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Model Class Reference
Inheritance diagram for Model:
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Detailed Description

Implementation of SBML's Model construct.

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 5.8.0 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 Version 1 Core, 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).

Checking consistency and adherence to SBML specifications

To make it easier for applications to do whatever they need, libSBML version 5.8.0 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 Version 1 Core. 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 Version 1 Core specification provides 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 Version 1 specification.

Public Member Functions

virtual bool accept (SBMLVisitor &v) const
 Accepts the given SBMLVisitor for this instance of Constraint. More...
 
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)
 Takes the contents of the passed-in Model, makes copies of everything, and appends those 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...
 
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...
 
int disablePackage (const std::string &pkgURI, const std::string &pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
int enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
virtual ListgetAllElements ()
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual ListgetAllElementsFromPlugins ()
 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. More...
 
const SBasegetAncestorOfType (int type, const std::string pkgName="core") const
 Returns the first ancestor object that has the given SBML type code. 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...
 
unsigned int getColumn () const
 Returns the column number on which 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...
 
virtual SBasegetElementByMetaId (std::string metaid)
 Returns the first child element it can find with the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (std::string id)
 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 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 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 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 on which 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 object. More...
 
std::string & getMetaId ()
 Returns the value of the "metaid" attribute of this object. More...
 
const ModelgetModel () const
 Returns the Model object 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...
 
virtual const std::string & getName () const
 Returns the value of the "name" attribute of this Model. More...
 
virtual XMLNamespacesgetNamespaces () const
 Returns a list of the XML Namespaces declared on this SBML document. 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 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 Specie 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...
 
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...
 
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 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 identifiers.org 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...
 
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 isPopulatedListFormulaUnitsData ()
 Predicate returning true if the list of FormulaUnitsData is populated. 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 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 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 populateListFormulaUnitsData ()
 Populates the list of FormulaDataUnits with the units derived for the model. 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 ()
 Finds this Model's parent SBMLDocument and calls setModel(NULL) on it, indirectly deleting itself. 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...
 
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="")
 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 (std::string oldid, std::string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
virtual void renameSIdRefs (std::string oldid, std::string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML. More...
 
virtual void renameUnitSIdRefs (std::string oldid, std::string newid)
 Renames all the UnitSIdRef attributes on this element. 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...
 
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 "metaid" attribute of this 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...
 
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 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 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, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object.
Note
Upon the addition of a Model object to an SBMLDocument (e.g., using SBMLDocument::setModel()), the SBML Level, SBML Version and XML namespace of the document override the values used when creating the Model object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a Model is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
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 this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.

Parameters
sbmlnsan SBMLNamespaces object.
Exceptions
SBMLConstructorExceptionThrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object.
Note
Upon the addition of a Model object to an SBMLDocument (e.g., using SBMLDocument::setModel()), the SBML XML namespace of the document overrides the value used when creating the Model object via this constructor. This is necessary to ensure that an SBML document is a consistent structure. Nevertheless, the ability to supply the values at the time of creation of a Model is an important aid to producing valid SBML. Knowledge of the intented SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument.
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.
Exceptions
SBMLConstructorExceptionThrown if the argument orig is NULL.

Member Function Documentation

bool Model::accept ( SBMLVisitor v) const
virtual

Accepts the given SBMLVisitor for this instance of Constraint.

Parameters
vthe SBMLVisitor instance to be used.
Returns
the result of calling v.visit().

Implements SBase.

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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createCompartment() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createCompartmentType() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createConstraint() for a method that does 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 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.
Warning
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 in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. 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.
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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createEvent() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createFunctionDefinition() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createInitialAssignment() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createParameter() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createReaction() for a method that does not lead to these issues.
See Also
createReaction()
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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 the methods Model::createAlgebraicRule(), Model::createAssignmentRule() and Model::createRateRule() for methods 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createSpecies() for a method that does not lead to these issues.
See Also
createSpecies()
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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createSpeciesType() for a method that does 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 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 in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. 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 Model::createUnitDefinition() for a method that does 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 possible values returned by this function are:
See Also
setAnnotation(const XMLNode* annotation)

Reimplemented from SBase.

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 possible values returned by this function are:
See Also
setAnnotation(const std::string& annotation)

Reimplemented from SBase.

int Model::appendFrom ( const Model model)
virtual

Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model.

Also calls 'appendFrom' on all plugin objects.

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 possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
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 possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
Model * Model::clone ( ) const
virtual

Creates and returns a deep copy of this Model object.

Returns
a (deep) copy of this Model.

