unsigned int n) const
 Get the nth SpeciesType object in this Model. More...
 
SpeciesTypegetSpeciesType (unsigned int n)
 Get the nth SpeciesType object in this Model. More...
 
const SpeciesTypegetSpeciesType (const std::string &sid) const
 Get a SpeciesType object based on its identifier. More...
 
SpeciesTypegetSpeciesType (const std::string &sid)
 Get a SpeciesType object based on its identifier. More...
 
const std::string & getSubstanceUnits () const
 Returns the value of the "substanceUnits" attribute of this Model. More...
 
const std::string & getTimeUnits () const
 Returns the value of the "timeUnits" attribute of this Model. More...
 
virtual int getTypeCode () const
 Returns the libSBML type code for this SBML object. More...
 
const UnitDefinitiongetUnitDefinition (unsigned int n) const
 Get the nth UnitDefinition object in this Model. More...
 
UnitDefinitiongetUnitDefinition (unsigned int n)
 Get the nth UnitDefinition object in this Model. More...
 
const UnitDefinitiongetUnitDefinition (const std::string &sid) const
 Get a UnitDefinition based on its identifier. More...
 
UnitDefinitiongetUnitDefinition (const std::string &sid)
 Get a UnitDefinition based on its identifier. More...
 
std::string getURI () const
 Gets the namespace URI to which this element belongs to. More...
 
void * getUserData () const
 Returns the user data that has been previously set via setUserData(). More...
 
unsigned int getVersion () const
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
const std::string & getVolumeUnits () const
 Returns the value of the "volumeUnits" attribute of this Model. More...
 
virtual bool hasRequiredElements () const
 Predicate returning true if all the required elements for this Model object have been set. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
bool isPackageEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (const std::string &pkgName) const
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (const std::string &pkgURI) const
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPopulatedAllElementIdList () const
 Predicate returning true if libSBML has a list of the ids of all components of this model. More...
 
bool isPopulatedAllElementMetaIdList () const
 Predicate returning true if libSBML has a list of the metaids of all components of this model. More...
 
bool isPopulatedListFormulaUnitsData ()
 Predicate returning true if libSBML has derived units for the components of this model. More...
 
bool isSetAnnotation () const
 Predicate returning true if this object's "annotation" subelement exists and has content. More...
 
bool isSetAreaUnits () const
 Predicate returning true if this Model's "areaUnits" attribute is set. More...
 
bool isSetConversionFactor () const
 Predicate returning true if this Model's "conversionFactor" attribute is set. More...
 
bool isSetExtentUnits () const
 Predicate returning true if this Model's "extentUnits" attribute is set. More...
 
virtual bool isSetId () const
 Predicate returning true if this Model's "id" attribute is set. More...
 
bool isSetIdAttribute () const
 Predicate returning true if this object's "id" attribute is set. More...
 
bool isSetLengthUnits () const
 Predicate returning true if this Model's "lengthUnits" attribute is set. More...
 
bool isSetMetaId () const
 Predicate returning true if this object's "metaid" attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
virtual bool isSetName () const
 Predicate returning true if this Model's "name" attribute is set. More...
 
bool isSetNotes () const
 Predicate returning true if this object's "notes" subelement exists and has content. More...
 
bool isSetSBOTerm () const
 Predicate returning true if this object's "sboTerm" attribute is set. More...
 
bool isSetSubstanceUnits () const
 Predicate returning true if this Model's "substanceUnits" attribute is set. More...
 
bool isSetTimeUnits () const
 Predicate returning true if this Model's "timeUnits" attribute is set. More...
 
bool isSetUserData () const
 Predicate returning true or false depending on whether the user data of this element has been set. More...
 
bool isSetVolumeUnits () const
 Predicate returning true if this Model's "volumeUnits" attribute is set. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (const SBase *sb) const
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
 Model (unsigned int level, unsigned int version)
 Creates a new Model using the given SBML level and version values. More...
 
 Model (SBMLNamespaces *sbmlns)
 Creates a new Model using the given SBMLNamespaces object sbmlns. More...
 
 Model (const Model &orig)
 Copy constructor; creates a (deep) copy of the given Model object. More...
 
Modeloperator= (const Model &rhs)
 Assignment operator for Model. More...
 
void populateAllElementIdList ()
 Populates the internal list of the identifiers of all elements within this Model object. More...
 
void populateAllElementMetaIdList ()
 Populates the internal list of the metaids of all elements within this Model object. More...
 
void populateListFormulaUnitsData ()
 Populates the internal list of derived units for this Model object. More...
 
void read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED)
 Reads (initializes) this SBML object by reading from the given XMLNode. More...
 
CompartmentremoveCompartment (unsigned int n)
 Removes the nth Compartment object from this Model object and returns a pointer to it. More...
 
CompartmentremoveCompartment (const std::string &sid)
 Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More...
 
CompartmentTyperemoveCompartmentType (unsigned int n)
 Removes the nth CompartmentType object from this Model object and returns a pointer to it. More...
 
CompartmentTyperemoveCompartmentType (const std::string &sid)
 Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More...
 
ConstraintremoveConstraint (unsigned int n)
 Removes the nth Constraint object from this Model object and returns a pointer to it. More...
 
EventremoveEvent (unsigned int n)
 Removes the nth Event object from this Model object and returns a pointer to it. More...
 
EventremoveEvent (const std::string &sid)
 Removes the Event object with the given identifier from this Model object and returns a pointer to it. More...
 
virtual int removeFromParentAndDelete ()
 Remove this Model from its parent SBMLDocument object. More...
 
FunctionDefinitionremoveFunctionDefinition (unsigned int n)
 Removes the nth FunctionDefinition object from this Model object and returns a pointer to it. More...
 
FunctionDefinitionremoveFunctionDefinition (const std::string &sid)
 Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it. More...
 
InitialAssignmentremoveInitialAssignment (unsigned int n)
 Removes the nth InitialAssignment object from this Model object and returns a pointer to it. More...
 
InitialAssignmentremoveInitialAssignment (const std::string &symbol)
 Removes the InitialAssignment object with the given "symbol" attribute from this Model object and returns a pointer to it. More...
 
ParameterremoveParameter (unsigned int n)
 Removes the nth Parameter object from this Model object and returns a pointer to it. More...
 
ParameterremoveParameter (const std::string &sid)
 Removes the Parameter object with the given identifier from this Model object and returns a pointer to it. More...
 
ReactionremoveReaction (unsigned int n)
 Removes the nth Reaction object from this Model object and returns a pointer to it. More...
 
ReactionremoveReaction (const std::string &sid)
 Removes the Reaction object with the given identifier from this Model object and returns a pointer to it. More...
 
RuleremoveRule (unsigned int n)
 Removes the nth Rule object from this Model object and returns a pointer to it. More...
 
RuleremoveRule (const std::string &variable)
 Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it. More...
 
RuleremoveRuleByVariable (const std::string &variable)
 Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it. More...
 
SpeciesremoveSpecies (unsigned int n)
 Removes the nth Species object from this Model object and returns a pointer to it. More...
 
SpeciesremoveSpecies (const std::string &sid)
 Removes the Species object with the given identifier from this Model object and returns a pointer to it. More...
 
SpeciesTyperemoveSpeciesType (unsigned int n)
 Removes the nth SpeciesType object from this Model object and returns a pointer to it. More...
 
SpeciesTyperemoveSpeciesType (const std::string &sid)
 Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More...
 
int removeTopLevelAnnotationElement (const std::string &elementName, const std::string elementURI="", bool removeEmpty=true)
 Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More...
 
UnitDefinitionremoveUnitDefinition (unsigned int n)
 Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More...
 
UnitDefinitionremoveUnitDefinition (const std::string &sid)
 Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More...
 
virtual void renameMetaIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given meta identifier attribute value with another value. More...
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given SIdRef type attribute value with another value. More...
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
 
int replaceTopLevelAnnotationElement (const XMLNode *annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (const std::string &annotation)
 Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More...
 
virtual int setAnnotation (const XMLNode *annotation)
 Sets the value of the "annotation" subelement of this SBML object to a copy of annotation. More...
 
virtual int setAnnotation (const std::string &annotation)
 Sets the value of the "annotation" subelement of this SBML object to a copy of annotation. More...
 
int setAreaUnits (const std::string &units)
 Sets the value of the "areaUnits" attribute of this Model. More...
 
int setConversionFactor (const std::string &units)
 Sets the value of the "conversionFactor" attribute of this Model. More...
 
int setExtentUnits (const std::string &units)
 Sets the value of the "extentUnits" attribute of this Model. More...
 
virtual int setId (const std::string &sid)
 Sets the value of the "id" attribute of this Model. More...
 
virtual int setIdAttribute (const std::string &sid)
 Sets the value of the "id" attribute of this SBML object. More...
 
int setLengthUnits (const std::string &units)
 Sets the value of the "lengthUnits" attribute of this Model. More...
 
int setMetaId (const std::string &metaid)
 Sets the value of the meta-identifier attribute of this SBML object. More...
 
int setModelHistory (ModelHistory *history)
 Sets the ModelHistory of this object. More...
 
virtual int setName (const std::string &name)
 Sets the value of the "name" attribute of this Model. More...
 
int setNamespaces (XMLNamespaces *xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (const XMLNode *notes)
 Sets the value of the "notes" subelement of this SBML object. More...
 
int setNotes (const std::string &notes, bool addXHTMLMarkup=false)
 Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More...
 
