Inheritance diagram for libsbmlcs.Model:

Detailed Description

An SBML model.

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

In SBML Level 1, the components are: UnitDefinition, Compartment, Species, Parameter, Rule, and Reaction. Instances of the classes are placed inside instances of classes ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, and ListOfReactions.
In SBML Level 2 Version 1, the components are: FunctionDefinition, UnitDefinition, Compartment, Species, Parameter, Rule, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, ListOfReactions, and ListOfEvents.
In SBML Level 2 Versions 2, 3 and 4, the components are: FunctionDefinition, UnitDefinition, CompartmentType, SpeciesType, Compartment, Species, Parameter, InitialAssignment, Rule, Constraint, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, and ListOfEvents.
In SBML Level 3 Version 1, the components are: FunctionDefinition, UnitDefinition, Compartment, Species, Parameter, InitialAssignment, Rule, Constraint, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, and ListOfEvents.

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

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

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

Approaches to creating objects using the libSBML API

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

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

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

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

Consistency and adherence to SBML specifications

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

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

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

Model attributes introduced in SBML Level 3

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

The 'substanceUnits' attribute

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

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

The 'timeUnits' attribute

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

The 'volumeUnits', 'areaUnits', and 'lengthUnits' attributes

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

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

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

The 'extentUnits' attribute

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

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

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

The 'conversionFactor' attribute

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

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

Public Member Functions
int	addCompartment (Compartment c)
	Adds a copy of the given Compartment object to this Model. More...

int	addCompartmentType (CompartmentType ct)
	Adds a copy of the given CompartmentType object to this Model. More...

void	addConstantAttribute ()

int	addConstraint (Constraint c)
	Adds a copy of the given Constraint object to this Model. More...

int	addCVTerm (CVTerm term, bool newBag)
	Adds a copy of the given CVTerm object to this SBML object. More...

int	addCVTerm (CVTerm term)
	Adds a copy of the given CVTerm object to this SBML object. More...

void	addDefinitionsForDefaultUnits ()

int	addEvent (Event e)
	Adds a copy of the given Event object to this Model. More...

int	addFunctionDefinition (FunctionDefinition fd)
	Adds a copy of the given FunctionDefinition object to this Model. More...

int	addInitialAssignment (InitialAssignment ia)
	Adds a copy of the given InitialAssignment object to this Model. More...

void	addModifiers ()

int	addParameter (Parameter p)
	Adds a copy of the given Parameter object to this Model. More...

int	addReaction (Reaction r)
	Adds a copy of the given Reaction object to this Model. More...

int	addRule (Rule r)
	Adds a copy of the given Rule object to this Model. More...

int	addSpecies (Species s)
	Adds a copy of the given Species object to this Model. More...

int	addSpeciesType (SpeciesType st)
	Adds a copy of the given SpeciesType object to this Model. More...

int	addUnitDefinition (UnitDefinition ud)
	Adds a copy of the given UnitDefinition object to this Model. More...

new int	appendAnnotation (XMLNode annotation)
	Appends annotation content to any existing content in the 'annotation' subelement of this object. More...

new int	appendAnnotation (string annotation)
	Appends annotation content to any existing content in the 'annotation' subelement of this object. More...

new int	appendFrom (Model model)
	Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model. More...

int	appendNotes (XMLNode notes)
	Appends the given `notes` to the 'notes' subelement of this object. More...

int	appendNotes (string notes)
	Appends the given `notes` to the 'notes' subelement of this object. More...

void	assignRequiredValues ()

int	checkCompatibility (SBase arg0)

string	checkMathMLNamespace (XMLToken elem)

void	clearAllElementIdList ()
	Clears the internal list of the identifiers of all elements within this Model object. More...

void	clearAllElementMetaIdList ()
	Clears the internal list of the metaids of all elements within this Model object. More...

new Model	clone ()
	Creates and returns a deep copy of this Model object. More...

override void	connectToChild ()

void	convertFromL3V2 (bool strict)

void	convertFromL3V2 ()

void	convertL1ToL2 ()

void	convertL1ToL3 (bool addDefaultUnits)

void	convertL1ToL3 ()

void	convertL2ToL1 (bool strict)

void	convertL2ToL1 ()

void	convertL2ToL3 (bool strict, bool addDefaultUnits)

void	convertL2ToL3 (bool strict)

void	convertL2ToL3 ()

void	convertL3ToL1 (bool strict)

void	convertL3ToL1 ()

void	convertL3ToL2 (bool strict)

void	convertL3ToL2 ()

void	convertParametersToLocals (long level, long version)

void	convertStoichiometryMath ()

AlgebraicRule	createAlgebraicRule ()
	Creates a new AlgebraicRule inside this Model and returns it. More...

AssignmentRule	createAssignmentRule ()
	Creates a new AssignmentRule inside this Model and returns it. More...

Compartment	createCompartment ()
	Creates a new Compartment inside this Model and returns it. More...

CompartmentType	createCompartmentType ()
	Creates a new CompartmentType inside this Model and returns it. More...

Constraint	createConstraint ()
	Creates a new Constraint inside this Model and returns it. More...

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

Event	createEvent ()
	Creates a new Event inside this Model and returns it. More...

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

FunctionDefinition	createFunctionDefinition ()
	Creates a new FunctionDefinition inside this Model and returns it. More...

InitialAssignment	createInitialAssignment ()
	Creates a new InitialAssignment inside this Model and returns it. More...

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

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

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

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

Parameter	createParameter ()
	Creates a new Parameter inside this Model and returns it. More...

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

RateRule	createRateRule ()
	Creates a new RateRule inside this Model and returns it. More...

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

Reaction	createReaction ()
	Creates a new Reaction inside this Model and returns it. More...

Species	createSpecies ()
	Creates a new Species inside this Model and returns it. More...

SpeciesType	createSpeciesType ()
	Creates a new SpeciesType inside this Model and returns it. More...

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

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

UnitDefinition	createUnitDefinition ()
	Creates a new UnitDefinition inside this Model and returns it. More...

void	dealWithDefaultValues ()

void	dealWithEvents (bool strict)

void	dealWithFast ()

void	dealWithL3Fast (long targetVersion)

void	dealWithModelUnits (bool strict)

void	dealWithModelUnits ()

void	dealWithStoichiometry ()

void	deleteDisabledPlugins (bool recursive)
	Deletes all information stored in disabled plugins. More...

void	deleteDisabledPlugins ()
	Deletes all information stored in disabled plugins. More...

int	disablePackage (string pkgURI, string pkgPrefix)
	Disables the given SBML Level 3 package on this object. More...

override void	Dispose ()

int	enablePackage (string pkgURI, string pkgPrefix, bool flag)
	Enables or disables the given SBML Level 3 package on this object. More...

override bool	Equals (Object sb)

IdList	getAllElementIdList ()
	Returns the internal list of the identifiers of all elements within this Model object. More...

IdList	getAllElementMetaIdList ()
	Returns the internal list of the metaids of all elements within this Model object. More...

SBase	getAncestorOfType (int type, string pkgName)
	Returns the first ancestor object that has the given SBML type code from the given package. More...

SBase	getAncestorOfType (int type)
	Returns the first ancestor object that has the given SBML type code from the given package. More...

XMLNode	getAnnotation ()
	Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...

string	getAnnotationString ()
	Returns the content of the 'annotation' subelement of this object as a character string. More...

string	getAreaUnits ()
	Returns the value of the 'areaUnits' attribute of this Model. More...

AssignmentRule	getAssignmentRule (string variable)
	Get a Rule object based on the variable to which it assigns a value. More...

AssignmentRule	getAssignmentRuleByVariable (string variable)
	Get a Rule object based on the variable to which it assigns a value. More...

long	getColumn ()
	Returns the column number where this object first appears in the XML representation of the SBML document. More...

Compartment	getCompartment (long n)
	Get the nth Compartment object in this Model. More...

Compartment	getCompartment (string sid)
	Get a Compartment object based on its identifier. More...

CompartmentType	getCompartmentType (long n)
	Get the nth CompartmentType object in this Model. More...

CompartmentType	getCompartmentType (string sid)
	Get a CompartmentType object based on its identifier. More...

Constraint	getConstraint (long n)
	Get the nth Constraint object in this Model. More...

string	getConversionFactor ()
	Returns the value of the 'conversionFactor' attribute of this Model. More...

CVTerm	getCVTerm (long n)
	Returns the nth CVTerm in the list of CVTerms of this SBML object. More...

CVTermList	getCVTerms ()
	Returns a list of CVTerm objects in the annotations of this SBML object. More...

SBasePlugin	getDisabledPlugin (long n)
	Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...

new SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid`. More...

new SBase	getElementBySId (string id)
	Returns the first child element found that has the given `id`. More...

new string	getElementName ()
	Returns the XML element name of this object, which for Model, is always `'model'`. More...

Event	getEvent (long n)
	Get the nth Event object in this Model. More...