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)
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 Delay 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)
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, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and NULL is returned instead.

Returns
the KineticLaw object created
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
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
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 ModifierSpeciesReference is not created and NULL is returned instead.

Returns
the SpeciesReference object created
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)
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
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
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)
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)
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 Trigger 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)
int SBase::disablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package.

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

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:
int SBase::enablePackage ( const std::string &  pkgURI,
const std::string &  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package.

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

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:
List * Model::getAllElements ( )
virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Returns
a List* of pointers to all children objects.

Reimplemented from SBase.

List * SBase::getAllElementsFromPlugins ( )
virtualinherited

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

This method walks down the list of all packages used by the enclosing Model and returns all objects contained in them.

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.

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. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

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.
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.

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. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

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.
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.

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()
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.

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.
unsigned int SBase::getColumn ( ) const
inherited

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

Returns
the column number of this SBML object.
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.

Returns
the nth Compartment of this Model.
Compartment * Model::getCompartment ( unsigned int  n)

Get the nth Compartment object in this Model.

Returns
the nth Compartment of this Model.
const Compartment * Model::getCompartment ( const std::string &  sid) const

Get a Compartment object based on its identifier.

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.

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.

Returns
the nth CompartmentType of 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.
CompartmentType * Model::getCompartmentType ( unsigned int  n)

Get the nth CompartmentType object in this Model.

Returns
the nth CompartmentType of 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 CompartmentType * Model::getCompartmentType ( const std::string &  sid) const

Get a CompartmentType object based on its identifier.

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.

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.

Returns
the nth Constraint of this Model.
Constraint * Model::getConstraint ( unsigned int  n)

Get the nth Constraint object in this Model.

Returns
the nth Constraint of this Model.
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.
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.
SBase * Model::getElementByMetaId ( std::string  metaid)
virtual

Returns the first child element it can find with the given metaid, or NULL if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.

Reimplemented from SBase.

SBase * Model::getElementBySId ( std::string  id)
virtual

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 of objects to find.
Returns
pointer to the first element found with the given id.

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".

Implements SBase.

Reimplemented in ModelDefinition.

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

Get the nth Event object in this Model.

Returns
the nth Event of this Model.
Event * Model::getEvent ( unsigned int  n)

Get the nth Event object in this Model.

Returns
the nth Event of this Model.
const Event * Model::getEvent ( const std::string &  sid) const

Get an Event object based on its identifier.

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.

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.

Returns
the nth FunctionDefinition of this Model.
FunctionDefinition * Model::getFunctionDefinition ( unsigned int  n)

Get the nth FunctionDefinitions object in this Model.

Returns
the nth FunctionDefinition of this Model.
const FunctionDefinition * Model::getFunctionDefinition ( const std::string &  sid) const

Get a FunctionDefinition object based on its identifier.

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.

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

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

Returns
the id of this Model.
const InitialAssignment * Model::getInitialAssignment ( unsigned int  n) const

Get the nth InitialAssignment object in this Model.

Returns
the nth InitialAssignment of this Model.
InitialAssignment * Model::getInitialAssignment ( unsigned int  n)

Get the nth InitialAssignment object in this Model.

Returns
the nth InitialAssignment of this Model.
const InitialAssignment * Model::getInitialAssignment ( const std::string &  symbol) const

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

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.

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.

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
unsigned int SBase::getLine ( ) const
inherited

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

Returns
the line number of this SBML object.
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 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. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.

Returns
the meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId(const std::string& metaid)
string & SBase::getMetaId ( )
inherited

Returns the value of the "metaid" attribute of this 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. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.

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 in which the current object is located.

Returns
the parent Model 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.
const string & Model::getName ( ) const
virtual

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

Returns
the name of this Model.
XMLNamespaces * SBase::getNamespaces ( ) const
virtualinherited

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

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

Returns
the XML Namespaces associated with this SBML object
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, 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 "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)
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, 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 "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)
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, 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.

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)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
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, 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.

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)
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.
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.
unsigned int Model::getNumConstraints ( ) const

Get the number of Constraint objects in this Model.

Returns
the number of Constraints in this Model.
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 Model::getNumEvents ( ) const

Get the number of Event objects in this Model.

Returns
the number of Events in this Model.
unsigned int Model::getNumFunctionDefinitions ( ) const

Get the number of FunctionDefinition objects in this Model.

Returns
the number of FunctionDefinitions in this Model.
unsigned int Model::getNumInitialAssignments ( ) const

Get the number of InitialAssignment objects in this Model.