virtual int setSBOTerm (int value)
 Sets the value of the "sboTerm" attribute. More...
 
virtual int setSBOTerm (const std::string &sboid)
 Sets the value of the "sboTerm" attribute by string. More...
 
int setSubstanceUnits (const std::string &units)
 Sets the value of the "substanceUnits" attribute of this Model. More...
 
int setTimeUnits (const std::string &units)
 Sets the value of the "timeUnits" attribute of this Model. More...
 
int setUserData (void *userData)
 Sets the user data of this element. More...
 
int setVolumeUnits (const std::string &units)
 Sets the value of the "volumeUnits" attribute of this Model. More...
 
char * toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
XMLNodetoXMLNode ()
 Returns this element as an XMLNode. More...
 
int unsetAnnotation ()
 Unsets the value of the "annotation" subelement of this SBML object. More...
 
int unsetAreaUnits ()
 Unsets the value of the "areaUnits" attribute of this Model. More...
 
int unsetConversionFactor ()
 Unsets the value of the "conversionFactor" attribute of this Model. More...
 
int unsetCVTerms ()
 Clears the list of CVTerm objects attached to this SBML object. More...
 
int unsetExtentUnits ()
 Unsets the value of the "extentUnits" attribute of this Model. More...
 
virtual int unsetId ()
 Unsets the value of the "id" attribute of this Model. More...
 
int unsetIdAttribute ()
 Unsets the value of the "id" attribute of this SBML object. More...
 
int unsetLengthUnits ()
 Unsets the value of the "lengthUnits" attribute of this Model. More...
 
int unsetMetaId ()
 Unsets the value of the "metaid" attribute of this SBML object. More...
 
int unsetModelHistory ()
 Unsets the ModelHistory object attached to this object. More...
 
virtual int unsetName ()
 Unsets the value of the "name" attribute of this Model. More...
 
int unsetNotes ()
 Unsets the value of the "notes" subelement of this SBML object. More...
 
int unsetSBOTerm ()
 Unsets the value of the "sboTerm" attribute of this SBML object. More...
 
int unsetSubstanceUnits ()
 Unsets the value of the "substanceUnits" attribute of this Model. More...
 
int unsetTimeUnits ()
 Unsets the value of the "timeUnits" attribute of this Model. More...
 
int unsetUserData ()
 Unsets the user data of this element. More...
 
int unsetVolumeUnits ()
 Unsets the value of the "volumeUnits" attribute of this Model. More...
 
virtual ~Model ()
 Destroys this Model. More...
 

Protected Member Functions

virtual void setElementText (const std::string &text)
 When overridden allows SBase elements to use the text included in between the elements tags. More...
 

Friends

class SBMLDocument
 

Constructor & Destructor Documentation

Model::Model ( unsigned int  level,
unsigned int  version 
)

Creates a new Model using the given SBML level and version values.

Parameters
levelan unsigned int, the SBML Level to assign to this Model.
versionan unsigned int, the SBML Version to assign to this Model.
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination are invalid or if this object is incompatible with the given level and version.
Note
Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.
Model::Model ( SBMLNamespaces sbmlns)

Creates a new Model using the given SBMLNamespaces object sbmlns.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sbmlnsan SBMLNamespaces object.
Exceptions
SBMLConstructorExceptionThrown if the given sbmlns is inconsistent or incompatible with this object.
Note
Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.
Model::~Model ( )
virtual

Destroys this Model.

Model::Model ( const Model orig)

Copy constructor; creates a (deep) copy of the given Model object.

Parameters
origthe object to copy.

Member Function Documentation

int Model::addCompartment ( const Compartment c)

Adds a copy of the given Compartment object to this Model.

Parameters
cthe Compartment object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createCompartment()
int Model::addCompartmentType ( const CompartmentType ct)

Adds a copy of the given CompartmentType object to this Model.

Parameters
ctthe CompartmentType object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
createCompartmentType()
int Model::addConstraint ( const Constraint c)

Adds a copy of the given Constraint object to this Model.

Parameters
cthe Constraint object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createConstraint()
int SBase::addCVTerm ( CVTerm term,
bool  newBag = false 
)
inherited

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
Since the CV Term uses the "metaid" attribute of the object as a reference, if the object has no "metaid" attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Examples:
addCVTerms.cpp, addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
int Model::addEvent ( const Event e)

Adds a copy of the given Event object to this Model.

Parameters
ethe Event object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createEvent()
int Model::addFunctionDefinition ( const FunctionDefinition fd)

Adds a copy of the given FunctionDefinition object to this Model.

Parameters
fdthe FunctionDefinition to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createFunctionDefinition()
int Model::addInitialAssignment ( const InitialAssignment ia)

Adds a copy of the given InitialAssignment object to this Model.

Parameters
iathe InitialAssignment object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createInitialAssignment()
int Model::addParameter ( const Parameter p)

Adds a copy of the given Parameter object to this Model.

Parameters
pthe Parameter object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createParameter()
int Model::addReaction ( const Reaction r)

Adds a copy of the given Reaction object to this Model.

Parameters
rthe Reaction object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createReaction()
Examples:
spec_example1.cpp, spec_example3.cpp, and spec_example4.cpp.
int Model::addRule ( const Rule r)

Adds a copy of the given Rule object to this Model.

Parameters
rthe Rule object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createAlgebraicRule()
createAssignmentRule()
createRateRule()
int Model::addSpecies ( const Species s)

Adds a copy of the given Species object to this Model.

Parameters
sthe Species object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createSpecies()
Examples:
spec_example1.cpp, spec_example3.cpp, and spec_example4.cpp.
int Model::addSpeciesType ( const SpeciesType st)

Adds a copy of the given SpeciesType object to this Model.

Parameters
stthe SpeciesType object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
createSpeciesType()
int Model::addUnitDefinition ( const UnitDefinition ud)

Adds a copy of the given UnitDefinition object to this Model.

Parameters
udthe UnitDefinition object to add.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createUnitDefinition()
int Model::appendAnnotation ( const XMLNode annotation)
virtual

Appends annotation content to any existing content in the "annotation" subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setAnnotation(const XMLNode* annotation)

Reimplemented from SBase.

Examples:
appendAnnotation.cpp.
int Model::appendAnnotation ( const std::string &  annotation)
virtual

Appends annotation content to any existing content in the "annotation" subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setAnnotation(const std::string& annotation)

Reimplemented from SBase.

int Model::appendFrom ( const Model model)
virtual

Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model.

This method also calls the appendFrom method on all libSBML plug-in objects.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
modelthe Model to merge with this one.
int SBase::appendNotes ( const XMLNode notes)
inherited

Appends the given notes to the "notes" subelement of this object.

The content of notes is copied.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the "notes" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::appendNotes ( const std::string &  notes)
inherited

Appends the given notes to the "notes" subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Parameters
notesan XML string that is to appended to the content of the "notes" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
void Model::clearAllElementIdList ( )

Clears the internal list of the identifiers of all elements within this Model object.

See also
populateAllElementIdList()
isPopulatedAllElementIdList()
void Model::clearAllElementMetaIdList ( )

Clears the internal list of the metaids of all elements within this Model object.

See also
populateAllElementMetaIdList()
isPopulatedAllElementMetaIdList()
Model * Model::clone ( ) const
virtual

Creates and returns a deep copy of this Model object.

Returns
the (deep) copy of this Model object.

Implements SBase.

Reimplemented in ModelDefinition.

AlgebraicRule * Model::createAlgebraicRule ( )

Creates a new AlgebraicRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the AlgebraicRule object created.
See also
addRule(const Rule* r)
AssignmentRule * Model::createAssignmentRule ( )

Creates a new AssignmentRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the AssignmentRule object created.
See also
addRule(const Rule* r)
Compartment * Model::createCompartment ( )

Creates a new Compartment inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Compartment object created.
See also
addCompartment(const Compartment *c)
Examples:
createExampleSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
CompartmentType * Model::createCompartmentType ( )

Creates a new CompartmentType inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the CompartmentType object created.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
addCompartmentType(const CompartmentType* ct)
Constraint * Model::createConstraint ( )

Creates a new Constraint inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Constraint object created.
See also
addConstraint(const Constraint *c)
Delay * Model::createDelay ( )

Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and NULL is returned instead.
Returns
the Delay object created.
Event * Model::createEvent ( )

Creates a new Event inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Event object created.
EventAssignment * Model::createEventAssignment ( )

Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and NULL is returned instead.
Returns
the EventAssignment object created.
FunctionDefinition * Model::createFunctionDefinition ( )

Creates a new FunctionDefinition inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the FunctionDefinition object created.
See also
addFunctionDefinition(const FunctionDefinition* fd)
Examples:
createExampleSBML.cpp.
InitialAssignment * Model::createInitialAssignment ( )

Creates a new InitialAssignment inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the InitialAssignment object created.
See also
addInitialAssignment(const InitialAssignment* ia)
KineticLaw * Model::createKineticLaw ( )

Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned instead.
Returns
the KineticLaw object created. If a Reaction does not exist for this model, or a Reaction does exist but already has a KineticLaw, a new KineticLaw is not created and NULL is returned.
LocalParameter * Model::createKineticLawLocalParameter ( )

Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction::createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and NULL is returned instead.
Returns
the Parameter object created. If a Reaction does not exist for this model, or a KineticLaw for the Reaction does not exist, a new Parameter is not created and NULL is returned.
Parameter * Model::createKineticLawParameter ( )

Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction::createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and NULL is returned instead.
Returns
the Parameter object created. If a Reaction does not exist for this model, or a KineticLaw for the Reaction does not exist, a new Parameter is not created and NULL is returned.
ModifierSpeciesReference * Model::createModifier ( )

Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned instead.
Returns
the SpeciesReference object created. If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned.
Parameter * Model::createParameter ( )

Creates a new Parameter inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Parameter object created.
See also
addParameter(const Parameter *p)
Examples:
createExampleSBML.cpp.
SpeciesReference * Model::createProduct ( )

Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned instead.
Returns
the SpeciesReference object created. If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned.
RateRule * Model::createRateRule ( )

Creates a new RateRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the RateRule object created.
See also
addRule(const Rule* r)
SpeciesReference * Model::createReactant ( )

Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned instead.
Returns
the SpeciesReference object created. If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL is returned.
Reaction * Model::createReaction ( )

Creates a new Reaction inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Reaction object created.
See also
addReaction(const Reaction *r)
Examples:
createExampleSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, and groups_example2.cpp.
Species * Model::createSpecies ( )

Creates a new Species inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Species object created.
See also
addSpecies(const Species *s)
Examples:
createExampleSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, and spec_example2.cpp.
SpeciesType * Model::createSpeciesType ( )

Creates a new SpeciesType inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the SpeciesType object created.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
addSpeciesType(const SpeciesType* st)
Trigger * Model::createTrigger ( )

Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and NULL is returned instead.
Returns
the Trigger object created.
Unit * Model::createUnit ( )

Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and NULL is returned instead.

Returns
the Unit object created.
See also
addUnitDefinition(const UnitDefinition* ud)
UnitDefinition * Model::createUnitDefinition ( )

Creates a new UnitDefinition inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the UnitDefinition object created.
See also
addUnitDefinition(const UnitDefinition* ud)
Examples:
createExampleSBML.cpp.
void SBase::deleteDisabledPlugins ( bool  recursive = true)
inherited

Deletes all information stored in disabled plugins.

If the plugin is re-enabled later, it will then not have any previously-stored information.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
recursiveif true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.
See also
getNumDisabledPlugins()
int SBase::disablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package on this object.

This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

// We read in an SBML L3V1 model that uses the 'comp'
// package namespace.
doc = readSBML("sbml-file-with-comp-elements.xml");
// We extract one of the species from the model.
Species* s1 = doc->getModel()->getSpecies(0);
// We construct a new model. This model does not use the
// 'comp' package.
Model * newModel = new Model(3,1);
// The following will fail with an error, because addSpecies()
// will first check that the parent of the given object has
// namespaces declared, and will discover that s1 does but
// newModel does not.
// newModel->addSpecies(s1);
// However, if we disable the 'comp' package on s1, then
// the call to addSpecies will work.
s1->disablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp");
newModel->addSpecies(s1);
Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
enablePackage(const std::string& pkgURI, const std::string& pkgPrefix, bool flag)
int SBase::enablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package.
flagwhether to enable (true) or disable (false) the package.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
disablePackage(const std::string& pkgURI, const std::string& pkgPrefix)
Examples:
addLayout.cpp.
IdList Model::getAllElementIdList ( ) const

Returns the internal list of the identifiers of all elements within this Model object.

Returns
an IdList of all the identifiers in the model.
See also
populateAllElementIdList()
isPopulatedAllElementIdList()
IdList Model::getAllElementMetaIdList ( ) const

Returns the internal list of the metaids of all elements within this Model object.

Returns
an IdList of all the metaids in the model.
See also
populateAllElementMetaIdList()
isPopulatedAllElementMetaIdList()
List * Model::getAllElements ( ElementFilter filter = NULL)
virtual

Returns a List of all child objects.

This returns all child objects nested to an arbitrary depth. If an optional element filter is provided, only those objects for which the filter's filter() method returns true will be added to the list.

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a List of pointers to all children objects.

Reimplemented from SBase.

List * SBase::getAllElementsFromPlugins ( ElementFilter filter = NULL)
virtualinherited

Returns a List of all child SBase objects contained in SBML package plug-ins.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a pointer to a List of pointers to all children objects from plug-ins.
SBase * SBase::getAncestorOfType ( int  type,
const std::string &  pkgName = "core" 
)
inherited

Returns the first ancestor object that has the given SBML type code from the given package.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought.
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong.
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBMLTypeCode_t value, or NULL if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.
const SBase * SBase::getAncestorOfType ( int  type,
const std::string  pkgName = "core" 
) const
inherited

Returns the first ancestor object that has the given SBML type code from the given package.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought.
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong.
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBMLTypeCode_t value, or NULL if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.
XMLNode * SBase::getAnnotation ( )
inherited

Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
XMLNode * SBase::getAnnotation ( ) const
inherited

Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
std::string SBase::getAnnotationString ( )
inherited

Returns the content of the "annotation" subelement of this object as a character string.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
Examples:
printAnnotation.cpp.
std::string SBase::getAnnotationString ( ) const
inherited

Returns the content of the "annotation" subelement of this object as a character string.

Whereas the SBML "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
const std::string & Model::getAreaUnits ( ) const

Returns the value of the "areaUnits" attribute of this Model.

Returns
the areaUnits of this Model.
Note
The "areaUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
const AssignmentRule * Model::getAssignmentRule ( const std::string &  variable) const

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
AssignmentRule * Model::getAssignmentRule ( const std::string &  variable)

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
const AssignmentRule * Model::getAssignmentRuleByVariable ( const std::string &  variable) const

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
AssignmentRule * Model::getAssignmentRuleByVariable ( const std::string &  variable)

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
unsigned int SBase::getColumn ( ) const
inherited

Returns the column number where this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getLine()
const Compartment * Model::getCompartment ( unsigned int  n) const

Get the nth Compartment object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Compartment of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Compartment * Model::getCompartment ( unsigned int  n)

Get the nth Compartment object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Compartment of this Model. If the index n is invalid, NULL is returned.
const Compartment * Model::getCompartment ( const std::string &  sid) const

Get a Compartment object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Compartment in this Model with the identifier sid or NULL if no such Compartment exists.
Compartment * Model::getCompartment ( const std::string &  sid)

Get a Compartment object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Compartment in this Model with the identifier sid or NULL if no such Compartment exists.
const CompartmentType * Model::getCompartmentType ( unsigned int  n) const

Get the nth CompartmentType object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth CompartmentType of this Model. If the index n is invalid, NULL is returned.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
CompartmentType * Model::getCompartmentType ( unsigned int  n)

Get the nth CompartmentType object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth CompartmentType of this Model. If the index n is invalid, NULL is returned.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
const CompartmentType * Model::getCompartmentType ( const std::string &  sid) const

Get a CompartmentType object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the CompartmentType in this Model with the identifier sid or NULL if no such CompartmentType exists.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
CompartmentType * Model::getCompartmentType ( const std::string &  sid)

Get a CompartmentType object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the CompartmentType in this Model with the identifier sid or NULL if no such CompartmentType exists.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
const Constraint * Model::getConstraint ( unsigned int  n) const

Get the nth Constraint object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Constraint of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printNotes.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Constraint * Model::getConstraint ( unsigned int  n)

Get the nth Constraint object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Constraint of this Model. If the index n is invalid, NULL is returned.
const std::string & Model::getConversionFactor ( ) const

Returns the value of the "conversionFactor" attribute of this Model.

Returns
the conversionFactor of this Model.
Note
The "conversionFactor" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
CVTerm * SBase::getCVTerm ( unsigned int  n)
inherited

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nunsigned int the index of the CVTerm to retrieve.
Returns
the nth CVTerm in the list of CVTerms for this SBML object. If the index n is invalid, NULL is returned.
List * SBase::getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
List * SBase::getCVTerms ( ) const
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n)
inherited

Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)
const SBasePlugin * SBase::getDisabledPlugin ( unsigned int  n) const
inherited

Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
nthe index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumDisabledPlugins()
getPlugin(const std::string& package)
const SBase * SBase::getElementByMetaId ( const std::string &  metaid) const
inherited

Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Parameters
metaidstring representing the "metaid" attribute value of the object to find.
Returns
pointer to the first element found with the given meta-identifier.
SBase * Model::getElementByMetaId ( const std::string &  metaid)
virtual

Returns the first child element it can find with the given metaid.

Parameters
metaidstring representing the meta-identifier of the object to find.
Returns
pointer to the first element found with the given metaid, or NULL if no such object is found.

Reimplemented from SBase.

const SBase * SBase::getElementBySId ( const std::string &  id) const
inherited

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters
idstring representing the "id" attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.
SBase * Model::getElementBySId ( const std::string &  id)
virtual

Returns the first child element found that has the given id.

This operation searches the model-wide SId identifier type namespace

Parameters
idstring representing the id of the object to find.
Returns
pointer to the first element found with the given id, or NULL if no such object is found.

Reimplemented from SBase.

const string & Model::getElementName ( ) const
virtual

Returns the XML element name of this object, which for Model, is always "model".

Returns
the name of this element, i.e., "model".

Reimplemented from SBase.

Reimplemented in ModelDefinition.

const Event * Model::getEvent ( unsigned int  n) const

Get the nth Event object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Event of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printMath.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Event * Model::getEvent ( unsigned int  n)

Get the nth Event object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Event of this Model. If the index n is invalid, NULL is returned.
const Event * Model::getEvent ( const std::string &  sid) const

Get an Event object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Event in this Model with the identifier sid or NULL if no such Event exists.
Event * Model::getEvent ( const std::string &  sid)

Get an Event object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Event in this Model with the identifier sid or NULL if no such Event exists.
const std::string & Model::getExtentUnits ( ) const

Returns the value of the "extentUnits" attribute of this Model.