Event	getEvent (string sid)
	Get an Event object based on its identifier. More...

string	getExtentUnits ()
	Returns the value of the 'extentUnits' attribute of this Model. More...

SWIGTYPE_p_FormulaUnitsData	getFormulaUnitsDataForAssignment (string sid)

SWIGTYPE_p_FormulaUnitsData	getFormulaUnitsDataForVariable (string sid)

FunctionDefinition	getFunctionDefinition (long n)
	Get the nth FunctionDefinitions object in this Model. More...

FunctionDefinition	getFunctionDefinition (string sid)
	Get a FunctionDefinition object based on its identifier. More...

override int	GetHashCode ()

new string	getId ()
	Returns the value of the 'id' attribute of this Model. More...

string	getIdAttribute ()
	Returns the value of the 'id' attribute of this SBML object. More...

InitialAssignment	getInitialAssignment (long n)
	Get the nth InitialAssignment object in this Model. More...

InitialAssignment	getInitialAssignment (string symbol)
	Get an InitialAssignment object based on the symbol to which it assigns a value. More...

InitialAssignment	getInitialAssignmentBySymbol (string symbol)
	Get an InitialAssignment object based on the symbol to which it assigns a value. More...

string	getLengthUnits ()
	Returns the value of the 'lengthUnits' attribute of this Model. More...

long	getLevel ()
	Returns the SBML Level of the SBMLDocument object containing this object. More...

long	getLine ()
	Returns the line number where this object first appears in the XML representation of the SBML document. More...

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

SBaseList	getListOfAllElementsFromPlugins (ElementFilter filter)

SBaseList	getListOfAllElementsFromPlugins ()

ListOfCompartments	getListOfCompartments ()
	Get the ListOfCompartments object in this Model. More...

ListOfCompartmentTypes	getListOfCompartmentTypes ()
	Get the ListOfCompartmentTypes object in this Model. More...

ListOfConstraints	getListOfConstraints ()
	Get the ListOfConstraints object in this Model. More...

ListOfEvents	getListOfEvents ()
	Get the ListOfEvents object in this Model. More...

ListOfFunctionDefinitions	getListOfFunctionDefinitions ()
	Get the ListOfFunctionDefinitions object in this Model. More...

ListOfInitialAssignments	getListOfInitialAssignments ()
	Get the ListOfInitialAssignments object in this Model. More...

ListOfParameters	getListOfParameters ()
	Get the ListOfParameters object in this Model. More...

ListOfReactions	getListOfReactions ()
	Get the ListOfReactions object in this Model. More...

ListOfRules	getListOfRules ()
	Get the ListOfRules object in this Model. More...

ListOfSpecies	getListOfSpecies ()
	Get the ListOfSpecies object in this Model. More...

ListOfSpeciesTypes	getListOfSpeciesTypes ()
	Get the ListOfSpeciesTypes object in this Model. More...

ListOfUnitDefinitions	getListOfUnitDefinitions ()
	Get the ListOfUnitDefinitions object in this Model. More...

string	getMetaId ()
	Returns the value of the 'metaid' attribute of this SBML object. More...

Model	getModel ()
	Returns the Model object for the SBML Document in which the current object is located. More...

ModelHistory	getModelHistory ()
	Returns the ModelHistory object, if any, attached to this object. More...

ModifierSpeciesReference	getModifierSpeciesReference (string sid)
	Get a ModifierSpeciesReference object based on its identifier. More...

new string	getName ()
	Returns the value of the 'name' attribute of this Model object. More...

new XMLNamespaces	getNamespaces ()
	Returns a list of the XML Namespaces declared on the SBML document owning this object. More...

XMLNode	getNotes ()
	Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...

string	getNotesString ()
	Returns the content of the 'notes' subelement of this object as a string. More...

long	getNumCompartments ()
	Get the number of Compartment objects in this Model. More...

long	getNumCompartmentTypes ()
	Get the number of CompartmentType objects in this Model. More...

long	getNumConstraints ()
	Get the number of Constraint objects in this Model. More...

long	getNumCVTerms ()
	Returns the number of CVTerm objects in the annotations of this SBML object. More...

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

long	getNumEvents ()
	Get the number of Event objects in this Model. More...

long	getNumFunctionDefinitions ()
	Get the number of FunctionDefinition objects in this Model. More...

long	getNumInitialAssignments ()
	Get the number of InitialAssignment objects in this Model. More...

long	getNumParameters ()
	Get the number of Parameter objects in this Model. More...

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

long	getNumReactions ()
	Get the number of Reaction objects in this Model. More...

long	getNumRules ()
	Get the number of Rule objects in this Model. More...

long	getNumSpecies ()
	Get the number of Species objects in this Model. More...

long	getNumSpeciesTypes ()
	Get the number of SpeciesType objects in this Model. More...

long	getNumSpeciesWithBoundaryCondition ()
	Get the number of Species in this Model having their 'boundaryCondition' attribute value set to `true`. More...

long	getNumUnitDefinitions ()
	Get the number of UnitDefinition objects in this Model. More...

long	getPackageCoreVersion ()
	Returns the SBML Core Version within the SBML Level of the actual object. More...

string	getPackageName ()
	Returns the name of the SBML Level 3 package in which this element is defined. More...

long	getPackageVersion ()
	Returns the Version of the SBML Level 3 package to which this element belongs to. More...

Parameter	getParameter (long n)
	Get the nth Parameter object in this Model. More...

Parameter	getParameter (string sid)
	Get a Parameter object based on its identifier. More...

SBase	getParentSBMLObject ()
	Returns the parent SBML object containing this object. More...

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

SBasePlugin	getPlugin (long n)
	Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...

string	getPrefix ()
	Returns the XML namespace prefix of this element. More...

RateRule	getRateRule (string variable)
	Get a Rule object based on the variable to which it assigns a value. More...

RateRule	getRateRuleByVariable (string variable)
	Get a Rule object based on the variable to which it assigns a value. More...

Reaction	getReaction (long n)
	Get the nth Reaction object in this Model. More...

Reaction	getReaction (string sid)
	Get a Reaction object based on its identifier. More...

int	getResourceBiologicalQualifier (string resource)
	Returns the MIRIAM biological qualifier associated with the given resource. More...

int	getResourceModelQualifier (string resource)
	Returns the MIRIAM model qualifier associated with the given resource. More...

Rule	getRule (long n)
	Get the nth Rule object in this Model. More...

Rule	getRule (string variable)
	Get a Rule object based on the variable to which it assigns a value. More...

Rule	getRuleByVariable (string variable)
	Get a Rule object based on the variable to which it assigns a value. More...

SBMLDocument	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

int	getSBOTerm ()
	Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...

string	getSBOTermAsURL ()
	Returns the URL representation of the 'sboTerm' attribute of this object. More...

string	getSBOTermID ()
	Returns the string representation of the 'sboTerm' attribute of this object. More...

Species	getSpecies (long n)
	Get the nth Species object in this Model. More...

Species	getSpecies (string sid)
	Get a Species object based on its identifier. More...

SpeciesReference	getSpeciesReference (string sid)
	Get a SpeciesReference object based on its identifier. More...

SpeciesType	getSpeciesType (long n)
	Get the nth SpeciesType object in this Model. More...

SpeciesType	getSpeciesType (string sid)
	Get a SpeciesType object based on its identifier. More...

string	getSubstanceUnits ()
	Returns the value of the 'substanceUnits' attribute of this Model. More...

string	getTimeUnits ()
	Returns the value of the 'timeUnits' attribute of this Model. More...

new int	getTypeCode ()
	Returns the libSBML type code for this SBML object. More...

UnitDefinition	getUnitDefinition (long n)
	Get the nth UnitDefinition object in this Model. More...