Returns
the number of InitialAssignments in this Model.
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.
unsigned int SBase::getNumPlugins ( ) const
inherited

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

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
unsigned int Model::getNumReactions ( ) const

Get the number of Reaction objects in this Model.

Returns
the number of Reactions in this Model.
unsigned int Model::getNumRules ( ) const

Get the number of Rule objects in this Model.

Returns
the number of Rules in this Model.
unsigned int Model::getNumSpecies ( ) const

Get the number of Specie objects in this Model.

Returns
the number of Species in this Model.
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.
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.
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.

Returns
the nth Parameter of this Model.
Parameter * Model::getParameter ( unsigned int  n)

Get the nth Parameter object in this Model.

Returns
the nth Parameter of this Model.
const Parameter * Model::getParameter ( const std::string &  sid) const

Get a Parameter object based on its identifier.

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.

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.

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.
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.

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.
SBasePlugin * SBase::getPlugin ( unsigned int  n)
inherited

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

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
const SBasePlugin * SBase::getPlugin ( unsigned int  n) const
inherited

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

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
const Reaction * Model::getReaction ( unsigned int  n) const

Get the nth Reaction object in this Model.

Returns
the nth Reaction of this Model.
Reaction * Model::getReaction ( unsigned int  n)

Get the nth Reaction object in this Model.

Returns
the nth Reaction of this Model.
const Reaction * Model::getReaction ( const std::string &  sid) const

Get a Reaction object based on its identifier.

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.

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.

Returns
the nth Rule of this Model.
Rule * Model::getRule ( unsigned int  n)

Get the nth Rule object in this Model.

Returns
the nth Rule of this Model.
const Rule * Model::getRule ( const std::string &  variable) const

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

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.

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 3, 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. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

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". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.

Returns
the value of the "sboTerm" attribute as an integer, or -1 if the value is not set.
std::string SBase::getSBOTermAsURL ( ) const
inherited

Returns the identifiers.org 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". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.

Returns
the value of the "sboTerm" attribute as an identifiers.org URL (its value will be of the form "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN"), 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 3, 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. This method returns the entire SBO identifier as a text string in the form "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". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.

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.

Returns
the nth Species of this Model.
Species * Model::getSpecies ( unsigned int  n)

Get the nth Species object in this Model.

Returns
the nth Species of this Model.
const Species * Model::getSpecies ( const std::string &  sid) const

Get a Species object based on its identifier.

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.

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.

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.

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.

Returns
the nth SpeciesType of 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.
SpeciesType * Model::getSpeciesType ( unsigned int  n)

Get the nth SpeciesType object in this Model.

Returns
the nth SpeciesType of 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 SpeciesType * Model::getSpeciesType ( const std::string &  sid) const

Get a SpeciesType object based on its identifier.

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.

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 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_.

Returns
the SBML type code for this object, or SBML_UNKNOWN (default).
See Also
getElementName()

Reimplemented from SBase.

Reimplemented in ModelDefinition.

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

Get the nth UnitDefinition object in this Model.

Returns
the nth UnitDefinition of this Model.
UnitDefinition * Model::getUnitDefinition ( unsigned int  n)

Get the nth UnitDefinition object in this Model.

Returns
the nth UnitDefinition of this Model.
const UnitDefinition * Model::getUnitDefinition ( const std::string &  sid) const

Get a UnitDefinition based on its identifier.

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.

Returns
the UnitDefinition in this Model with the identifier sid or NULL if no such UnitDefinition exists.
void * SBase::getUserData ( ) const
inherited

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

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.

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
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.

Note
The required elements for a Model object are: listOfCompartments (L1 only); listOfSpecies (L1V1 only); listOfReactions(L1V1 only)
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 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/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::isPopulatedListFormulaUnitsData ( )

Predicate returning true if the list of FormulaUnitsData is populated.

Returns
true if the list of FormulaUnitsData is populated, 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()
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.

Returns
true if the "id" attribute of this Model is set, false otherwise.
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. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.

Returns
true if the "metaid" attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(const std::string& metaid)
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.

Returns
true if the "name" attribute of this Model is set, false otherwise.
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)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
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.
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 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.

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.

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.

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.

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.
Exceptions
SBMLConstructorExceptionThrown if the argument rhs is NULL.
void Model::populateListFormulaUnitsData ( )

Populates the list of FormulaDataUnits with the units derived for the model.

The list contains elements of class FormulaUnitsData.

The first element of the list refers to the default units of 'substance per time' derived from the model and has the unitReferenceId 'subs_per_time'. This facilitates the comparison of units derived from mathematical formula with the expected units.