Returns
the extentUnits of this Model.
Note
The "extentUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
const FunctionDefinition * Model::getFunctionDefinition ( unsigned int  n) const

Get the nth FunctionDefinitions object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth FunctionDefinition of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printMath.cpp, printNotes.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
FunctionDefinition * Model::getFunctionDefinition ( unsigned int  n)

Get the nth FunctionDefinitions object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth FunctionDefinition of this Model. If the index n is invalid, NULL is returned.
const FunctionDefinition * Model::getFunctionDefinition ( const std::string &  sid) const

Get a FunctionDefinition object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the FunctionDefinition in this Model with the identifier sid or NULL if no such FunctionDefinition exists.
FunctionDefinition * Model::getFunctionDefinition ( const std::string &  sid)

Get a FunctionDefinition object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the FunctionDefinition in this Model with the identifier sid or NULL if no such FunctionDefinition exists.
virtual const std::string& Model::getId ( ) const
virtual

Returns the value of the "id" attribute of this Model.

Note
Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() function instead.
The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
the id of this Model.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()

Reimplemented from SBase.

Examples:
createExampleSBML.cpp, printSBML.cpp, and SBMLHttpResolverExample.cpp.
const string & SBase::getIdAttribute ( ) const
inherited

Returns the value of the "id" attribute of this SBML object.

The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.
Note
Because of the inconsistent behavior of this function with respect to assignments and rules, callers should use getIdAttribute() instead.
See also
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()
const InitialAssignment * Model::getInitialAssignment ( unsigned int  n) const

Get the nth InitialAssignment object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth InitialAssignment of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
InitialAssignment * Model::getInitialAssignment ( unsigned int  n)

Get the nth InitialAssignment object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth InitialAssignment of this Model. If the index n is invalid, NULL is returned.
const InitialAssignment * Model::getInitialAssignment ( const std::string &  symbol) const

Get an InitialAssignment object based on the symbol to which it assigns a value.

Parameters
symbolthe symbol to search for.
Returns
the InitialAssignment in this Model with the given "symbol" attribute value or NULL if no such InitialAssignment exists.
InitialAssignment * Model::getInitialAssignment ( const std::string &  symbol)

Get an InitialAssignment object based on the symbol to which it assigns a value.

Parameters
symbolthe symbol to search for.
Returns
the InitialAssignment in this Model with the given "symbol" attribute value or NULL if no such InitialAssignment exists.
const InitialAssignment * Model::getInitialAssignmentBySymbol ( const std::string &  symbol) const

Get an InitialAssignment object based on the symbol to which it assigns a value.

Parameters
symbolthe symbol to search for.
Returns
the InitialAssignment in this Model with the given "symbol" attribute value or NULL if no such InitialAssignment exists.
InitialAssignment * Model::getInitialAssignmentBySymbol ( const std::string &  symbol)

Get an InitialAssignment object based on the symbol to which it assigns a value.

Parameters
symbolthe symbol to search for.
Returns
the InitialAssignment in this Model with the given "symbol" attribute value or NULL if no such InitialAssignment exists.
const std::string & Model::getLengthUnits ( ) const

Returns the value of the "lengthUnits" attribute of this Model.

Returns
the lengthUnits of this Model.
Note
The "lengthUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
unsigned int SBase::getLevel ( ) const
inherited

Returns the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.
unsigned int SBase::getLine ( ) const
inherited

Returns the line number where this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getColumn()
const ListOfCompartments * Model::getListOfCompartments ( ) const

Get the ListOfCompartments object in this Model.

Returns
the list of Compartments for this Model.
ListOfCompartments * Model::getListOfCompartments ( )

Get the ListOfCompartments object in this Model.

Returns
the list of Compartments for this Model.
const ListOfCompartmentTypes * Model::getListOfCompartmentTypes ( ) const

Get the ListOfCompartmentTypes object in this Model.

Returns
the list of CompartmentTypes for this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
ListOfCompartmentTypes * Model::getListOfCompartmentTypes ( )

Get the ListOfCompartmentTypes object in this Model.

Returns
the list of CompartmentTypes for this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
const ListOfConstraints * Model::getListOfConstraints ( ) const

Get the ListOfConstraints object in this Model.

Returns
the list of Constraints for this Model.
ListOfConstraints * Model::getListOfConstraints ( )

Get the ListOfConstraints object in this Model.

Returns
the list of Constraints for this Model.
const ListOfEvents * Model::getListOfEvents ( ) const

Get the ListOfEvents object in this Model.

Returns
the list of Events for this Model.
ListOfEvents * Model::getListOfEvents ( )

Get the ListOfEvents object in this Model.

Returns
the list of Events for this Model.
const ListOfFunctionDefinitions * Model::getListOfFunctionDefinitions ( ) const

Get the ListOfFunctionDefinitions object in this Model.

Returns
the list of FunctionDefinitions for this Model.
ListOfFunctionDefinitions * Model::getListOfFunctionDefinitions ( )

Get the ListOfFunctionDefinitions object in this Model.

Returns
the list of FunctionDefinitions for this Model.
const ListOfInitialAssignments * Model::getListOfInitialAssignments ( ) const

Get the ListOfInitialAssignments object in this Model.

Returns
the list of InitialAssignments for this Model.
ListOfInitialAssignments * Model::getListOfInitialAssignments ( )

Get the ListOfInitialAssignments object in this Model.

Returns
the list of InitialAssignment for this Model.
const ListOfParameters * Model::getListOfParameters ( ) const

Get the ListOfParameters object in this Model.

Returns
the list of Parameters for this Model.
ListOfParameters * Model::getListOfParameters ( )

Get the ListOfParameters object in this Model.

Returns
the list of Parameters for this Model.
const ListOfReactions * Model::getListOfReactions ( ) const

Get the ListOfReactions object in this Model.

Returns
the list of Reactions for this Model.
ListOfReactions * Model::getListOfReactions ( )

Get the ListOfReactions object in this Model.

Returns
the list of Reactions for this Model.
const ListOfRules * Model::getListOfRules ( ) const

Get the ListOfRules object in this Model.

Returns
the list of Rules for this Model.
ListOfRules * Model::getListOfRules ( )

Get the ListOfRules object in this Model.

Returns
the list of Rules for this Model.
const ListOfSpecies * Model::getListOfSpecies ( ) const

Get the ListOfSpecies object in this Model.

Returns
the list of Species for this Model.
ListOfSpecies * Model::getListOfSpecies ( )

Get the ListOfSpecies object in this Model.

Returns
the list of Species for this Model.
const ListOfSpeciesTypes * Model::getListOfSpeciesTypes ( ) const

Get the ListOfSpeciesTypes object in this Model.

Returns
the list of SpeciesTypes for this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
ListOfSpeciesTypes * Model::getListOfSpeciesTypes ( )

Get the ListOfSpeciesTypes object in this Model.

Returns
the list of SpeciesTypes for this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
const ListOfUnitDefinitions * Model::getListOfUnitDefinitions ( ) const

Get the ListOfUnitDefinitions object in this Model.

Returns
the list of UnitDefinitions for this Model.
ListOfUnitDefinitions * Model::getListOfUnitDefinitions ( )

Get the ListOfUnitDefinitions object in this Model.

Returns
the list of UnitDefinitions for this Model.
const string & SBase::getMetaId ( ) const
inherited

Returns the value of the "metaid" attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_2.cpp.
string & SBase::getMetaId ( )
inherited

Returns the value of the "metaid" attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object, as a string.
See also
isSetMetaId()
setMetaId(const std::string& metaid)
const Model * SBase::getModel ( ) const
inherited

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()
ModelHistory * SBase::getModelHistory ( ) const
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or NULL if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
ModelHistory * SBase::getModelHistory ( )
inherited

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or NULL if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
ModifierSpeciesReference * Model::getModifierSpeciesReference ( const std::string &  sid)

Get a ModifierSpeciesReference object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the ModifierSpeciesReference in this Model with the identifier sid or NULL if no such ModifierSpeciesReference exists.
const ModifierSpeciesReference * Model::getModifierSpeciesReference ( const std::string &  sid) const

Get a ModifierSpeciesReference object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the ModifierSpeciesReference in this Model with the identifier sid or NULL if no such ModifierSpeciesReference exists.
const string & Model::getName ( ) const
virtual

Returns the value of the "name" attribute of this Model object.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The "name" attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of "name" is the type string defined in XML Schema. SBML imposes no restrictions as to the content of "name" attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling "name" is as follows. If a software tool has the capability for displaying the content of "name" attributes, it should display this content to the user as a component's label instead of the component's "id". If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the "name" attribute is missing on a given component, then the user interface should display the value of the "id" attribute instead. (Script language interpreters are especially likely to display "id" instead of "name".)

As a consequence of the above, authors of systems that automatically generate the values of "id" attributes should be aware some systems may display the "id"'s to the user. Authors therefore may wish to take some care to have their software create "id" values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the "id" attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of "id" values, there are no restrictions on the uniqueness of "name" values in a model. This allows software applications leeway in assigning component identifiers.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns
the name of this SBML object, or the empty string if not set or unsettable.
See also
getIdAttribute()
isSetName()
setName(const std::string& sid)
unsetName()

Reimplemented from SBase.