UnitDefinition	getUnitDefinition (string sid)
	Get a UnitDefinition based on its identifier. More...

string	getURI ()
	Gets the namespace URI to which this element belongs to. More...

long	getVersion ()
	Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...

string	getVolumeUnits ()
	Returns the value of the 'volumeUnits' attribute of this Model. More...

new bool	hasRequiredElements ()
	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 (string pkgName)
	Predicate returning `true` if the given SBML Level 3 package is enabled with this object. More...

bool	isPackageURIEnabled (string pkgURI)
	Predicate returning `true` if an SBML Level 3 package with the given URI is enabled with this object. More...

bool	isPkgEnabled (string pkgName)
	Predicate returning `true` if the given SBML Level 3 package is enabled with this object. More...

bool	isPkgURIEnabled (string pkgURI)
	Predicate returning `true` if an SBML Level 3 package with the given URI is enabled with this object. More...

bool	isPopulatedAllElementIdList ()
	Predicate returning `true` if libSBML has a list of the ids of all components of this model. More...

bool	isPopulatedAllElementMetaIdList ()
	Predicate returning `true` if libSBML has a list of the metaids of all components of this model. More...

bool	isPopulatedListFormulaUnitsData ()
	Predicate returning `true` if libSBML has derived units for the components of this model. More...

bool	isSetAnnotation ()
	Predicate returning `true` if this object's 'annotation' subelement exists and has content. More...

bool	isSetAreaUnits ()
	Predicate returning `true` if this Model's 'areaUnits' attribute is set. More...

bool	isSetConversionFactor ()
	Predicate returning `true` if this Model's 'conversionFactor' attribute is set. More...

bool	isSetExtentUnits ()
	Predicate returning `true` if this Model's 'extentUnits' attribute is set. More...

new bool	isSetId ()
	Predicate returning `true` if this Model's 'id' attribute is set. More...

bool	isSetIdAttribute ()
	Predicate returning `true` if this object's 'id' attribute is set. More...

bool	isSetLengthUnits ()
	Predicate returning `true` if this Model's 'lengthUnits' attribute is set. More...

bool	isSetMetaId ()
	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...

new bool	isSetName ()
	Predicate returning `true` if this Model's 'name' attribute is set. More...

bool	isSetNotes ()
	Predicate returning `true` if this object's 'notes' subelement exists and has content. More...

bool	isSetSBOTerm ()
	Predicate returning `true` if this object's 'sboTerm' attribute is set. More...

bool	isSetSubstanceUnits ()
	Predicate returning `true` if this Model's 'substanceUnits' attribute is set. More...

bool	isSetTimeUnits ()
	Predicate returning `true` if this Model's 'timeUnits' attribute is set. More...

bool	isSetUserData ()
	Predicate returning true or false depending on whether the user data of this element has been set. More...

bool	isSetVolumeUnits ()
	Predicate returning `true` if this Model's 'volumeUnits' attribute is set. More...

bool	matchesRequiredSBMLNamespacesForAddition (SBase sb)
	Returns `true` if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...

bool	matchesSBMLNamespaces (SBase sb)
	Returns `true` if this object's set of XML namespaces are the same as the given object's XML namespaces. More...

	Model (long level, long 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 (Model orig)
	Copy constructor; creates a (deep) copy of the given Model object. More...

void	populateAllElementIdList ()
	Populates the internal list of the identifiers of all elements within this Model object. More...

void	populateAllElementMetaIdList ()
	Populates the internal list of the metaids of all elements within this Model object. More...

void	populateListFormulaUnitsData ()
	Populates the internal list of derived units for this Model object. More...

Compartment	removeCompartment (long n)
	Removes the nth Compartment object from this Model object and returns a pointer to it. More...

Compartment	removeCompartment (string sid)
	Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More...

CompartmentType	removeCompartmentType (long n)
	Removes the nth CompartmentType object from this Model object and returns a pointer to it. More...

CompartmentType	removeCompartmentType (string sid)
	Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More...

void	removeCompartmentTypes ()

Constraint	removeConstraint (long n)
	Removes the nth Constraint object from this Model object and returns a pointer to it. More...

Event	removeEvent (long n)
	Removes the nth Event object from this Model object and returns a pointer to it. More...

Event	removeEvent (string sid)
	Removes the Event object with the given identifier from this Model object and returns a pointer to it. More...

new int	removeFromParentAndDelete ()
	Remove this Model from its parent SBMLDocument object. More...

FunctionDefinition	removeFunctionDefinition (long n)
	Removes the nth FunctionDefinition object from this Model object and returns a pointer to it. More...

FunctionDefinition	removeFunctionDefinition (string sid)
	Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it. More...

InitialAssignment	removeInitialAssignment (long n)
	Removes the nth InitialAssignment object from this Model object and returns a pointer to it. More...

InitialAssignment	removeInitialAssignment (string symbol)
	Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it. More...

Parameter	removeParameter (long n)
	Removes the nth Parameter object from this Model object and returns a pointer to it. More...

Parameter	removeParameter (string sid)
	Removes the Parameter object with the given identifier from this Model object and returns a pointer to it. More...

void	removeParameterRuleUnits (bool strict)

Reaction	removeReaction (long n)
	Removes the nth Reaction object from this Model object and returns a pointer to it. More...

Reaction	removeReaction (string sid)
	Removes the Reaction object with the given identifier from this Model object and returns a pointer to it. More...

Rule	removeRule (long n)
	Removes the nth Rule object from this Model object and returns a pointer to it. More...

Rule	removeRule (string variable)
	Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it. More...

Rule	removeRuleByVariable (string variable)
	Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it. More...

Species	removeSpecies (long n)
	Removes the nth Species object from this Model object and returns a pointer to it. More...

Species	removeSpecies (string sid)
	Removes the Species object with the given identifier from this Model object and returns a pointer to it. More...

SpeciesType	removeSpeciesType (long n)
	Removes the nth SpeciesType object from this Model object and returns a pointer to it. More...

SpeciesType	removeSpeciesType (string sid)
	Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More...

void	removeSpeciesTypes ()

int	removeTopLevelAnnotationElement (string elementName, string elementURI, bool removeEmpty)
	Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...

int	removeTopLevelAnnotationElement (string elementName, string elementURI)
	Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...

int	removeTopLevelAnnotationElement (string elementName)
	Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...

UnitDefinition	removeUnitDefinition (long n)
	Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More...

UnitDefinition	removeUnitDefinition (string sid)
	Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More...

void	renameIDs (SBaseList elements, IdentifierTransformer idTransformer)

new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

int	replaceTopLevelAnnotationElement (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 (string annotation)
	Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...

new int	setAnnotation (XMLNode annotation)
	Sets the value of the 'annotation' subelement of this SBML object to a copy of `annotation`. More...

new int	setAnnotation (string annotation)
	Sets the value of the 'annotation' subelement of this SBML object to a copy of `annotation`. More...

int	setAreaUnits (string units)
	Sets the value of the 'areaUnits' attribute of this Model. More...

int	setConversionFactor (string units)
	Sets the value of the 'conversionFactor' attribute of this Model. More...

int	setExtentUnits (string units)
	Sets the value of the 'extentUnits' attribute of this Model. More...

new int	setId (string sid)
	Sets the value of the 'id' attribute of this Model. More...

new int	setIdAttribute (string sid)
	Sets the value of the 'id' attribute of this SBML object. More...

int	setLengthUnits (string units)
	Sets the value of the 'lengthUnits' attribute of this Model. More...

int	setMetaId (string metaid)
	Sets the value of the meta-identifier attribute of this SBML object. More...

int	setModelHistory (ModelHistory history)
	Sets the ModelHistory of this object. More...

new int	setName (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 (XMLNode notes)
	Sets the value of the 'notes' subelement of this SBML object. More...

int	setNotes (string notes, bool addXHTMLMarkup)
	Sets the value of the 'notes' subelement of this SBML object to a copy of the string `notes`. More...

int	setNotes (string notes)
	Sets the value of the 'notes' subelement of this SBML object to a copy of the string `notes`. More...

void	setSBMLNamespacesAndOwn (SBMLNamespaces disownedNs)

new int	setSBOTerm (int value)
	Sets the value of the 'sboTerm' attribute. More...

new int	setSBOTerm (string sboid)
	Sets the value of the 'sboTerm' attribute by string. More...

void	setSpatialDimensions (double dims)

void	setSpatialDimensions ()

void	setSpeciesReferenceConstantValueAndStoichiometry ()

int	setSubstanceUnits (string units)
	Sets the value of the 'substanceUnits' attribute of this Model. More...

int	setTimeUnits (string units)
	Sets the value of the 'timeUnits' attribute of this Model. More...

int	setVolumeUnits (string units)
	Sets the value of the 'volumeUnits' attribute of this Model. More...

string	toSBML ()
	Returns a string consisting of a partial SBML corresponding to just this object. More...

XMLNode	toXMLNode ()
	Returns this element as an XMLNode. More...

int	unsetAnnotation ()
	Unsets the value of the 'annotation' subelement of this SBML object. More...

int	unsetAreaUnits ()
	Unsets the value of the 'areaUnits' attribute of this Model. More...

int	unsetConversionFactor ()
	Unsets the value of the 'conversionFactor' attribute of this Model. More...

int	unsetCVTerms ()
	Clears the list of CVTerm objects attached to this SBML object. More...

int	unsetExtentUnits ()
	Unsets the value of the 'extentUnits' attribute of this Model. More...

new int	unsetId ()
	Unsets the value of the 'id' attribute of this Model. More...

int	unsetIdAttribute ()
	Unsets the value of the 'id' attribute of this SBML object. More...

int	unsetLengthUnits ()
	Unsets the value of the 'lengthUnits' attribute of this Model. More...

int	unsetMetaId ()
	Unsets the value of the 'metaid' attribute of this SBML object. More...

int	unsetModelHistory ()
	Unsets the ModelHistory object attached to this object. More...

new int	unsetName ()
	Unsets the value of the 'name' attribute of this Model. More...

int	unsetNotes ()
	Unsets the value of the 'notes' subelement of this SBML object. More...

int	unsetSBOTerm ()
	Unsets the value of the 'sboTerm' attribute of this SBML object. More...

int	unsetSubstanceUnits ()
	Unsets the value of the 'substanceUnits' attribute of this Model. More...

int	unsetTimeUnits ()
	Unsets the value of the 'timeUnits' attribute of this Model. More...

int	unsetUserData ()
	Unsets the user data of this element. More...

int	unsetVolumeUnits ()
	Unsets the value of the 'volumeUnits' attribute of this Model. More...