The next elements of the list record the units of the compartments and species established from either explicitly declared or default units.

The next elements record the units of any parameters.

Subsequent elements of the list record the units derived for each mathematical expression encountered within the model.

Note
This function is utilised by the Unit Consistency Validator. The list is populated prior to running the validation and thus the consistency of units can be checked by accessing the members of the list and comparing the appropriate data.
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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the Compartment objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the Compartment object to remove
Returns
the Compartment object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the CompartmentType objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the object to remove
Returns
the CompartmentType object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the Event objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the Event object to remove
Returns
the Event object removed. As mentioned above, the caller owns the returned object. NULL is returned if no Event object with the identifier exists in this Model object.
int Model::removeFromParentAndDelete ( )
virtual

Finds this Model's parent SBMLDocument and calls 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the FunctionDefinition objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the FunctionDefinition object to remove
Returns
the FunctionDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the InitialAssignment objects in this Model object have the "symbol" attribute symbol, then NULL is returned.

Parameters
symbolthe "symbol" attribute of the InitialAssignment object to remove
Returns
the InitialAssignment object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the Parameter objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the Parameter object to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the Reaction objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the Reaction object to remove
Returns
the Reaction object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the Rule objects in this Model object have the "variable" attribute variable, then NULL is returned.

Parameters
variablethe "variable" attribute of the Rule object to remove
Returns
the Rule object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the Species objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the Species object to remove
Returns
the Species object removed. As mentioned above, the caller owns the returned object. NULL is returned 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the SpeciesType objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the SpeciesType object to remove
Returns
the SpeciesType object removed. As mentioned above, the caller owns the returned object. NULL is returned if no SpeciesType object with the identifier exists in this Model object.
int SBase::removeTopLevelAnnotationElement ( const std::string  elementName,
const std::string  elementURI = "" 
)
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
Returns
integer value indicating success/failure of the function. 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. As mentioned above, the caller owns the returned item. NULL is returned 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. If none of the UnitDefinition objects in this Model object have the identifier sid, then NULL is returned.

Parameters
sidthe identifier of the UnitDefinition object to remove
Returns
the UnitDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if no UnitDefinition object with the identifier exists in this Model object.
void SBase::renameMetaIdRefs ( std::string  oldid,
std::string  newid 
)
virtualinherited

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-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.

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

Renames all the SIdRef attributes on this element, including any found in MathML.

Reimplemented from SBase.

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

Renames all the UnitSIdRef attributes on this element.

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); 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 possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI)
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); 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 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 possible values returned by this function are:
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 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 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 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 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. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:

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. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

Parameters
sidthe string to use as the identifier of this Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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 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 "metaid" attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the "metaid" attribute, callers 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.

Parameters
metaidthe identifier string to use as the value of the "metaid" attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
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 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::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 Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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 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 possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
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 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 3, 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". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(const std::string &sboid)
int SBase::setSBOTerm ( const std::string &  sboid)
virtualinherited

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

Beginning with SBML Level 2 Version 3, 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. This method lets you set the value of "sboTerm" as a complete string of the form "SBO:NNNNNNN", whereas setSBOTerm(int value) allows you to set it using the integer form.

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". Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the "sboTerm" attribute.

Parameters
sboidthe SBO identifier string of the form "SBO:NNNNNNN"
Returns
integer value indicating success/failure of the function. 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 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 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.

This can be used by the application developer to attach custom information to the node. In case of a deep copy this attribute will passed as it is. The attribute will be never interpreted by this class.

Parameters
userDataspecifies the new user data.
Returns
integer value indicating success/failure of the function. 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 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.
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 possible values returned by this function are:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(const XMLNode* annotation)
setAnnotation(const std::string& annotation)
appendAnnotation(const XMLNode* annotation)
appendAnnotation(const std::string& annotation)
int Model::unsetAreaUnits ( )

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

Returns
integer value indicating success/failure of the function. 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 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 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 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.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

Reimplemented from SBase.

int Model::unsetLengthUnits ( )

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

Returns
integer value indicating success/failure of the function. 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. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The "metaid" value serves to identify a model component for purposes such as referencing that component from metadata placed within "annotation" subelements.

Returns
integer value indicating success/failure of the function. 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 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.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

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 possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(const XMLNode* notes)
setNotes(const std::string& notes)
appendNotes(const XMLNode* notes)
appendNotes(const std::string& notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
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 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 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 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 Model::unsetVolumeUnits ( )

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

Returns
integer value indicating success/failure of the function. 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