XMLNamespaces * SBase::getNamespaces ( ) const
virtualinherited

Returns a list of the XML Namespaces declared on the SBML document owning this object.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Returns
the XML Namespaces associated with this SBML object, or NULL in certain very usual circumstances where a namespace is not set.
See also
getLevel()
getVersion()

Reimplemented in SBMLDocument.

XMLNode * SBase::getNotes ( )
inherited

Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the "notes" subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
XMLNode * SBase::getNotes ( ) const
inherited

Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

The "notes" element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the "notes" subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
std::string SBase::getNotesString ( )
inherited

Returns the content of the "notes" subelement of this object as a string.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the "notes" subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
printNotes.cpp, and SBMLHttpResolverExample.cpp.
std::string SBase::getNotesString ( ) const
inherited

Returns the content of the "notes" subelement of this object as a string.

The optional SBML element named "notes", present on every major SBML component type (and in SBML Level 3, the "message" subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the "notes" subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
unsigned int Model::getNumCompartments ( ) const

Get the number of Compartment objects in this Model.

Returns
the number of Compartments in this Model.
Examples:
printAnnotation.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumCompartmentTypes ( ) const

Get the number of CompartmentType objects in this Model.

Returns
the number of CompartmentTypes in this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
Examples:
printSBML.cpp.
unsigned int Model::getNumConstraints ( ) const

Get the number of Constraint objects in this Model.

Returns
the number of Constraints in this Model.
Examples:
printAnnotation.cpp, printNotes.cpp, printSBML.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int SBase::getNumCVTerms ( )
inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
unsigned int SBase::getNumDisabledPlugins ( ) const
inherited

Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Returns
the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
unsigned int Model::getNumEvents ( ) const

Get the number of Event objects in this Model.

Returns
the number of Events in this Model.
Examples:
printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumFunctionDefinitions ( ) const

Get the number of FunctionDefinition objects in this Model.

Returns
the number of FunctionDefinitions in this Model.
Examples:
printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumInitialAssignments ( ) const

Get the number of InitialAssignment objects in this Model.

Returns
the number of InitialAssignments in this Model.
Examples:
printAnnotation.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumParameters ( ) const

Get the number of Parameter objects in this Model.

Returns
the number of Parameters in this Model. Parameters defined in KineticLaws are not included.
Examples:
printAnnotation.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int SBase::getNumPlugins ( ) const
inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
See also
getPlugin(unsigned int n)
unsigned int Model::getNumReactions ( ) const

Get the number of Reaction objects in this Model.

Returns
the number of Reactions in this Model.
Examples:
addingEvidenceCodes_1.cpp, printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumRules ( ) const

Get the number of Rule objects in this Model.

Returns
the number of Rules in this Model.
Examples:
printAnnotation.cpp, printMath.cpp, printNotes.cpp, printSBML.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumSpecies ( ) const
unsigned int Model::getNumSpeciesTypes ( ) const

Get the number of SpeciesType objects in this Model.

Returns
the number of SpeciesTypes in this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
Examples:
printAnnotation.cpp, printNotes.cpp, printSBML.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int Model::getNumSpeciesWithBoundaryCondition ( ) const

Get the number of Species in this Model having their "boundaryCondition" attribute value set to true.

Returns
the number of Species in this Model with boundaryCondition set to true.
unsigned int Model::getNumUnitDefinitions ( ) const

Get the number of UnitDefinition objects in this Model.

Returns
the number of UnitDefinitions in this Model.
Examples:
printAnnotation.cpp, printNotes.cpp, printSBML.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
unsigned int SBase::getPackageCoreVersion ( ) const
inherited

Returns the SBML Core Version within the SBML Level of the actual object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML core version of this SBML object.
const std::string & SBase::getPackageName ( ) const
inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
unsigned int SBase::getPackageVersion ( ) const
inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See also
getLevel()
getVersion()
const Parameter * Model::getParameter ( unsigned int  n) const

Get the nth Parameter object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Parameter of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Parameter * Model::getParameter ( unsigned int  n)

Get the nth Parameter object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Parameter of this Model. If the index n is invalid, NULL is returned.
const Parameter * Model::getParameter ( const std::string &  sid) const

Get a Parameter object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Parameter in this Model with the identifier sid or NULL if no such Parameter exists.
Parameter * Model::getParameter ( const std::string &  sid)

Get a Parameter object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Parameter in this Model with the identifier sid or NULL if no such Parameter exists.
SBase * SBase::getParentSBMLObject ( )
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
const SBase * SBase::getParentSBMLObject ( ) const
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
SBasePlugin * SBase::getPlugin ( const std::string &  package)
inherited

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
See also
getPlugin(unsigned int n)
Examples:
addLayout.cpp, convertLayout.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, fbc_example1.cpp, groups_example1.cpp, groups_example2.cpp, qual_example1.cpp, SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
const SBasePlugin * SBase::getPlugin ( const std::string &  package) const
inherited

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
See also
getPlugin(unsigned int n)
SBasePlugin * SBase::getPlugin ( unsigned int  n)
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumPlugins()
getPlugin(const std::string& package)
const SBasePlugin * SBase::getPlugin ( unsigned int  n) const
inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.

If no such plugin exists, NULL is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, NULL is returned.
See also
getNumPlugins()
getPlugin(const std::string& package)
std::string SBase::getPrefix ( ) const
inherited

Returns the XML namespace prefix of this element.

This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.

Returns
a text string representing the XML namespace prefix.
const RateRule * Model::getRateRule ( const std::string &  variable) const

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe symbol to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
RateRule * Model::getRateRule ( const std::string &  variable)

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
const RateRule * Model::getRateRuleByVariable ( const std::string &  variable) const

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
RateRule * Model::getRateRuleByVariable ( const std::string &  variable)

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
const Reaction * Model::getReaction ( unsigned int  n) const

Get the nth Reaction object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Reaction of this Model. If the index n is invalid, NULL is returned.
Examples:
addingEvidenceCodes_1.cpp, printAnnotation.cpp, printMath.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Reaction * Model::getReaction ( unsigned int  n)

Get the nth Reaction object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Reaction of this Model. If the index n is invalid, NULL is returned.
const Reaction * Model::getReaction ( const std::string &  sid) const

Get a Reaction object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Reaction in this Model with the identifier sid or NULL if no such Reaction exists.
Reaction * Model::getReaction ( const std::string &  sid)

Get a Reaction object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Reaction in this Model with the identifier sid or NULL if no such Reaction exists.
BiolQualifierType_t SBase::getResourceBiologicalQualifier ( std::string  resource)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values from the enumeration type BiolQualifierType_t.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value from the enumeration type BiolQualifierType_t.

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration BiolQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
ModelQualifierType_t SBase::getResourceModelQualifier ( std::string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is "isDerivedFrom", to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values from the enumeration type ModelQualifierType_t.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value from the enumeration type ModelQualifierType_t.

Parameters
resourcestring representing the resource; e.g., "http://www.geneontology.org/#GO:0005892".
Returns
the ModelQualifierType_t value associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values in the enumeration ModelQualifierType_t are up to date with MIRIAM at the time of a given libSBML release. The set of values may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
const Rule * Model::getRule ( unsigned int  n) const

Get the nth Rule object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Rule of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printMath.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Rule * Model::getRule ( unsigned int  n)

Get the nth Rule object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Rule of this Model. If the index n is invalid, NULL is returned.
const Rule * Model::getRule ( const std::string &  variable) const

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
Rule * Model::getRule ( const std::string &  variable)

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
const Rule * Model::getRuleByVariable ( const std::string &  variable) const

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
Rule * Model::getRuleByVariable ( const std::string &  variable)

Get a Rule object based on the variable to which it assigns a value.

Parameters
variablethe variable to search for.
Returns
the Rule in this Model with the given "variable" attribute value or NULL if no such Rule exists.
const SBMLDocument * SBase::getSBMLDocument ( ) const
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
SBMLDocument * SBase::getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
int SBase::getSBOTerm ( ) const
inherited

Returns the integer portion of the value of the "sboTerm" attribute of this object.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the "sboTerm" attribute as an integer, or -1 if the value is not set.
Examples:
printSBML.cpp.
std::string SBase::getSBOTermAsURL ( ) const
inherited

Returns the URL representation of the "sboTerm" attribute of this object.