Static Public Member Functions
static bool	operator!= (SBase lhs, SBase rhs)

static bool	operator== (SBase lhs, SBase rhs)

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.Model.Model	(	long	level,
		long	version
	)

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

Parameters

level	a long integer, the SBML Level to assign to this Model.
version	a long integer, the SBML Version to assign to this Model.

Exceptions

SBMLConstructorException Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version.

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

libsbmlcs.Model.Model ( SBMLNamespaces sbmlns )

Creates a new Model using the given SBMLNamespaces object sbmlns.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sbmlns an SBMLNamespaces object.

Exceptions

SBMLConstructorException Thrown if the given sbmlns is inconsistent or incompatible with this object.

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

libsbmlcs.Model.Model ( Model orig )

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

Parameters

orig	the object to copy.

Member Function Documentation

int libsbmlcs.Model.addCompartment ( Compartment c )

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

Parameters

c	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createCompartment()

int libsbmlcs.Model.addCompartmentType ( CompartmentType ct )

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

Parameters

ct	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.; The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

See also: createCompartmentType()

void libsbmlcs.Model.addConstantAttribute ( )

int libsbmlcs.Model.addConstraint ( Constraint c )

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

Parameters

c	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createConstraint()

int libsbmlcs.SBase.addCVTerm	(	CVTerm	term,
		bool	newBag
	)

inherited

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

Parameters

term	the CVTerm to assign.
newBag	if `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:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE, if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note: Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.; This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

int libsbmlcs.SBase.addCVTerm ( CVTerm term )

inherited

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

Parameters

term	the CVTerm to assign.
newBag	if `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:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE, if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note: Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.; This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

void libsbmlcs.Model.addDefinitionsForDefaultUnits ( )

int libsbmlcs.Model.addEvent ( Event e )

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

Parameters

e	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createEvent()

int libsbmlcs.Model.addFunctionDefinition ( FunctionDefinition fd )

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

Parameters

fd	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createFunctionDefinition()

int libsbmlcs.Model.addInitialAssignment ( InitialAssignment ia )

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

Parameters

ia	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createInitialAssignment()

void libsbmlcs.Model.addModifiers ( )

int libsbmlcs.Model.addParameter ( Parameter p )

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

Parameters

p	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createParameter()

int libsbmlcs.Model.addReaction ( Reaction r )

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

Parameters

r	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createReaction()

int libsbmlcs.Model.addRule ( Rule r )

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

Parameters

r	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createAlgebraicRule(); createAssignmentRule(); createRateRule()

int libsbmlcs.Model.addSpecies ( Species s )

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

Parameters

s	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createSpecies()

int libsbmlcs.Model.addSpeciesType ( SpeciesType st )

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

Parameters

st	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.; The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

See also: createSpeciesType()

int libsbmlcs.Model.addUnitDefinition ( UnitDefinition ud )

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

Parameters

ud	the 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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createUnitDefinition()

new int libsbmlcs.Model.appendAnnotation ( XMLNode annotation )

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

annotation an 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(XMLNode annotation)

new int libsbmlcs.Model.appendAnnotation ( string annotation )

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

annotation an 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(string annotation)

new int libsbmlcs.Model.appendFrom ( Model model )

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

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

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

Parameters

model the Model to merge with this one.

int libsbmlcs.SBase.appendNotes ( 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

notes an 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(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.appendNotes ( 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

notes an 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(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

void libsbmlcs.Model.assignRequiredValues ( )

int libsbmlcs.SBase.checkCompatibility ( SBase arg0 )

inherited

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken elem )

inherited

void libsbmlcs.Model.clearAllElementIdList ( )

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

See also: populateAllElementIdList(); isPopulatedAllElementIdList()

void libsbmlcs.Model.clearAllElementMetaIdList ( )

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

See also: populateAllElementMetaIdList(); isPopulatedAllElementMetaIdList()

new Model libsbmlcs.Model.clone ( )

Creates and returns a deep copy of this Model object.

Returns: the (deep) copy of this Model object.

override void libsbmlcs.Model.connectToChild ( )

virtual

Reimplemented from libsbmlcs.SBase.

void libsbmlcs.Model.convertFromL3V2 ( bool strict )

void libsbmlcs.Model.convertFromL3V2 ( )

void libsbmlcs.Model.convertL1ToL2 ( )

void libsbmlcs.Model.convertL1ToL3 ( bool addDefaultUnits )

void libsbmlcs.Model.convertL1ToL3 ( )

void libsbmlcs.Model.convertL2ToL1 ( bool strict )

void libsbmlcs.Model.convertL2ToL1 ( )

void libsbmlcs.Model.convertL2ToL3	(	bool	strict,
		bool	addDefaultUnits
	)

void libsbmlcs.Model.convertL2ToL3 ( bool strict )

void libsbmlcs.Model.convertL2ToL3 ( )

void libsbmlcs.Model.convertL3ToL1 ( bool strict )

void libsbmlcs.Model.convertL3ToL1 ( )

void libsbmlcs.Model.convertL3ToL2 ( bool strict )

void libsbmlcs.Model.convertL3ToL2 ( )

void libsbmlcs.Model.convertParametersToLocals	(	long	level,
		long	version
	)

void libsbmlcs.Model.convertStoichiometryMath ( )

AlgebraicRule libsbmlcs.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(Rule r)

AssignmentRule libsbmlcs.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(Rule r)

Compartment libsbmlcs.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(Compartment c)

CompartmentType libsbmlcs.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(CompartmentType ct)

Constraint libsbmlcs.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(Constraint c)

Delay libsbmlcs.Model.createDelay ( )

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

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

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

Returns: the Delay object created.

Event libsbmlcs.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 libsbmlcs.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 libsbmlcs.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(FunctionDefinition fd)

InitialAssignment libsbmlcs.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(InitialAssignment ia)

KineticLaw libsbmlcs.Model.createKineticLaw ( )

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

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

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

Returns: the KineticLaw object created. If a Reaction does not exist for this model, or a Reaction does exist but already has a KineticLaw, a new KineticLaw is not created and null is returned.

LocalParameter libsbmlcs.Model.createKineticLawLocalParameter ( )

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

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

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

Returns: the Parameter object created. If a Reaction does not exist for this model, or a KineticLaw for the Reaction does not exist, a new Parameter is not created and null is returned.

Parameter libsbmlcs.Model.createKineticLawParameter ( )

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

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

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

Returns: the Parameter object created. If a Reaction does not exist for this model, or a KineticLaw for the Reaction does not exist, a new Parameter is not created and null is returned.

ModifierSpeciesReference libsbmlcs.Model.createModifier ( )

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

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

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

Returns: the SpeciesReference object created. If a Reaction does not exist for this model, a new SpeciesReference is not created and null is returned.

Parameter libsbmlcs.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(Parameter p)

SpeciesReference libsbmlcs.Model.createProduct ( )

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

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

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

Returns: the SpeciesReference object created. If a Reaction does not exist for this model, a new SpeciesReference is not created and null is returned.

RateRule libsbmlcs.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(Rule r)

SpeciesReference libsbmlcs.Model.createReactant ( )

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

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

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

Returns: the SpeciesReference object created. If a Reaction does not exist for this model, a new SpeciesReference is not created and null is returned.

Reaction libsbmlcs.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(Reaction r)

Species libsbmlcs.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(Species s)

SpeciesType libsbmlcs.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(SpeciesType st)

Trigger libsbmlcs.Model.createTrigger ( )

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

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

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

Returns: the Trigger object created.

Unit libsbmlcs.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(UnitDefinition ud)

UnitDefinition libsbmlcs.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(UnitDefinition ud)

void libsbmlcs.Model.dealWithDefaultValues ( )

void libsbmlcs.Model.dealWithEvents ( bool strict )

void libsbmlcs.Model.dealWithFast ( )

void libsbmlcs.Model.dealWithL3Fast ( long targetVersion )

void libsbmlcs.Model.dealWithModelUnits ( bool strict )

void libsbmlcs.Model.dealWithModelUnits ( )

void libsbmlcs.Model.dealWithStoichiometry ( )

void libsbmlcs.SBase.deleteDisabledPlugins ( bool recursive )

inherited

Deletes all information stored in disabled plugins.

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

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

recursive if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.

See also: getNumDisabledPlugins()

void libsbmlcs.SBase.deleteDisabledPlugins ( )

inherited

Deletes all information stored in disabled plugins.

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

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

recursive if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.

See also: getNumDisabledPlugins()

int libsbmlcs.SBase.disablePackage	(	string	pkgURI,
		string	pkgPrefix
	)

inherited

Disables the given SBML Level 3 package on this object.

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

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

Parameters

pkgURI	the URI of the package.
pkgPrefix	the XML prefix of the package.

Returns

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

See also: enablePackage(string pkgURI, string pkgPrefix, bool flag)

override void libsbmlcs.Model.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBase.

Reimplemented in libsbmlcs.ModelDefinition.

int libsbmlcs.SBase.enablePackage	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

inherited

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

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

Parameters

pkgURI	the URI of the package.
pkgPrefix	the XML prefix of the package.
flag	whether to enable (`true`) or disable (`false`) the package.

Returns

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

See also: disablePackage(string pkgURI, string pkgPrefix)

override bool libsbmlcs.SBase.Equals ( Object sb )

inherited

IdList libsbmlcs.Model.getAllElementIdList ( )

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

Returns: an IdList of all the identifiers in the model.

See also: populateAllElementIdList(); isPopulatedAllElementIdList()

IdList libsbmlcs.Model.getAllElementMetaIdList ( )

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

Returns: an IdList of all the metaids in the model.

See also: populateAllElementMetaIdList(); isPopulatedAllElementMetaIdList()

SBase libsbmlcs.SBase.getAncestorOfType	(	int	type,
		string	pkgName
	)

inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_. This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters

type	the 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 SBML object type code, or null if no ancestor exists.

Warning: The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return null.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

SBase libsbmlcs.SBase.getAncestorOfType ( int type )

inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_. This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters

type	the 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 SBML object type code, or null if no ancestor exists.

Warning: The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return null.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

XMLNode libsbmlcs.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(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

string libsbmlcs.SBase.getAnnotationString ( )

inherited

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

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

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

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

Returns: the annotation of this SBML object as a character string.

See also: getAnnotation(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

string libsbmlcs.Model.getAreaUnits ( )

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.

AssignmentRule libsbmlcs.Model.getAssignmentRule ( string variable )

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

Parameters

variable the variable to search for.

Returns: the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.

AssignmentRule libsbmlcs.Model.getAssignmentRuleByVariable ( string variable )

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

Parameters

variable the variable to search for.

Returns: the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.

long libsbmlcs.SBase.getColumn ( )

inherited

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

Returns: the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.

Note: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getLine()

Compartment libsbmlcs.Model.getCompartment ( long n )

Get the nth Compartment object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Compartment of this Model. If the index n is invalid, null is returned.

Compartment libsbmlcs.Model.getCompartment ( string sid )

Get a Compartment object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the Compartment in this Model with the identifier sid or null if no such Compartment exists.

CompartmentType libsbmlcs.Model.getCompartmentType ( long n )

Get the nth CompartmentType object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth CompartmentType of this Model. If the index n is invalid, null is returned.

Note: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

CompartmentType libsbmlcs.Model.getCompartmentType ( string sid )

Get a CompartmentType object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the CompartmentType in this Model with the identifier sid or null if no such CompartmentType exists.

Note: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

Constraint libsbmlcs.Model.getConstraint ( long n )

Get the nth Constraint object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Constraint of this Model. If the index n is invalid, null is returned.

string libsbmlcs.Model.getConversionFactor ( )

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 libsbmlcs.SBase.getCVTerm ( long n )

inherited

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

Parameters

n	unsigned int the index of the CVTerm to retrieve.

Returns: the nth CVTerm in the list of CVTerms for this SBML object. If the index n is invalid, null is returned.

CVTermList libsbmlcs.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.

SBasePlugin libsbmlcs.SBase.getDisabledPlugin ( long n )

inherited

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

If no such plugin exists, null is returned.

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

n	the index of the disabled plug-in to return.

Returns: the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, null is returned.

See also: getNumDisabledPlugins(); getPlugin(string package)

new SBase libsbmlcs.Model.getElementByMetaId ( string metaid )

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

Parameters

metaid string representing the meta-identifier of the object to find.

Returns: pointer to the first element found with the given metaid, or null if no such object is found.

new SBase libsbmlcs.Model.getElementBySId ( string id )

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

This operation searches the model-wide SId identifier type namespace

Parameters

id	string representing the id of the object to find.

Returns: pointer to the first element found with the given id, or null if no such object is found.

new string libsbmlcs.Model.getElementName ( )

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

Returns: the name of this element, i.e., 'model'.

Event libsbmlcs.Model.getEvent ( long n )

Get the nth Event object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Event of this Model. If the index n is invalid, null is returned.

Event libsbmlcs.Model.getEvent ( string sid )

Get an Event object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the Event in this Model with the identifier sid or null if no such Event exists.

string libsbmlcs.Model.getExtentUnits ( )

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.

SWIGTYPE_p_FormulaUnitsData libsbmlcs.Model.getFormulaUnitsDataForAssignment ( string sid )

SWIGTYPE_p_FormulaUnitsData libsbmlcs.Model.getFormulaUnitsDataForVariable ( string sid )

FunctionDefinition libsbmlcs.Model.getFunctionDefinition ( long n )

Get the nth FunctionDefinitions object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth FunctionDefinition of this Model. If the index n is invalid, null is returned.

FunctionDefinition libsbmlcs.Model.getFunctionDefinition ( string sid )

Get a FunctionDefinition object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the FunctionDefinition in this Model with the identifier sid or null if no such FunctionDefinition exists.

override int libsbmlcs.SBase.GetHashCode ( )

inherited

new string libsbmlcs.Model.getId ( )

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

Note: Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() function instead.

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns: the id of this Model.

See also: getIdAttribute(); setIdAttribute(string sid); isSetIdAttribute(); unsetIdAttribute()

string libsbmlcs.SBase.getIdAttribute ( )

inherited

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

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns: the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.

Note: Because of the inconsistent behavior of this function with respect to assignments and rules, callers should use getIdAttribute() instead.

See also: setIdAttribute(string sid); isSetIdAttribute(); unsetIdAttribute()

InitialAssignment libsbmlcs.Model.getInitialAssignment ( long n )

Get the nth InitialAssignment object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth InitialAssignment of this Model. If the index n is invalid, null is returned.

InitialAssignment libsbmlcs.Model.getInitialAssignment ( string symbol )

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

Parameters

symbol the symbol to search for.

Returns: the InitialAssignment in this Model with the given 'symbol' attribute value or null if no such InitialAssignment exists.

InitialAssignment libsbmlcs.Model.getInitialAssignmentBySymbol ( string symbol )

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

Parameters

symbol the symbol to search for.

Returns: the InitialAssignment in this Model with the given 'symbol' attribute value or null if no such InitialAssignment exists.

string libsbmlcs.Model.getLengthUnits ( )

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.

long libsbmlcs.SBase.getLevel ( )

inherited

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

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

Returns: the SBML level of this SBML object.

See also: getVersion(); getNamespaces(); getPackageVersion()

long libsbmlcs.SBase.getLine ( )

inherited

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

Returns: the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.

Note: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getColumn()

SBaseList libsbmlcs.SBase.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElements ( )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBase.getListOfAllElementsFromPlugins ( )

inherited

ListOfCompartments libsbmlcs.Model.getListOfCompartments ( )

Get the ListOfCompartments object in this Model.

Returns: the list of Compartments for this Model.

ListOfCompartmentTypes libsbmlcs.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.

ListOfConstraints libsbmlcs.Model.getListOfConstraints ( )

Get the ListOfConstraints object in this Model.

Returns: the list of Constraints for this Model.

ListOfEvents libsbmlcs.Model.getListOfEvents ( )

Get the ListOfEvents object in this Model.

Returns: the list of Events for this Model.

ListOfFunctionDefinitions libsbmlcs.Model.getListOfFunctionDefinitions ( )

Get the ListOfFunctionDefinitions object in this Model.

Returns: the list of FunctionDefinitions for this Model.

ListOfInitialAssignments libsbmlcs.Model.getListOfInitialAssignments ( )

Get the ListOfInitialAssignments object in this Model.

Returns: the list of InitialAssignments for this Model.

ListOfParameters libsbmlcs.Model.getListOfParameters ( )

Get the ListOfParameters object in this Model.

Returns: the list of Parameters for this Model.

ListOfReactions libsbmlcs.Model.getListOfReactions ( )

Get the ListOfReactions object in this Model.

Returns: the list of Reactions for this Model.

ListOfRules libsbmlcs.Model.getListOfRules ( )

Get the ListOfRules object in this Model.

Returns: the list of Rules for this Model.

ListOfSpecies libsbmlcs.Model.getListOfSpecies ( )

Get the ListOfSpecies object in this Model.

Returns: the list of Species for this Model.

ListOfSpeciesTypes libsbmlcs.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.

ListOfUnitDefinitions libsbmlcs.Model.getListOfUnitDefinitions ( )

Get the ListOfUnitDefinitions object in this Model.

Returns: the list of UnitDefinitions for this Model.

string libsbmlcs.SBase.getMetaId ( )

inherited

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

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

Returns: the meta-identifier of this SBML object.