This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the "sboTerm" attribute as an identifiers.org URL, or an empty string if the value is not set.
std::string SBase::getSBOTermID ( ) const
inherited

Returns the string representation of the "sboTerm" attribute of this object.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the "sboTerm" attribute as a string (its value will be of the form "SBO:NNNNNNN"), or an empty string if the value is not set.
const Species * Model::getSpecies ( unsigned int  n) const

Get the nth Species object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Species of this Model. If the index n is invalid, NULL is returned.
Examples:
addCVTerms.cpp, addingEvidenceCodes_2.cpp, appendAnnotation.cpp, printAnnotation.cpp, printNotes.cpp, printUnits.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
Species * Model::getSpecies ( unsigned int  n)

Get the nth Species object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth Species of this Model. If the index n is invalid, NULL is returned.
const Species * Model::getSpecies ( const std::string &  sid) const

Get a Species object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Species in this Model with the identifier sid or NULL if no such Species exists.
Species * Model::getSpecies ( const std::string &  sid)

Get a Species object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the Species in this Model with the identifier sid or NULL if no such Species exists.
SpeciesReference * Model::getSpeciesReference ( const std::string &  sid)

Get a SpeciesReference object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the SpeciesReference in this Model with the identifier sid or NULL if no such SpeciesReference exists.
const SpeciesReference * Model::getSpeciesReference ( const std::string &  sid) const

Get a SpeciesReference object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the SpeciesReference in this Model with the identifier sid or NULL if no such SpeciesReference exists.
const SpeciesType * Model::getSpeciesType ( unsigned int  n) const

Get the nth SpeciesType object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth SpeciesType of this Model. If the index n is invalid, NULL is returned.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
Examples:
printAnnotation.cpp, printNotes.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
SpeciesType * Model::getSpeciesType ( unsigned int  n)

Get the nth SpeciesType object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth SpeciesType of this Model. If the index n is invalid, NULL is returned.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
const SpeciesType * Model::getSpeciesType ( const std::string &  sid) const

Get a SpeciesType object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the SpeciesType in this Model with the identifier sid or NULL if no such SpeciesType exists.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
SpeciesType * Model::getSpeciesType ( const std::string &  sid)

Get a SpeciesType object based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the SpeciesType in this Model with the identifier sid or NULL if no such SpeciesType exists.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
const std::string & Model::getSubstanceUnits ( ) const

Returns the value of the "substanceUnits" attribute of this Model.

Returns
the substanceUnits of this Model.
Note
The "substanceUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
const std::string & Model::getTimeUnits ( ) const

Returns the value of the "timeUnits" attribute of this Model.

Returns
the timeUnits of this Model.
Note
The "timeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::getTypeCode ( ) const
virtual

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase::getPackageName() method on the object.

The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.

Returns
the SBML type code for this object: SBML_MODEL (default).
Warning
The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf::getItemTypeCode()).
See also
getElementName()
getPackageName()

Reimplemented from SBase.

Reimplemented in ModelDefinition.

const UnitDefinition * Model::getUnitDefinition ( unsigned int  n) const

Get the nth UnitDefinition object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth UnitDefinition of this Model. If the index n is invalid, NULL is returned.
Examples:
printAnnotation.cpp, printNotes.cpp, unsetAnnotation.cpp, and unsetNotes.cpp.
UnitDefinition * Model::getUnitDefinition ( unsigned int  n)

Get the nth UnitDefinition object in this Model.

Parameters
nthe index of the object to return.
Returns
the nth UnitDefinition of this Model. If the index n is invalid, NULL is returned.
const UnitDefinition * Model::getUnitDefinition ( const std::string &  sid) const

Get a UnitDefinition based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the UnitDefinition in this Model with the identifier sid or NULL if no such UnitDefinition exists.
UnitDefinition * Model::getUnitDefinition ( const std::string &  sid)

Get a UnitDefinition based on its identifier.

Parameters
sidthe identifier to search for.
Returns
the UnitDefinition in this Model with the identifier sid or NULL if no such UnitDefinition exists.
std::string SBase::getURI ( ) const
inherited

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1".

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.

Returns
the URI of this element, as a text string.
See also
getSBMLDocument()
getPackageName()
void * SBase::getUserData ( ) const
inherited

Returns the user data that has been previously set via setUserData().

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
the user data of this node, or NULL if no user data has been set.
See also
ASTNode::setUserData(void *userData)
unsigned int SBase::getVersion ( ) const
inherited

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
Examples:
addLayout.cpp, convertSBML.cpp, and printSBML.cpp.
const std::string & Model::getVolumeUnits ( ) const

Returns the value of the "volumeUnits" attribute of this Model.

Returns
the volumeUnits of this Model.
Note
The "volumeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool Model::hasRequiredElements ( ) const
virtual

Predicate returning true if all the required elements for this Model object have been set.

Returns
a boolean value indicating whether all the required elements for this object have been defined.
bool SBase::hasValidLevelVersionNamespaceCombination ( )
inherited

Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

  • Level 1 Version 2: "http://www.sbml.org/sbml/level1"
  • Level 2 Version 1: "http://www.sbml.org/sbml/level2"
  • Level 2 Version 2: "http://www.sbml.org/sbml/level2/version2"
  • Level 2 Version 3: "http://www.sbml.org/sbml/level2/version3"
  • Level 2 Version 4: "http://www.sbml.org/sbml/level2/version4"
  • Level 2 Version 5: "http://www.sbml.org/sbml/level2/version5"
  • Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
  • Level 3 Version 2 Core: "http://www.sbml.org/sbml/level3/version2/core"
Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
bool SBase::isPackageEnabled ( const std::string &  pkgName) const
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPackageURIEnabled()
bool SBase::isPackageURIEnabled ( const std::string &  pkgURI) const
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPackageEnabled()
bool SBase::isPkgEnabled ( const std::string &  pkgName) const
inherited

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPkgURIEnabled()
bool SBase::isPkgURIEnabled ( const std::string &  pkgURI) const
inherited

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package.
Returns
true if the given package is enabled within this object, false otherwise.
See also
isPkgEnabled()
bool Model::isPopulatedAllElementIdList ( ) const

Predicate returning true if libSBML has a list of the ids of all components of this model.

Returns
true if the id list has already been populated, false otherwise.
bool Model::isPopulatedAllElementMetaIdList ( ) const

Predicate returning true if libSBML has a list of the metaids of all components of this model.

Returns
true if the metaid list has already been populated, false otherwise.
bool Model::isPopulatedListFormulaUnitsData ( )

Predicate returning true if libSBML has derived units for the components of this model.

LibSBML can infer the units of measurement associated with different elements of a model. When libSBML does that, it builds a complex internal structure during a resource-intensive operation. This is done automatically only when callers invoke validation (via SBMLDocument::checkConsistency()) and have not turned off the unit validation option.

Callers can force units to be recalculated by calling populateListFormulaUnitsData(). To avoid calling that method unnecessarily, calling programs may first want to invoke this method (isPopulatedListFormulaUnitsData()) to determine whether it is even necessary.

Returns
true if the units have already been computed, false otherwise.
bool SBase::isSetAnnotation ( ) const
inherited

Predicate returning true if this object's "annotation" subelement exists and has content.

Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
true if a "annotation" subelement exists, false otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
unsetAnnotation()
Examples:
printAnnotation.cpp.
bool Model::isSetAreaUnits ( ) const

Predicate returning true if this Model's "areaUnits" attribute is set.

Returns
true if the "areaUnits" attribute of this Model is set, false otherwise.
Note
The "areaUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool Model::isSetConversionFactor ( ) const

Predicate returning true if this Model's "conversionFactor" attribute is set.

Returns
true if the "conversionFactor" attribute of this Model is set, false otherwise.
Note
The "conversionFactor" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool Model::isSetExtentUnits ( ) const

Predicate returning true if this Model's "extentUnits" attribute is set.

Returns
true if the "extentUnits" attribute of this Model is set, false otherwise.
Note
The "extentUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool Model::isSetId ( ) const
virtual

Predicate returning true if this Model's "id" attribute is set.

The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
true if the "id" attribute of this SBML object is set, false otherwise.
Note
Because of the inconsistent behavior of this function with respect to assignments and rules, it is recommended that callers use isSetIdAttribute() instead.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
unsetIdAttribute()
isSetIdAttribute()

Reimplemented from SBase.

Examples:
printSBML.cpp, and SBMLHttpResolverExample.cpp.
bool SBase::isSetIdAttribute ( ) const
inherited

Predicate returning true if this object's "id" attribute is set.

The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
true if the "id" attribute of this SBML object is set, false otherwise.
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
unsetIdAttribute()
bool Model::isSetLengthUnits ( ) const

Predicate returning true if this Model's "lengthUnits" attribute is set.

Returns
true if the "lengthUnits" attribute of this Model is set, false otherwise.
Note
The "lengthUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool SBase::isSetMetaId ( ) const
inherited

Predicate returning true if this object's "metaid" attribute is set.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
true if the "metaid" attribute of this SBML object is set, false otherwise.
See also
getMetaId()
setMetaId(const std::string& metaid)
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
bool SBase::isSetModelHistory ( )
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
bool Model::isSetName ( ) const
virtual

Predicate returning true if this Model's "name" attribute is set.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The "name" attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of "name" is the type string defined in XML Schema. SBML imposes no restrictions as to the content of "name" attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling "name" is as follows. If a software tool has the capability for displaying the content of "name" attributes, it should display this content to the user as a component's label instead of the component's "id". If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the "name" attribute is missing on a given component, then the user interface should display the value of the "id" attribute instead. (Script language interpreters are especially likely to display "id" instead of "name".)

As a consequence of the above, authors of systems that automatically generate the values of "id" attributes should be aware some systems may display the "id"'s to the user. Authors therefore may wish to take some care to have their software create "id" values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the "id" attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of "id" values, there are no restrictions on the uniqueness of "name" values in a model. This allows software applications leeway in assigning component identifiers.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns
true if the "name" attribute of this SBML object is set, false otherwise.
See also
getName()
setName(const std::string& sid)
unsetName()

Reimplemented from SBase.

bool SBase::isSetNotes ( ) const
inherited

Predicate returning true if this object's "notes" subelement exists and has content.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Returns
true if a "notes" subelement exists, false otherwise.
See also
getNotes()
getNotesString()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
getAllElementsWithNotes.cpp, printNotes.cpp, and SBMLHttpResolverExample.cpp.
bool SBase::isSetSBOTerm ( ) const
inherited

Predicate returning true if this object's "sboTerm" attribute is set.

Returns
true if the "sboTerm" attribute of this SBML object is set, false otherwise.
Examples:
printSBML.cpp.
bool Model::isSetSubstanceUnits ( ) const

Predicate returning true if this Model's "substanceUnits" attribute is set.

Returns
true if the "substanceUnits" attribute of this Model is set, false otherwise.
Note
The "substanceUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool Model::isSetTimeUnits ( ) const

Predicate returning true if this Model's "timeUnits" attribute is set.

Returns
true if the "timeUnits" attribute of this Model is set, false otherwise.
Note
The "substanceUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool SBase::isSetUserData ( ) const
inherited

Predicate returning true or false depending on whether the user data of this element has been set.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
boolean, true if this object's user data has been set, false otherwise.
bool Model::isSetVolumeUnits ( ) const

Predicate returning true if this Model's "volumeUnits" attribute is set.

Returns
true if the "volumeUnits" attribute of this Model is set, false otherwise.
Note
The "volumeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb)
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesRequiredSBMLNamespacesForAddition ( const SBase sb) const
inherited

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb)
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
bool SBase::matchesSBMLNamespaces ( const SBase sb) const
inherited

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces.
Returns
boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.
Model & Model::operator= ( const Model rhs)

Assignment operator for Model.

Parameters
rhsthe object whose values are used as the basis of the assignment.
void Model::populateAllElementIdList ( )

Populates the internal list of the identifiers of all elements within this Model object.

This method tells libSBML to retrieve the identifiers of all elements of the enclosing Model object. The result is stored in an internal list of ids. Users can access the resulting data by calling the method getAllElementIdList().

Warning
Retrieving all elements within a model is a time-consuming operation. Callers may want to call isPopulatedAllElementIdList() to determine whether the id list may already have been populated.
See also
isPopulatedAllElementIdList()
void Model::populateAllElementMetaIdList ( )

Populates the internal list of the metaids of all elements within this Model object.

This method tells libSBML to retrieve the identifiers of all elements of the enclosing Model object. The result is stored in an internal list of metaids. Users can access the resulting data by calling the method getAllElementMetaIdList().

Warning
Retrieving all elements within a model is a time-consuming operation. Callers may want to call isPopulatedAllElementMetaIdList() to determine whether the metaid list may already have been populated.
See also
isPopulatedAllElementMetaIdList()
void Model::populateListFormulaUnitsData ( )

Populates the internal list of derived units for this Model object.

This method tells libSBML to (re)calculate all units for all components of the enclosing Model object. The result is stored in an internal list of unit data. Users can access the resulting data by calling the method SBase::getDerivedUnitDefinition() available on most objects. (The name "formula units data" is drawn from the name of the internal objects libSBML uses to store the data; note that these internal objects are not exposed to callers, because callers can interact with the results using the ordinary SBML unit objects.)

This method is used by libSBML itself in the validator concerned with unit consistency. The unit consistency validator (like all other validators in libSBML) is invoked by using SBMLDocument::checkConsistency(), with the consistency checks for the category LIBSBML_CAT_UNITS_CONSISTENCY turned on. The method populateListFormulaUnitsData() does not need to be called prior to invoking the validator if unit consistency checking has not been turned off. This method is only provided for cases when callers have a special need to force the unit data to be recalculated. For instance, during construction of a model, a caller may want to interrogate libSBML's inferred units without invoking full-blown model validation; this is a scenario in which calling populateListFormulaUnitsData() may be useful.

Warning
Computing and inferring units is a time-consuming operation. Callers may want to call isPopulatedListFormulaUnitsData() to determine whether the units may already have been computed, to save themselves the need of invoking unit inference unnecessarily.
See also
isPopulatedListFormulaUnitsData()
void SBase::read ( XMLNode node,
XMLErrorSeverityOverride_t  flag = LIBSBML_OVERRIDE_DISABLED 
)
inherited

Reads (initializes) this SBML object by reading from the given XMLNode.

Parameters
nodethe XMLNode to read from.
flagan optional flag that determines how how errors are logged during the reading process.
Warning
This method is computationally expensive, because the given node has to be serialized to a string first. Attempting to serialize a large tree structure (e.g., a large Model) may consume significant computer memory and time.
Compartment * Model::removeCompartment ( unsigned int  n)

Removes the nth Compartment object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Compartment object to remove.
Returns
the Compartment object removed, or NULL if the given index is out of range.
Compartment * Model::removeCompartment ( const std::string &  sid)

Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the Compartment object to remove.
Returns
the Compartment object removed, or NULL if no Compartment object with the identifier exists in this Model object.
CompartmentType * Model::removeCompartmentType ( unsigned int  n)

Removes the nth CompartmentType object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the CompartmentType object to remove.
Returns
the ComapartmentType object removed, or NULL if the given index is out of range.
CompartmentType * Model::removeCompartmentType ( const std::string &  sid)

Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the object to remove.
Returns
the CompartmentType object removed, or NULL if no CompartmentType object with the identifier exists in this Model object.
Constraint * Model::removeConstraint ( unsigned int  n)

Removes the nth Constraint object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Constraint object to remove.
Returns
the Constraint object removed, or NULL if the given index is out of range.
Event * Model::removeEvent ( unsigned int  n)

Removes the nth Event object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Event object to remove.
Returns
the Event object removed, or NULL if the given index is out of range.
Event * Model::removeEvent ( const std::string &  sid)

Removes the Event object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the Event object to remove.
Returns
the Event object removed, or NULL if no Event object with the identifier exists in this Model object.
int Model::removeFromParentAndDelete ( )
virtual

Remove this Model from its parent SBMLDocument object.

This works by finding this Model's parent SBMLDocument and then calling setModel(NULL) on it, indirectly deleting itself. Overridden from the SBase function since the parent is not a ListOf.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented from SBase.

Reimplemented in ModelDefinition.

FunctionDefinition * Model::removeFunctionDefinition ( unsigned int  n)

Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the FunctionDefinition object to remove.
Returns
the FunctionDefinition object removed, or NULL if the given index is out of range.
FunctionDefinition * Model::removeFunctionDefinition ( const std::string &  sid)

Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the FunctionDefinition object to remove.
Returns
the FunctionDefinition object removed, or NULL if no FunctionDefinition object with the identifier exists in this Model object.
InitialAssignment * Model::removeInitialAssignment ( unsigned int  n)

Removes the nth InitialAssignment object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the InitialAssignment object to remove.
Returns
the InitialAssignment object removed, or NULL if the given index is out of range.
InitialAssignment * Model::removeInitialAssignment ( const std::string &  symbol)

Removes the InitialAssignment object with the given "symbol" attribute from this Model object and returns a pointer to it.

Removes the InitialAssignment object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
symbolthe "symbol" attribute of the InitialAssignment object to remove.
Returns
the InitialAssignment object removed, or NULL if no InitialAssignment object with the "symbol" attribute exists in this Model object.
Parameter * Model::removeParameter ( unsigned int  n)

Removes the nth Parameter object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Parameter object to remove.
Returns
the Parameter object removed, or NULL if the given index is out of range.
Parameter * Model::removeParameter ( const std::string &  sid)

Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the Parameter object to remove.
Returns
the Parameter object removed, or NULL if no Parameter object with the identifier exists in this Model object.
Reaction * Model::removeReaction ( unsigned int  n)

Removes the nth Reaction object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Reaction object to remove.
Returns
the Reaction object removed, or NULL if the given index is out of range.
Reaction * Model::removeReaction ( const std::string &  sid)

Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the Reaction object to remove.
Returns
the Reaction object removed, or NULL if no Reaction object with the identifier exists in this Model object.
Rule * Model::removeRule ( unsigned int  n)

Removes the nth Rule object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Rule object to remove.
Returns
the Rule object removed, or NULL if the given index is out of range.
Rule * Model::removeRule ( const std::string &  variable)

Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it.

Removes the Rule object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
variablethe "variable" attribute of the Rule object to remove.
Returns
the Rule object removed, or NULL if no Rule object with the "variable" attribute exists in this Model object.
Rule * Model::removeRuleByVariable ( const std::string &  variable)

Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it.

Removes the Rule object with the given variable from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
variablethe "variable" attribute of the Rule object to remove.
Returns
the Rule object removed, or NULL if no Rule object with the "variable" attribute exists in this Model object.
Species * Model::removeSpecies ( unsigned int  n)

Removes the nth Species object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Species object to remove.
Returns
the Species object removed, or NULL if the given index is out of range.
Species * Model::removeSpecies ( const std::string &  sid)

Removes the Species object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the Species object to remove.
Returns
the Species object removed, or NULL if no Species object with the identifier exists in this Model object.
SpeciesType * Model::removeSpeciesType ( unsigned int  n)

Removes the nth SpeciesType object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the SpeciesType object to remove.
Returns
the SpeciesType object removed, or NULL if the given index is out of range.
SpeciesType * Model::removeSpeciesType ( const std::string &  sid)

Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the SpeciesType object to remove.
Returns
the SpeciesType object removed, or NULL if no SpeciesType object with the identifier exists in this Model object.
int SBase::removeTopLevelAnnotationElement ( const std::string &  elementName,
const std::string  elementURI = "",
bool  removeEmpty = true 
)
inherited

Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed.
elementURIan optional string that is used to check both the name and URI of the top level element to be removed.
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement(const XMLNode *)
replaceTopLevelAnnotationElement(const std::string&)
UnitDefinition * Model::removeUnitDefinition ( unsigned int  n)

Removes the nth UnitDefinition object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the UnitDefinition object to remove.
Returns
the UnitDefinition object removed., or NULL if the given index is out of range.
UnitDefinition * Model::removeUnitDefinition ( const std::string &  sid)

Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe identifier of the UnitDefinition object to remove.
Returns
the UnitDefinition object removed, or NULL if no UnitDefinition object with the identifier exists in this Model object.
void SBase::renameMetaIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented in Port, and GraphicalObject.

void Model::renameSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtual

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented from SBase.

void Model::renameUnitSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtual

Replaces all uses of a given UnitSIdRef type attribute value with another value.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier.
newidthe new identifier.