See also: isSetMetaId(); setMetaId(string metaid)

Model libsbmlcs.SBase.getModel ( )

inherited

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

Returns: the Model object for the SBML Document of this SBML object.

See also: getParentSBMLObject(); getSBMLDocument()

ModelHistory libsbmlcs.SBase.getModelHistory ( )

inherited

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

Returns: the ModelHistory object attached to this object, or null if none exist.

Note: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

ModifierSpeciesReference libsbmlcs.Model.getModifierSpeciesReference ( string sid )

Get a ModifierSpeciesReference object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the ModifierSpeciesReference in this Model with the identifier sid or null if no such ModifierSpeciesReference exists.

new string libsbmlcs.Model.getName ( )

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

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

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

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

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

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

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

Returns: the name of this SBML object, or the empty string if not set or unsettable.

See also: getIdAttribute(); isSetName(); setName(string sid); unsetName()

new XMLNamespaces libsbmlcs.SBase.getNamespaces ( )

inherited

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

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

Returns: the XML Namespaces associated with this SBML object, or null in certain very usual circumstances where a namespace is not set.

See also: getLevel(); getVersion()

XMLNode libsbmlcs.SBase.getNotes ( )

inherited

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

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

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

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

Returns: the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.

See also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

string libsbmlcs.SBase.getNotesString ( )

inherited

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

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

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

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

Returns: the content of the 'notes' subelement of this SBML object as a string.

See also: getNotes(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

long libsbmlcs.Model.getNumCompartments ( )

Get the number of Compartment objects in this Model.

Returns: the number of Compartments in this Model.

long libsbmlcs.Model.getNumCompartmentTypes ( )

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.

long libsbmlcs.Model.getNumConstraints ( )

Get the number of Constraint objects in this Model.

Returns: the number of Constraints in this Model.

long libsbmlcs.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.

long libsbmlcs.SBase.getNumDisabledPlugins ( )

inherited

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

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Returns: the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.

long libsbmlcs.Model.getNumEvents ( )

Get the number of Event objects in this Model.

Returns: the number of Events in this Model.

long libsbmlcs.Model.getNumFunctionDefinitions ( )

Get the number of FunctionDefinition objects in this Model.

Returns: the number of FunctionDefinitions in this Model.

long libsbmlcs.Model.getNumInitialAssignments ( )

Get the number of InitialAssignment objects in this Model.

Returns: the number of InitialAssignments in this Model.

long libsbmlcs.Model.getNumParameters ( )

Get the number of Parameter objects in this Model.

Returns: the number of Parameters in this Model. Parameters defined in KineticLaws are not included.

long libsbmlcs.SBase.getNumPlugins ( )

inherited

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

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

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

See also: getPlugin(unsigned int n)

long libsbmlcs.Model.getNumReactions ( )

Get the number of Reaction objects in this Model.

Returns: the number of Reactions in this Model.

long libsbmlcs.Model.getNumRules ( )

Get the number of Rule objects in this Model.

Returns: the number of Rules in this Model.

long libsbmlcs.Model.getNumSpecies ( )

Get the number of Species objects in this Model.

Returns: the number of Species in this Model.

long libsbmlcs.Model.getNumSpeciesTypes ( )

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.

long libsbmlcs.Model.getNumSpeciesWithBoundaryCondition ( )

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.

long libsbmlcs.Model.getNumUnitDefinitions ( )

Get the number of UnitDefinition objects in this Model.

Returns: the number of UnitDefinitions in this Model.

long libsbmlcs.SBase.getPackageCoreVersion ( )

inherited

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

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

Returns: the SBML core version of this SBML object.

string libsbmlcs.SBase.getPackageName ( )

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.

long libsbmlcs.SBase.getPackageVersion ( )

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()

Parameter libsbmlcs.Model.getParameter ( long n )

Get the nth Parameter object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Parameter of this Model. If the index n is invalid, null is returned.

Parameter libsbmlcs.Model.getParameter ( string sid )

Get a Parameter object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the Parameter in this Model with the identifier sid or null if no such Parameter exists.

SBase libsbmlcs.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()

SBasePlugin libsbmlcs.SBase.getPlugin ( string package )

inherited

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

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

If no such plugin exists, null is returned.

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

Parameters

package the name or URI of the package.

Returns: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

See also: getPlugin(unsigned int n)

SBasePlugin libsbmlcs.SBase.getPlugin ( long n )

inherited

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

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

If no such plugin exists, null is returned.

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

Parameters

n	the index of the plug-in to return.

Returns: the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, null is returned.

See also: getNumPlugins(); getPlugin(string package)

string libsbmlcs.SBase.getPrefix ( )

inherited

Returns the XML namespace prefix of this element.

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

Returns: a text string representing the XML namespace prefix.

RateRule libsbmlcs.Model.getRateRule ( string variable )

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

Parameters

variable the symbol to search for.

Returns: the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.

RateRule libsbmlcs.Model.getRateRuleByVariable ( string variable )

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

Parameters

variable the variable to search for.

Returns: the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.

Reaction libsbmlcs.Model.getReaction ( long n )

Get the nth Reaction object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Reaction of this Model. If the index n is invalid, null is returned.

Reaction libsbmlcs.Model.getReaction ( string sid )

Get a Reaction object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the Reaction in this Model with the identifier sid or null if no such Reaction exists.

int libsbmlcs.SBase.getResourceBiologicalQualifier ( 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 valueswhose names begin with BQB_ in the interface class libsbml. 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 valuewhose names begin with BQB_ in the interface class libsbml.

Parameters

resource string 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 are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

int libsbmlcs.SBase.getResourceModelQualifier ( 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 valueswhose names begin with BQB_ in the interface class libsbml. 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 valuewhose names begin with BQB_ in the interface class libsbml.

Parameters

resource string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.

Returns: the model qualifier typeassociated with the resource, or BQM_UNKNOWN if the resource does not exist.

Note: The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

Rule libsbmlcs.Model.getRule ( long n )

Get the nth Rule object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Rule of this Model. If the index n is invalid, null is returned.

Rule libsbmlcs.Model.getRule ( string variable )

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

Parameters

variable the variable to search for.

Returns: the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.

Rule libsbmlcs.Model.getRuleByVariable ( string variable )

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

Parameters

variable the variable to search for.

Returns: the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.

SBMLDocument libsbmlcs.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 libsbmlcs.SBase.getSBOTerm ( )

inherited

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

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns: the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.

string libsbmlcs.SBase.getSBOTermAsURL ( )

inherited

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

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns: the value of the 'sboTerm' attribute as an identifiers.org URL, or an empty string if the value is not set.

string libsbmlcs.SBase.getSBOTermID ( )

inherited

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

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns: the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.

Species libsbmlcs.Model.getSpecies ( long n )

Get the nth Species object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth Species of this Model. If the index n is invalid, null is returned.

Species libsbmlcs.Model.getSpecies ( string sid )

Get a Species object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the Species in this Model with the identifier sid or null if no such Species exists.

SpeciesReference libsbmlcs.Model.getSpeciesReference ( string sid )

Get a SpeciesReference object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the SpeciesReference in this Model with the identifier sid or null if no such SpeciesReference exists.

SpeciesType libsbmlcs.Model.getSpeciesType ( long n )

Get the nth SpeciesType object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth SpeciesType of this Model. If the index n is invalid, null is returned.

Note: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

SpeciesType libsbmlcs.Model.getSpeciesType ( string sid )

Get a SpeciesType object based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the SpeciesType in this Model with the identifier sid or null if no such SpeciesType exists.

Note: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

string libsbmlcs.Model.getSubstanceUnits ( )

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.

string libsbmlcs.Model.getTimeUnits ( )

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.

new int libsbmlcs.Model.getTypeCode ( )

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml.Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase::getPackageName() method on the object.

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

Returns: the SBML type code for this object: SBML_MODEL (default).

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

See also: getElementName(); getPackageName()

UnitDefinition libsbmlcs.Model.getUnitDefinition ( long n )

Get the nth UnitDefinition object in this Model.

Parameters

n	the index of the object to return.

Returns: the nth UnitDefinition of this Model. If the index n is invalid, null is returned.

UnitDefinition libsbmlcs.Model.getUnitDefinition ( string sid )

Get a UnitDefinition based on its identifier.

Parameters

sid	the identifier to search for.

Returns: the UnitDefinition in this Model with the identifier sid or null if no such UnitDefinition exists.

string libsbmlcs.SBase.getURI ( )

inherited

Gets the namespace URI to which this element belongs to.

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

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

Returns: the URI of this element, as a text string.

See also: getSBMLDocument(); getPackageName()

long libsbmlcs.SBase.getVersion ( )

inherited

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

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

Returns: the SBML version of this SBML object.