Reimplemented from SBase.

int SBase::replaceTopLevelAnnotationElement ( const XMLNode annotation)
inherited

Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI, bool removeEmpty)
replaceTopLevelAnnotationElement(const std::string&)
int SBase::replaceTopLevelAnnotationElement ( const std::string &  annotation)
inherited

Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
replaceTopLevelAnnotationElement(const XMLNode*)
int Model::setAnnotation ( const XMLNode annotation)
virtual

Sets the value of the "annotation" subelement of this SBML object to a copy of annotation.

Any existing content of the "annotation" subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters
annotationan XML structure that is to be used as the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
appendAnnotation(const XMLNode* annotation)

Reimplemented from SBase.

int Model::setAnnotation ( const std::string &  annotation)
virtual

Sets the value of the "annotation" subelement of this SBML object to a copy of annotation.

Any existing content of the "annotation" subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters
annotationan XML string that is to be used as the content of the "annotation" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
appendAnnotation(const std::string& annotation)

Reimplemented from SBase.

int Model::setAreaUnits ( const std::string &  units)

Sets the value of the "areaUnits" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new areaUnits for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "areaUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::setConversionFactor ( const std::string &  units)

Sets the value of the "conversionFactor" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new conversionFactor for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "conversionFactor" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
void SBase::setElementText ( const std::string &  text)
protectedvirtualinherited

When overridden allows SBase elements to use the text included in between the elements tags.

The default implementation does nothing.

Parameters
textthe text string found between the element tags.
int Model::setExtentUnits ( const std::string &  units)

Sets the value of the "extentUnits" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new extentUnits for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "extentUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::setId ( const std::string &  sid)
virtual

Sets the value of the "id" attribute of this Model.

The string sid is copied.
The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Parameters
sidthe string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()

Reimplemented from SBase.

Examples:
createExampleSBML.cpp, example1-L3.cpp, example1.cpp, example2-L3.cpp, example2.cpp, example3-L3.cpp, example3.cpp, groups_example2.cpp, spec_example1.cpp, spec_example3.cpp, and spec_example4.cpp.
int SBase::setIdAttribute ( const std::string &  sid)
virtualinherited

Sets the value of the "id" attribute of this SBML object.

The string sid is copied.
The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Parameters
sidthe string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()
int Model::setLengthUnits ( const std::string &  units)

Sets the value of the "lengthUnits" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new lengthUnits for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "lengthUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int SBase::setMetaId ( const std::string &  metaid)
inherited

Sets the value of the meta-identifier attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the "metaid" attribute.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
Examples:
addingEvidenceCodes_1.cpp, and addingEvidenceCodes_2.cpp.
int SBase::setModelHistory ( ModelHistory history)
inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
Examples:
addModelHistory.cpp.
int Model::setName ( const std::string &  name)
virtual

Sets the value of the "name" attribute of this Model.

The string in name is copied.

Parameters
namethe new name for the SBML object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented from SBase.

Examples:
spec_example1.cpp, and spec_example4.cpp.
int SBase::setNamespaces ( XMLNamespaces xmlns)
inherited

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::setNotes ( const XMLNode notes)
inherited

Sets the value of the "notes" subelement of this SBML object.

The content of notes is copied, and any existing content of this object's "notes" subelement is deleted.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the "notes" subelement of this object.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
createExampleSBML.cpp.
int SBase::setNotes ( const std::string &  notes,
bool  addXHTMLMarkup = false 
)
inherited

Sets the value of the "notes" subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's "notes" subelement is deleted.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

SBMLDocument* s = new SBMLDocument(3, 1);
s->setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>");
Parameters
notesan XML string that is to be used as the content of the "notes" subelement of this object.
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int SBase::setSBOTerm ( int  value)
virtualinherited

Sets the value of the "sboTerm" attribute.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Parameters
valuethe NNNNNNN integer portion of the SBO identifier.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setSBOTerm(const std::string &sboid)
Examples:
groups_example1.cpp, and qual_example1.cpp.
int SBase::setSBOTerm ( const std::string &  sboid)
virtualinherited

Sets the value of the "sboTerm" attribute by string.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named "sboTerm" for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form "SBO:NNNNNNN", where "NNNNNNN" is a seven digit integer number; libSBML simplifies the representation by only storing the "NNNNNNN" integer portion. Thus, in libSBML, the "sboTerm" attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for "sboTerm". More details can be found in SBML specifications for Level 2 Version 2 and above.
Parameters
sboidthe SBO identifier string of the form "SBO:NNNNNNN".
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
setSBOTerm(int value)
int Model::setSubstanceUnits ( const std::string &  units)

Sets the value of the "substanceUnits" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new substanceUnits for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "substanceUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::setTimeUnits ( const std::string &  units)

Sets the value of the "timeUnits" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new timeUnits for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "timeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int SBase::setUserData ( void *  userData)
inherited

Sets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Parameters
userDataspecifies the new user data.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int Model::setVolumeUnits ( const std::string &  units)

Sets the value of the "volumeUnits" attribute of this Model.

The string in units is copied.

Parameters
unitsthe new volumeUnits for the Model.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "volumeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
char * SBase::toSBML ( )
inherited

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
XMLNode* SBase::toXMLNode ( )
inherited

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
int SBase::unsetAnnotation ( )
inherited

Unsets the value of the "annotation" subelement of this SBML object.

Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
Examples:
unsetAnnotation.cpp.
int Model::unsetAreaUnits ( )

Unsets the value of the "areaUnits" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "areaUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::unsetConversionFactor ( )

Unsets the value of the "conversionFactor" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "conversionFactor" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int SBase::unsetCVTerms ( )
inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int Model::unsetExtentUnits ( )

Unsets the value of the "extentUnits" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "extentUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::unsetId ( )
virtual

Unsets the value of the "id" attribute of this Model.

The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of "id" is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
     letter ::= 'a'..'z','A'..'Z'
     digit  ::= '0'..'9'
     idChar ::= letter | digit | '_'
     SId    ::= ( letter | '_' ) idChar*
   
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined "id" and "name" attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have "id" or "name" attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: "variable" (for the rules and event assignments), "symbol" (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.

With the addition of "id" and "name" attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original "id" methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual "id" attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an "id" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write "id" attributes for those objects.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
unsetIdAttribute()

Reimplemented from SBase.

int SBase::unsetIdAttribute ( )
inherited

Unsets the value of the "id" attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: "id" and "name". The identifier given by an object's "id" attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getIdAttribute()
setIdAttribute(const std::string& sid)
isSetIdAttribute()
int Model::unsetLengthUnits ( )

Unsets the value of the "lengthUnits" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "lengthUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int SBase::unsetMetaId ( )
inherited

Unsets the value of the "metaid" attribute of this SBML object.

The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the "metaid" attribute used by SBML—something to be aware of if your application-specific XML content inside the "annotation" subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the "metaid" attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the "annotation" subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBase::unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
int Model::unsetName ( )
virtual

Unsets the value of the "name" attribute of this Model.

In SBML Level 3 Version 2, the "id" and "name" attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The "name" attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of "name" is the type string defined in XML Schema. SBML imposes no restrictions as to the content of "name" attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling "name" is as follows. If a software tool has the capability for displaying the content of "name" attributes, it should display this content to the user as a component's label instead of the component's "id". If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the "name" attribute is missing on a given component, then the user interface should display the value of the "id" attribute instead. (Script language interpreters are especially likely to display "id" instead of "name".)

As a consequence of the above, authors of systems that automatically generate the values of "id" attributes should be aware some systems may display the "id"'s to the user. Authors therefore may wish to take some care to have their software create "id" values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the "id" attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of "id" values, there are no restrictions on the uniqueness of "name" values in a model. This allows software applications leeway in assigning component identifiers.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a "name" attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write "name" attributes for those objects.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
See also
getName()
setName(const std::string& sid)
isSetName()

Reimplemented from SBase.

int SBase::unsetNotes ( )
inherited

Unsets the value of the "notes" subelement of this SBML object.

The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.

The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
See also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes, bool addXHTMLMarkup)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
Examples:
unsetNotes.cpp.
int SBase::unsetSBOTerm ( )
inherited

Unsets the value of the "sboTerm" attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int Model::unsetSubstanceUnits ( )

Unsets the value of the "substanceUnits" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "substanceUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int Model::unsetTimeUnits ( )

Unsets the value of the "timeUnits" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "timeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int SBase::unsetUserData ( )
inherited

Unsets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this attribute will passed as it is. The attribute will never be interpreted by libSBML.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int Model::unsetVolumeUnits ( )

Unsets the value of the "volumeUnits" attribute of this Model.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Note
The "volumeUnits" attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

Friends And Related Function Documentation

friend class SBMLDocument
friend