See also: getLevel(); getNamespaces()

string libsbmlcs.Model.getVolumeUnits ( )

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.

new bool libsbmlcs.Model.hasRequiredElements ( )

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

Returns: a boolean value indicating whether all the required elements for this object have been defined.

bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )

inherited

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

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

Level 1 Version 2: "http://www.sbml.org/sbml/level1"
Level 2 Version 1: "http://www.sbml.org/sbml/level2"
Level 2 Version 2: "http://www.sbml.org/sbml/level2/version2"
Level 2 Version 3: "http://www.sbml.org/sbml/level2/version3"
Level 2 Version 4: "http://www.sbml.org/sbml/level2/version4"
Level 2 Version 5: "http://www.sbml.org/sbml/level2/version5"
Level 3 Version 1 Core: "http://www.sbml.org/sbml/level3/version1/core"
Level 3 Version 2 Core: "http://www.sbml.org/sbml/level3/version2/core"

Returns: true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.

bool libsbmlcs.SBase.isPackageEnabled ( string pkgName )

inherited

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

The search ignores the package version.

Parameters

pkgName the name of the package.

Returns: true if the given package is enabled within this object, false otherwise.

See also: isPackageURIEnabled()

bool libsbmlcs.SBase.isPackageURIEnabled ( string pkgURI )

inherited

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

Parameters

pkgURI the URI of the package.

Returns: true if the given package is enabled within this object, false otherwise.

See also: isPackageEnabled()

bool libsbmlcs.SBase.isPkgEnabled ( string pkgName )

inherited

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

The search ignores the package version.

Parameters

pkgName the name of the package.

Returns: true if the given package is enabled within this object, false otherwise.

See also: isPkgURIEnabled()

bool libsbmlcs.SBase.isPkgURIEnabled ( string pkgURI )

inherited

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

Parameters

pkgURI the URI of the package.

Returns: true if the given package is enabled within this object, false otherwise.

See also: isPkgEnabled()

bool libsbmlcs.Model.isPopulatedAllElementIdList ( )

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

Returns: true if the id list has already been populated, false otherwise.

bool libsbmlcs.Model.isPopulatedAllElementMetaIdList ( )

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

Returns: true if the metaid list has already been populated, false otherwise.

bool libsbmlcs.Model.isPopulatedListFormulaUnitsData ( )

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

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

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

Returns: true if the units have already been computed, false otherwise.

bool libsbmlcs.SBase.isSetAnnotation ( )

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(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation); unsetAnnotation()

bool libsbmlcs.Model.isSetAreaUnits ( )

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 libsbmlcs.Model.isSetConversionFactor ( )

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 libsbmlcs.Model.isSetExtentUnits ( )

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.

new bool libsbmlcs.Model.isSetId ( )

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

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns: true if the 'id' attribute of this SBML object is set, false otherwise.

Note: Because of the inconsistent behavior of this function with respect to assignments and rules, it is recommended that callers use isSetIdAttribute() instead.

See also: getIdAttribute(); setIdAttribute(string sid); unsetIdAttribute(); isSetIdAttribute()

bool libsbmlcs.SBase.isSetIdAttribute ( )

inherited

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

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns: true if the 'id' attribute of this SBML object is set, false otherwise.

See also: getIdAttribute(); setIdAttribute(string sid); unsetIdAttribute()

bool libsbmlcs.Model.isSetLengthUnits ( )

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 libsbmlcs.SBase.isSetMetaId ( )

inherited

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

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

Returns: true if the 'metaid' attribute of this SBML object is set, false otherwise.

See also: getMetaId(); setMetaId(string metaid)

bool libsbmlcs.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.

new bool libsbmlcs.Model.isSetName ( )

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

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

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

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

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

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

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

Returns: true if the 'name' attribute of this SBML object is set, false otherwise.

See also: getName(); setName(string sid); unsetName()

bool libsbmlcs.SBase.isSetNotes ( )

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(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

bool libsbmlcs.SBase.isSetSBOTerm ( )

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 libsbmlcs.Model.isSetSubstanceUnits ( )

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 libsbmlcs.Model.isSetTimeUnits ( )

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 libsbmlcs.SBase.isSetUserData ( )

inherited

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

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns: boolean, true if this object's user data has been set, false otherwise.

bool libsbmlcs.Model.isSetVolumeUnits ( )

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 libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase sb )

inherited

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

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sb	an 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 libsbmlcs.SBase.matchesSBMLNamespaces ( SBase sb )

inherited

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

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

sb	an 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.

static bool libsbmlcs.SBase.operator!=	(	SBase	lhs,
		SBase	rhs
	)

staticinherited

static bool libsbmlcs.SBase.operator==	(	SBase	lhs,
		SBase	rhs
	)

staticinherited

void libsbmlcs.Model.populateAllElementIdList ( )

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

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

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

See also: isPopulatedAllElementIdList()

void libsbmlcs.Model.populateAllElementMetaIdList ( )

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

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

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

See also: isPopulatedAllElementMetaIdList()

void libsbmlcs.Model.populateListFormulaUnitsData ( )

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

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

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

Warning: Computing and inferring units is a time-consuming operation. Callers may want to call isPopulatedListFormulaUnitsData() to determine whether the units may already have been computed, to save themselves the need of invoking unit inference unnecessarily.

See also: isPopulatedListFormulaUnitsData()

Compartment libsbmlcs.Model.removeCompartment ( long 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

n	the index of the Compartment object to remove.

Returns: the Compartment object removed, or null if the given index is out of range.

Compartment libsbmlcs.Model.removeCompartment ( string sid )

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

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

Parameters

sid	the identifier of the Compartment object to remove.

Returns: the Compartment object removed, or null if no Compartment object with the identifier exists in this Model object.

CompartmentType libsbmlcs.Model.removeCompartmentType ( long 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

n	the index of the CompartmentType object to remove.

Returns: the ComapartmentType object removed, or null if the given index is out of range.

CompartmentType libsbmlcs.Model.removeCompartmentType ( string sid )

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

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

Parameters

sid	the identifier of the object to remove.

Returns: the CompartmentType object removed, or null if no CompartmentType object with the identifier exists in this Model object.

void libsbmlcs.Model.removeCompartmentTypes ( )

Constraint libsbmlcs.Model.removeConstraint ( long 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

n	the index of the Constraint object to remove.

Returns: the Constraint object removed, or null if the given index is out of range.

Event libsbmlcs.Model.removeEvent ( long 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

n	the index of the Event object to remove.

Returns: the Event object removed, or null if the given index is out of range.

Event libsbmlcs.Model.removeEvent ( string sid )

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

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

Parameters

sid	the identifier of the Event object to remove.

Returns: the Event object removed, or null if no Event object with the identifier exists in this Model object.

new int libsbmlcs.Model.removeFromParentAndDelete ( )

Remove this Model from its parent SBMLDocument object.

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

Returns

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

FunctionDefinition libsbmlcs.Model.removeFunctionDefinition ( long 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

n	the index of the FunctionDefinition object to remove.

Returns: the FunctionDefinition object removed, or null if the given index is out of range.

FunctionDefinition libsbmlcs.Model.removeFunctionDefinition ( string sid )

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

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

Parameters

sid	the identifier of the FunctionDefinition object to remove.

Returns: the FunctionDefinition object removed, or null if no FunctionDefinition object with the identifier exists in this Model object.

InitialAssignment libsbmlcs.Model.removeInitialAssignment ( long 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

n	the index of the InitialAssignment object to remove.

Returns: the InitialAssignment object removed, or null if the given index is out of range.

InitialAssignment libsbmlcs.Model.removeInitialAssignment ( string symbol )

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

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

Parameters

symbol the 'symbol' attribute of the InitialAssignment object to remove.

Returns: the InitialAssignment object removed, or null if no InitialAssignment object with the 'symbol' attribute exists in this Model object.

Parameter libsbmlcs.Model.removeParameter ( long 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

n	the index of the Parameter object to remove.

Returns: the Parameter object removed, or null if the given index is out of range.

Parameter libsbmlcs.Model.removeParameter ( string sid )

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

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

Parameters

sid	the identifier of the Parameter object to remove.

Returns: the Parameter object removed, or null if no Parameter object with the identifier exists in this Model object.

void libsbmlcs.Model.removeParameterRuleUnits ( bool strict )

Reaction libsbmlcs.Model.removeReaction ( long 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

n	the index of the Reaction object to remove.

Returns: the Reaction object removed, or null if the given index is out of range.

Reaction libsbmlcs.Model.removeReaction ( string sid )

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

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

Parameters

sid	the identifier of the Reaction object to remove.

Returns: the Reaction object removed, or null if no Reaction object with the identifier exists in this Model object.

Rule libsbmlcs.Model.removeRule ( long 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

n	the index of the Rule object to remove.

Returns: the Rule object removed, or null if the given index is out of range.

Rule libsbmlcs.Model.removeRule ( string variable )

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

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

Parameters

variable the 'variable' attribute of the Rule object to remove.

Returns: the Rule object removed, or null if no Rule object with the 'variable' attribute exists in this Model object.

Rule libsbmlcs.Model.removeRuleByVariable ( string variable )

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

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

Parameters

variable the 'variable' attribute of the Rule object to remove.

Returns: the Rule object removed, or null if no Rule object with the 'variable' attribute exists in this Model object.

Species libsbmlcs.Model.removeSpecies ( long 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

n	the index of the Species object to remove.

Returns: the Species object removed, or null if the given index is out of range.

Species libsbmlcs.Model.removeSpecies ( string sid )

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

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

Parameters

sid	the identifier of the Species object to remove.

Returns: the Species object removed, or null if no Species object with the identifier exists in this Model object.

SpeciesType libsbmlcs.Model.removeSpeciesType ( long 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

n	the index of the SpeciesType object to remove.

Returns: the SpeciesType object removed, or null if the given index is out of range.

SpeciesType libsbmlcs.Model.removeSpeciesType ( string sid )

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

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

Parameters

sid	the identifier of the SpeciesType object to remove.

Returns: the SpeciesType object removed, or null if no SpeciesType object with the identifier exists in this Model object.

void libsbmlcs.Model.removeSpeciesTypes ( )

int libsbmlcs.SBase.removeTopLevelAnnotationElement	(	string	elementName,
		string	elementURI,
		bool	removeEmpty
	)

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

elementName	a string representing the name of the top level annotation element that is to be removed.
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed.
removeEmpty	if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).

Returns

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

See also: replaceTopLevelAnnotationElement(XMLNode ); replaceTopLevelAnnotationElement(string)

int libsbmlcs.SBase.removeTopLevelAnnotationElement	(	string	elementName,
		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

elementName	a string representing the name of the top level annotation element that is to be removed.
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed.
removeEmpty	if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).

Returns

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

See also: replaceTopLevelAnnotationElement(XMLNode ); replaceTopLevelAnnotationElement(string)

int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string elementName )

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

elementName	a string representing the name of the top level annotation element that is to be removed.
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed.
removeEmpty	if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).

Returns

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

See also: replaceTopLevelAnnotationElement(XMLNode ); replaceTopLevelAnnotationElement(string)

UnitDefinition libsbmlcs.Model.removeUnitDefinition ( long 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

n	the index of the UnitDefinition object to remove.

Returns: the UnitDefinition object removed., or null if the given index is out of range.

UnitDefinition libsbmlcs.Model.removeUnitDefinition ( string sid )

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

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

Parameters

sid	the identifier of the UnitDefinition object to remove.

Returns: the UnitDefinition object removed, or null if no UnitDefinition object with the identifier exists in this Model object.

void libsbmlcs.Model.renameIDs	(	SBaseList	elements,
		IdentifierTransformer	idTransformer
	)

new void libsbmlcs.SBase.renameMetaIdRefs	(	string	oldid,
		string	newid
	)

inherited

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

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

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

Parameters

oldid	the old identifier.
newid	the new identifier.

new void libsbmlcs.Model.renameSIdRefs	(	string	oldid,
		string	newid
	)

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

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

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

Parameters

oldid	the old identifier.
newid	the new identifier.

new void libsbmlcs.Model.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

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

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

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

Parameters

oldid	the old identifier.
newid	the new identifier.

int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( XMLNode annotation )

inherited

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

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

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

Parameters

annotation XMLNode 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(string elementName, string elementURI, bool removeEmpty); replaceTopLevelAnnotationElement(string)

int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string annotation )

inherited

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

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

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

Parameters

annotation string 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(string elementName, string elementURI); replaceTopLevelAnnotationElement(XMLNode)

new int libsbmlcs.Model.setAnnotation ( XMLNode annotation )

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

annotation an 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. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: appendAnnotation(XMLNode annotation)

new int libsbmlcs.Model.setAnnotation ( string annotation )

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

annotation an 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(string annotation)

int libsbmlcs.Model.setAreaUnits ( string units )

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

The string in units is copied.

Parameters

units the 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 libsbmlcs.Model.setConversionFactor ( string units )

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

The string in units is copied.

Parameters

units the 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.

int libsbmlcs.Model.setExtentUnits ( string units )

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

The string in units is copied.

Parameters

units the 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.

new int libsbmlcs.Model.setId ( string sid )

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

The string sid is copied.

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Parameters

sid	the string to use as the identifier of this object.

Returns

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

See also: getIdAttribute(); setIdAttribute(string sid); isSetIdAttribute(); unsetIdAttribute()

new int libsbmlcs.SBase.setIdAttribute ( string sid )

inherited

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

The string sid is copied.

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Parameters

sid	the string to use as the identifier of this object.

Returns

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

See also: getIdAttribute(); setIdAttribute(string sid); isSetIdAttribute(); unsetIdAttribute()

int libsbmlcs.Model.setLengthUnits ( string units )

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

The string in units is copied.

Parameters

units the 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 libsbmlcs.SBase.setMetaId ( string metaid )

inherited

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

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

The string metaid is copied.

Parameters

metaid the 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 libsbmlcs.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

history ModelHistory 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.

new int libsbmlcs.Model.setName ( string name )

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

The string in name is copied.

Parameters

name	the new name for the SBML object.

Returns

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

int libsbmlcs.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

xmlns the namespaces to set.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.SBase.setNotes ( 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

notes an 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(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.setNotes	(	string	notes,
		bool	addXHTMLMarkup
	)

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

notes	an XML string that is to be used as the content of the 'notes' subelement of this object.
addXHTMLMarkup	a 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(XMLNode notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.SBase.setNotes ( string notes )

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

notes	an XML string that is to be used as the content of the 'notes' subelement of this object.
addXHTMLMarkup	a 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(XMLNode notes); appendNotes(XMLNode notes); appendNotes(string notes); unsetNotes(); SyntaxChecker::hasExpectedXHTMLSyntax()

void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces disownedNs )

inherited

new int libsbmlcs.SBase.setSBOTerm ( int value )

inherited

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Parameters

value the 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(string &sboid)

new int libsbmlcs.SBase.setSBOTerm ( string sboid )

inherited

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

Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Parameters

sboid the 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)

void libsbmlcs.Model.setSpatialDimensions ( double dims )

void libsbmlcs.Model.setSpatialDimensions ( )

void libsbmlcs.Model.setSpeciesReferenceConstantValueAndStoichiometry ( )

int libsbmlcs.Model.setSubstanceUnits ( string units )

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

The string in units is copied.

Parameters

units the 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 libsbmlcs.Model.setTimeUnits ( string units )

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

The string in units is copied.

Parameters

units the 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 libsbmlcs.Model.setVolumeUnits ( string units )

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

The string in units is copied.

Parameters

units the 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.

string libsbmlcs.SBase.toSBML ( )

inherited

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

Returns: the partial SBML that describes this SBML object.

Warning: This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

XMLNode libsbmlcs.SBase.toXMLNode ( )

inherited

Returns this element as an XMLNode.

Returns: this element as an XMLNode.

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

int libsbmlcs.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. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getAnnotation(); getAnnotationString(); isSetAnnotation(); setAnnotation(XMLNode annotation); setAnnotation(string annotation); appendAnnotation(XMLNode annotation); appendAnnotation(string annotation)

int libsbmlcs.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 libsbmlcs.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 libsbmlcs.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 libsbmlcs.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.

new int libsbmlcs.Model.unsetId ( )

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

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:

  letter ::= 'a'..'z','A'..'Z'
  digit  ::= '0'..'9'
  idChar ::= letter | digit | '_'
  SId    ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns

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

See also: getIdAttribute(); setIdAttribute(string sid); isSetIdAttribute(); unsetIdAttribute()

int libsbmlcs.SBase.unsetIdAttribute ( )

inherited

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

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

Returns

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

See also: getIdAttribute(); setIdAttribute(string sid); isSetIdAttribute()

int libsbmlcs.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 libsbmlcs.SBase.unsetMetaId ( )

inherited

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

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

Returns

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

int libsbmlcs.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.

new int libsbmlcs.Model.unsetName ( )

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

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

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

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

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

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

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

Returns

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

See also: getName(); setName(string sid); isSetName()

int libsbmlcs.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. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getNotesString(); isSetNotes(); setNotes(XMLNode notes); setNotes(string notes, bool addXHTMLMarkup); appendNotes(XMLNode notes); appendNotes(string notes); SyntaxChecker::hasExpectedXHTMLSyntax()

int libsbmlcs.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 libsbmlcs.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 libsbmlcs.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 libsbmlcs.SBase.unsetUserData ( )

inherited

Unsets the user data of this element.

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns

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

int libsbmlcs.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.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn

protectedinherited

Detailed Description

Approaches to creating objects using the libSBML API

Consistency and adherence to SBML specifications

Model attributes introduced in SBML Level 3

The 'substanceUnits' attribute

The 'timeUnits' attribute

The 'volumeUnits', 'areaUnits', and 'lengthUnits' attributes

The 'extentUnits' attribute

The 'conversionFactor' attribute

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation