Inheritance diagram for libsbmlcs.ModelDefinition:

Detailed Description

{comp}

comp Implementation of the ModelDefinition construct from the “comp” package.

The comp package (“comp”) allows multiple Model objects to be defined in a single SBMLDocument. While these new Model objects are not new SBML classes, they are given a new name, <modelDefinition>, and reside in ListOfModelDefinition objects. In libSBML, this class inherits from the Model class, changing only the expected parent of the object, and the XML name.

An additional restriction is placed on the 'id' attribute of ModelDefinition objects: not only must it be unique across all such attributes of type SId within the ModelDefintion, it must also be unique across all Model, ModelDefinition, and ExternalModelDefinition objects in the same SBMLDocument.

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...

int	appendFrom (Model model)
	Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model. More...

int	appendNotes (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)

SBase	clone ()
	Creates and returns a deep copy of this ModelDefinition object. More...

void	connectToParent (SBase parent)
	Sets the parent SBML object of this SBML object. More...

bool	containsUndeclaredUnits ()

void	convertL1ToL2 ()

void	convertL1ToL3 ()

void	convertL2ToL1 (bool strict)

void	convertL2ToL1 ()

void	convertL2ToL3 ()

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	dealWithEvents (bool strict)

void	dealWithModelUnits ()

void	dealWithStoichiometry ()

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

override void	Dispose ()

void	divideAssignmentsToSIdByFunction (string id, ASTNode function)
	If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...

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)

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 on which 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...

UnitDefinition	getDerivedUnitDefinition ()

SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid`, or null if no such object is found. More...

SBase	getElementBySId (string id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace, or `null` if no such object is found. More...

SBase	getElementFromPluginsByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid` from all plug-ins associated with this element, or `null` if no such object is found. More...

SBase	getElementFromPluginsBySId (string id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace from all plug-ins associated with this element, or `null` if no such object is found. More...

string	getElementName ()
	The only difference between a Model and a ModelDefinition is the element name ('modelDefinition') 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...

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 on which 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 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. More...

XMLNamespaces	getNamespaces ()
	Returns a list of the XML Namespaces declared on this SBML document. 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	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 Specie 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...

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 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...

SBMLNamespaces	getSBMLNamespaces ()

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

string	getSBOTermAsURL ()
	Returns the identifiers.org 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...

int	getTypeCode ()
	Returns the libSBML type code of this object instance. 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...

bool	hasNonstandardIdentifierBeginningWith (string prefix)
	Check to see if the given prefix is used by any of the IDs defined by extension elements excluding 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More...

bool	hasRequiredAttributes ()

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	isPopulatedListFormulaUnitsData ()
	Predicate returning `true` if the list of FormulaUnitsData is populated. 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	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	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...

	ModelDefinition (long level, long version, long pkgVersion)
	Creates a new ModelDefinition with the given level, version, and package version. More...

	ModelDefinition (long level, long version)
	Creates a new ModelDefinition with the given level, version, and package version. More...

	ModelDefinition (long level)
	Creates a new ModelDefinition with the given level, version, and package version. More...

	ModelDefinition ()
	Creates a new ModelDefinition with the given level, version, and package version. More...

	ModelDefinition (CompPkgNamespaces compns)
	Creates a new ModelDefinition with the given CompPkgNamespaces object. More...

	ModelDefinition (Model source)
	Copy constructor from base Model object. More...

void	multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
	If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...

void	populateListFormulaUnitsData ()
	Populates the list of FormulaDataUnits with the units derived for the model. More...

int	prependStringToAllIdentifiers (string prefix)
	Add the given string to all identifiers in the 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...

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...

int	removeFromParentAndDelete ()
	Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself. 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...

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...

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...

int	renameAllIds (IdentifierTransformer idTransformer, ElementFilter filter)

int	renameAllIds (IdentifierTransformer idTransformer)

void	renameIDs (SBaseList elements, IdentifierTransformer idTransformer)

void	renameMetaIdRefs (string oldid, string newid)
	Renames all the meta-identifier attributes on this element. More...

void	renameSIdRefs (string oldid, string newid)
	Renames all the `SIdRef` attributes on this element, including any found in MathML. More...

void	renameUnitSIdRefs (string oldid, string newid)
	Renames all the `UnitSIdRef` attributes on this element. More...

void	replaceSIDWithFunction (string id, ASTNode function)
	If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. 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...

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 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 sbmlns)

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

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	transformIdentifiers (IdentifierTransformer idTransformer)

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

void	writeExtensionElements (XMLOutputStream stream)
	Writes out contained SBML objects of package extensions (if any) as XML elements. 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.ModelDefinition.ModelDefinition	(	long	level,
		long	version,
		long	pkgVersion
	)

Creates a new ModelDefinition with the given level, version, and package version.

Parameters

level	the SBML Level
version	the Version within the SBML Level
pkgVersion	the version of the package

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

Creates a new ModelDefinition with the given level, version, and package version.

Parameters

level	the SBML Level
version	the Version within the SBML Level
pkgVersion	the version of the package

libsbmlcs.ModelDefinition.ModelDefinition ( long level )

Creates a new ModelDefinition with the given level, version, and package version.

Parameters

level	the SBML Level
version	the Version within the SBML Level
pkgVersion	the version of the package

libsbmlcs.ModelDefinition.ModelDefinition ( )

Creates a new ModelDefinition with the given level, version, and package version.

Parameters

level	the SBML Level
version	the Version within the SBML Level
pkgVersion	the version of the package

libsbmlcs.ModelDefinition.ModelDefinition ( CompPkgNamespaces compns )

Creates a new ModelDefinition with the given CompPkgNamespaces object.

Parameters

compns the namespace to use

libsbmlcs.ModelDefinition.ModelDefinition ( Model source )

Copy constructor from base Model object.

Member Function Documentation

int libsbmlcs.Model.addCompartment ( Compartment c )

inherited

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 )

inherited

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 ( )

inherited

int libsbmlcs.Model.addConstraint ( Constraint c )

inherited

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.

*

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.

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.

*

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.

void libsbmlcs.Model.addDefinitionsForDefaultUnits ( )

inherited

int libsbmlcs.Model.addEvent ( Event e )

inherited

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 )

inherited

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 )

inherited

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 ( )

inherited

int libsbmlcs.Model.addParameter ( Parameter p )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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)

int libsbmlcs.Model.appendFrom ( Model model )

inherited

Takes the contents of the passed-in Model, makes copies of everything, and appends those 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 ( )

inherited

int libsbmlcs.SBase.checkCompatibility ( SBase arg0 )

inherited

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken elem )

inherited

SBase libsbmlcs.ModelDefinition.clone ( )

Creates and returns a deep copy of this ModelDefinition object.

Returns: a (deep) copy of this ModelDefinition object

void libsbmlcs.SBase.connectToParent ( SBase parent )

inherited

Sets the parent SBML object of this SBML object.

(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).

Parameters

parent the SBML object to use

bool libsbmlcs.SBase.containsUndeclaredUnits ( )

inherited

void libsbmlcs.Model.convertL1ToL2 ( )

inherited

void libsbmlcs.Model.convertL1ToL3 ( )

inherited

void libsbmlcs.Model.convertL2ToL1 ( bool strict )

inherited

void libsbmlcs.Model.convertL2ToL1 ( )

inherited

void libsbmlcs.Model.convertL2ToL3 ( )

inherited

void libsbmlcs.Model.convertL3ToL1 ( )

inherited

void libsbmlcs.Model.convertL3ToL2 ( bool strict )

inherited

void libsbmlcs.Model.convertL3ToL2 ( )

inherited

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

inherited

void libsbmlcs.Model.convertStoichiometryMath ( )

inherited

AlgebraicRule libsbmlcs.Model.createAlgebraicRule ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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

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

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

Returns: the Delay object created

Event libsbmlcs.Model.createEvent ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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

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

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

Returns: the KineticLaw object created

LocalParameter libsbmlcs.Model.createKineticLawLocalParameter ( )

inherited

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

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

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

Returns: the Parameter object created

Parameter libsbmlcs.Model.createKineticLawParameter ( )

inherited

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

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

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

Returns: the Parameter object created

ModifierSpeciesReference libsbmlcs.Model.createModifier ( )

inherited

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

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

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

Returns: the SpeciesReference object created

Parameter libsbmlcs.Model.createParameter ( )

inherited

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 ( )

inherited

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

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

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

Returns: the SpeciesReference object created

RateRule libsbmlcs.Model.createRateRule ( )

inherited

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 ( )

inherited

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

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

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

Returns: the SpeciesReference object created

Reaction libsbmlcs.Model.createReaction ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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

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

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

Returns: the Trigger object created

Unit libsbmlcs.Model.createUnit ( )

inherited

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 ( )

inherited

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.dealWithEvents ( bool strict )

inherited

void libsbmlcs.Model.dealWithModelUnits ( )

inherited

void libsbmlcs.Model.dealWithStoichiometry ( )

inherited

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 another 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.ModelDefinition.Dispose ( )

virtual

Reimplemented from libsbmlcs.Model.

void libsbmlcs.SBase.divideAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note: This function does nothing itself—subclasses with ASTNode subelements must override this function.

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

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.

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.

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 ( )

inherited

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 )

inherited

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

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

AssignmentRule libsbmlcs.Model.getAssignmentRuleByVariable ( string variable )

inherited

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

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

long libsbmlcs.SBase.getColumn ( )

inherited

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

Returns: the column number of this SBML object.

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

See also: getLine()

Compartment libsbmlcs.Model.getCompartment ( long n )

inherited

Get the nth Compartment object in this Model.

Returns: the nth Compartment of this Model.

Compartment libsbmlcs.Model.getCompartment ( string sid )

inherited

Get a Compartment object based on its identifier.

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

CompartmentType libsbmlcs.Model.getCompartmentType ( long n )

inherited

Get the nth CompartmentType object in this Model.

Returns: the nth CompartmentType of this Model.

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

CompartmentType libsbmlcs.Model.getCompartmentType ( string sid )

inherited

Get a CompartmentType object based on its identifier.

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

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

Constraint libsbmlcs.Model.getConstraint ( long n )

inherited

Get the nth Constraint object in this Model.

Returns: the nth Constraint of this Model.

string libsbmlcs.Model.getConversionFactor ( )

inherited

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	long the index of the CVTerm to retrieve

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

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.

UnitDefinition libsbmlcs.SBase.getDerivedUnitDefinition ( )

inherited

SBase libsbmlcs.Model.getElementByMetaId ( string metaid )

inherited

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

Parameters

metaid string representing the metaid of objects to find

Returns: pointer to the first element found with the given metaid.

SBase libsbmlcs.Model.getElementBySId ( string id )

inherited

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

Parameters

id	string representing the id of objects to find.

Returns: pointer to the first element found with the given id.

SBase libsbmlcs.SBase.getElementFromPluginsByMetaId ( string metaid )

inherited

Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found.

Parameters

metaid string representing the metaid of objects to find

Returns: pointer to the first element found with the given metaid.

SBase libsbmlcs.SBase.getElementFromPluginsBySId ( string id )

inherited

Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found.

Parameters

id	string representing the id of objects to find

Returns: pointer to the first element found with the given id.

string libsbmlcs.ModelDefinition.getElementName ( )

The only difference between a Model and a ModelDefinition is the element name ('modelDefinition')

Returns: the string of the name of this element ('modelDefintion').

See also: getTypeCode()

Event libsbmlcs.Model.getEvent ( long n )

inherited

Get the nth Event object in this Model.

Returns: the nth Event of this Model.

Event libsbmlcs.Model.getEvent ( string sid )

inherited

Get an Event object based on its identifier.

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

string libsbmlcs.Model.getExtentUnits ( )

inherited

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 )

inherited

SWIGTYPE_p_FormulaUnitsData libsbmlcs.Model.getFormulaUnitsDataForVariable ( string sid )

inherited

FunctionDefinition libsbmlcs.Model.getFunctionDefinition ( long n )

inherited

Get the nth FunctionDefinitions object in this Model.

Returns: the nth FunctionDefinition of this Model.

FunctionDefinition libsbmlcs.Model.getFunctionDefinition ( string sid )

inherited

Get a FunctionDefinition object based on its identifier.

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

override int libsbmlcs.SBase.GetHashCode ( )

inherited

new string libsbmlcs.Model.getId ( )

inherited

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

Returns: the id of this Model.

InitialAssignment libsbmlcs.Model.getInitialAssignment ( long n )

inherited

Get the nth InitialAssignment object in this Model.

Returns: the nth InitialAssignment of this Model.

InitialAssignment libsbmlcs.Model.getInitialAssignment ( string symbol )

inherited

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

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

InitialAssignment libsbmlcs.Model.getInitialAssignmentBySymbol ( string symbol )

inherited

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

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

string libsbmlcs.Model.getLengthUnits ( )

inherited

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

Returns: the line number of this SBML object.

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

See also: getColumn()

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 ( )

inherited

Get the ListOfCompartments object in this Model.

Returns: the list of Compartments for this Model.

ListOfCompartmentTypes libsbmlcs.Model.getListOfCompartmentTypes ( )

inherited

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 ( )

inherited

Get the ListOfConstraints object in this Model.

Returns: the list of Constraints for this Model.

ListOfEvents libsbmlcs.Model.getListOfEvents ( )

inherited

Get the ListOfEvents object in this Model.

Returns: the list of Events for this Model.

ListOfFunctionDefinitions libsbmlcs.Model.getListOfFunctionDefinitions ( )

inherited

Get the ListOfFunctionDefinitions object in this Model.

Returns: the list of FunctionDefinitions for this Model.

ListOfInitialAssignments libsbmlcs.Model.getListOfInitialAssignments ( )

inherited

Get the ListOfInitialAssignments object in this Model.

Returns: the list of InitialAssignments for this Model.

ListOfParameters libsbmlcs.Model.getListOfParameters ( )

inherited

Get the ListOfParameters object in this Model.

Returns: the list of Parameters for this Model.

ListOfReactions libsbmlcs.Model.getListOfReactions ( )

inherited

Get the ListOfReactions object in this Model.

Returns: the list of Reactions for this Model.

ListOfRules libsbmlcs.Model.getListOfRules ( )

inherited

Get the ListOfRules object in this Model.

Returns: the list of Rules for this Model.

ListOfSpecies libsbmlcs.Model.getListOfSpecies ( )

inherited

Get the ListOfSpecies object in this Model.

Returns: the list of Species for this Model.

ListOfSpeciesTypes libsbmlcs.Model.getListOfSpeciesTypes ( )

inherited

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 ( )

inherited

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 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 )

inherited

Get a ModifierSpeciesReference object based on its identifier.

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

new string libsbmlcs.Model.getName ( )

inherited

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

Returns: the name of this Model.

XMLNamespaces libsbmlcs.SBase.getNamespaces ( )

inherited

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

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

inherited

Get the number of Compartment objects in this Model.

Returns: the number of Compartments in this Model.

long libsbmlcs.Model.getNumCompartmentTypes ( )

inherited

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 ( )

inherited

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.Model.getNumEvents ( )

inherited

Get the number of Event objects in this Model.

Returns: the number of Events in this Model.

long libsbmlcs.Model.getNumFunctionDefinitions ( )

inherited

Get the number of FunctionDefinition objects in this Model.

Returns: the number of FunctionDefinitions in this Model.

long libsbmlcs.Model.getNumInitialAssignments ( )

inherited

Get the number of InitialAssignment objects in this Model.

Returns: the number of InitialAssignments in this Model.

long libsbmlcs.Model.getNumParameters ( )

inherited

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.

long libsbmlcs.Model.getNumReactions ( )

inherited

Get the number of Reaction objects in this Model.

Returns: the number of Reactions in this Model.

long libsbmlcs.Model.getNumRules ( )

inherited

Get the number of Rule objects in this Model.

Returns: the number of Rules in this Model.

long libsbmlcs.Model.getNumSpecies ( )

inherited

Get the number of Specie objects in this Model.

Returns: the number of Species in this Model.

long libsbmlcs.Model.getNumSpeciesTypes ( )

inherited

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 ( )

inherited

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 ( )

inherited

Get the number of UnitDefinition objects in this Model.

Returns: the number of UnitDefinitions in this Model.

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 )

inherited

Get the nth Parameter object in this Model.

Returns: the nth Parameter of this Model.

Parameter libsbmlcs.Model.getParameter ( string sid )

inherited

Get a Parameter object based on its identifier.

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

SBase 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.

*

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.

SBasePlugin libsbmlcs.SBase.getPlugin ( long n )

inherited

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

*

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

string libsbmlcs.SBase.getPrefix ( )

inherited

Returns the namespace prefix of this element.

RateRule libsbmlcs.Model.getRateRule ( string variable )

inherited

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

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

RateRule libsbmlcs.Model.getRateRuleByVariable ( string variable )

inherited

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

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

Reaction libsbmlcs.Model.getReaction ( long n )

inherited

Get the nth Reaction object in this Model.

Returns: the nth Reaction of this Model.

Reaction libsbmlcs.Model.getReaction ( string sid )

inherited

Get a Reaction object based on its identifier.

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

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 )

inherited

Get the nth Rule object in this Model.

Returns: the nth Rule of this Model.

Rule libsbmlcs.Model.getRule ( string variable )

inherited

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

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

Rule libsbmlcs.Model.getRuleByVariable ( string variable )

inherited

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

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

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()

SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )

inherited

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 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

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

string libsbmlcs.SBase.getSBOTermAsURL ( )

inherited

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

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns: the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.

string libsbmlcs.SBase.getSBOTermID ( )

inherited

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

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

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

Species libsbmlcs.Model.getSpecies ( long n )

inherited

Get the nth Species object in this Model.

Returns: the nth Species of this Model.

Species libsbmlcs.Model.getSpecies ( string sid )

inherited

Get a Species object based on its identifier.

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

SpeciesReference libsbmlcs.Model.getSpeciesReference ( string sid )

inherited

Get a SpeciesReference object based on its identifier.

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

SpeciesType libsbmlcs.Model.getSpeciesType ( long n )

inherited

Get the nth SpeciesType object in this Model.

Returns: the nth SpeciesType of this Model.

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

SpeciesType libsbmlcs.Model.getSpeciesType ( string sid )

inherited

Get a SpeciesType object based on its identifier.

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

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

string libsbmlcs.Model.getSubstanceUnits ( )

inherited

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 ( )

inherited

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

Returns: the timeUnits of this Model.

Note: The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

int libsbmlcs.ModelDefinition.getTypeCode ( )

Returns the libSBML type code of this object instance.

*

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 getPackageName() method on the object.

Returns: the SBML type code for this object: SBML_COMP_MODELDEFINITION

*

Warning: The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().

See also: getElementName(); getPackageName()

UnitDefinition libsbmlcs.Model.getUnitDefinition ( long n )

inherited

Get the nth UnitDefinition object in this Model.

Returns: the nth UnitDefinition of this Model.

UnitDefinition libsbmlcs.Model.getUnitDefinition ( string sid )

inherited

Get a UnitDefinition based on its identifier.

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 willreturn the XML namespace to which this element belongs.

Returns: the URI of this element

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 ( )

inherited

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

Returns: the volumeUnits of this Model.

Note: The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

bool libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string prefix )

inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').

bool libsbmlcs.SBase.hasRequiredAttributes ( )

inherited

new bool libsbmlcs.Model.hasRequiredElements ( )

inherited

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

Note: The required elements for a Model object are: listOfCompartments (L1 only); listOfSpecies (L1V1 only); listOfReactions(L1V1 only)

Returns: a bool 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 3 Version 1 Core: 'http://www.sbml.org/sbml/level3/version1/core'

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

bool 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.isPopulatedListFormulaUnitsData ( )

inherited

Predicate returning true if the list of FormulaUnitsData is populated.

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

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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

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

bool libsbmlcs.Model.isSetLengthUnits ( )

inherited

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 ( )

inherited

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

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

bool 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 ( )

inherited

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 ( )

inherited

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.Model.isSetVolumeUnits ( )

inherited

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: bool, 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: bool, true if this object's collection of namespaces is the same as sb's, false otherwise.

void libsbmlcs.SBase.multiplyAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

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

staticinherited

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

staticinherited

void libsbmlcs.Model.populateListFormulaUnitsData ( )

inherited

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

The list contains elements of class FormulaUnitsData.

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

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

The next elements record the units of any parameters.

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

Note: This function is utilised by the Unit Consistency Validator. The list is populated prior to running the validation and thus the consistency of units can be checked by accessing the members of the list and comparing the appropriate data.

int libsbmlcs.SBase.prependStringToAllIdentifiers ( string prefix )

inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

Compartment libsbmlcs.Model.removeCompartment ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Compartment libsbmlcs.Model.removeCompartment ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the Compartment objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the Compartment object to remove

Returns: the Compartment object removed. As mentioned above, the caller owns the returned object. null is returned if no Compartment object with the identifier exists in this Model object.

CompartmentType libsbmlcs.Model.removeCompartmentType ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

CompartmentType libsbmlcs.Model.removeCompartmentType ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the CompartmentType objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the object to remove

Returns: the CompartmentType object removed. As mentioned above, the caller owns the returned object. null is returned if no CompartmentType object with the identifier exists in this Model object.

Constraint libsbmlcs.Model.removeConstraint ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Event libsbmlcs.Model.removeEvent ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Event libsbmlcs.Model.removeEvent ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the Event objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the Event object to remove

Returns: the Event object removed. As mentioned above, the caller owns the returned object. null is returned if no Event object with the identifier exists in this Model object.

int libsbmlcs.ModelDefinition.removeFromParentAndDelete ( )

Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself.

This method actually just calls the SBase function, since the Model class overrides it, but that's actually what we want to happen here.

Returns

integer value indicating success/failure of the operation. The possible return values are:

FunctionDefinition libsbmlcs.Model.removeFunctionDefinition ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

FunctionDefinition libsbmlcs.Model.removeFunctionDefinition ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the FunctionDefinition objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the FunctionDefinition object to remove

Returns: the FunctionDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if no FunctionDefinition object with the identifier exists in this Model object.

InitialAssignment libsbmlcs.Model.removeInitialAssignment ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

InitialAssignment libsbmlcs.Model.removeInitialAssignment ( string symbol )

inherited

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. If none of the InitialAssignment objects in this Model object have the 'symbol' attribute symbol, then null is returned.

Parameters

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

Returns: the InitialAssignment object removed. As mentioned above, the caller owns the returned object. null is returned if no InitialAssignment object with the 'symbol' attribute exists in this Model object.

Parameter libsbmlcs.Model.removeParameter ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Parameter libsbmlcs.Model.removeParameter ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the Parameter objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the Parameter object to remove

Returns: the Parameter object removed. As mentioned above, the caller owns the returned object. null is returned if no Parameter object with the identifier exists in this Model object.

void libsbmlcs.Model.removeParameterRuleUnits ( bool strict )

inherited

Reaction libsbmlcs.Model.removeReaction ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Reaction libsbmlcs.Model.removeReaction ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the Reaction objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the Reaction object to remove

Returns: the Reaction object removed. As mentioned above, the caller owns the returned object. null is returned if no Reaction object with the identifier exists in this Model object.

Rule libsbmlcs.Model.removeRule ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Rule libsbmlcs.Model.removeRule ( string variable )

inherited

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. If none of the Rule objects in this Model object have the 'variable' attribute variable, then null is returned.

Parameters

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

Returns: the Rule object removed. As mentioned above, the caller owns the returned object. null is returned if no Rule object with the 'variable' attribute exists in this Model object.

Species libsbmlcs.Model.removeSpecies ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

Species libsbmlcs.Model.removeSpecies ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the Species objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the Species object to remove

Returns: the Species object removed. As mentioned above, the caller owns the returned object. null is returned if no Species object with the identifier exists in this Model object.

SpeciesType libsbmlcs.Model.removeSpeciesType ( long n )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

SpeciesType libsbmlcs.Model.removeSpeciesType ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the SpeciesType objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the SpeciesType object to remove

Returns: the SpeciesType object removed. As mentioned above, the caller owns the returned object. null is returned if no SpeciesType object with the identifier exists in this Model object.

int 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 )

inherited

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. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.

UnitDefinition libsbmlcs.Model.removeUnitDefinition ( string sid )

inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the UnitDefinition objects in this Model object have the identifier sid, then null is returned.

Parameters

sid	the identifier of the UnitDefinition object to remove

Returns: the UnitDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if no UnitDefinition object with the identifier exists in this Model object.

int libsbmlcs.Model.renameAllIds	(	IdentifierTransformer	idTransformer,
		ElementFilter	filter
	)

inherited

int libsbmlcs.Model.renameAllIds ( IdentifierTransformer idTransformer )

inherited

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

inherited

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

inherited

Renames all the meta-identifier attributes on this element.

*

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

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

inherited

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

*

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 SIdRefin 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, 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

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

inherited

Renames all the UnitSIdRef attributes on this element.

*

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 unit 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

void libsbmlcs.SBase.replaceSIDWithFunction	(	string	id,
		ASTNode	function
	)

inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note: This function does nothing itself—subclasses with ASTNode subelements must override this function.

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); 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 )

inherited

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. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also: appendAnnotation(XMLNode annotation)

new int libsbmlcs.Model.setAnnotation ( string annotation )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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 )

inherited

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

The string sid is copied.

*

SBML has strict requirements for the syntax of identifiers, that is, the values of the 'id' attribute present on most types of SBML objects. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact details of the uniqueness requirements.

Parameters

sid	the string to use as the identifier of this Model

Returns

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

int libsbmlcs.Model.setLengthUnits ( string units )

inherited

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 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 )

inherited

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

The string in name is copied.

Parameters

name	the new name for the Model

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 bool 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 bool 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 sbmlns )

inherited

int libsbmlcs.SBase.setSBOTerm ( int value )

inherited

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters

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)

int libsbmlcs.SBase.setSBOTerm ( string sboid )

inherited

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

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters

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 )

inherited

void libsbmlcs.Model.setSpatialDimensions ( )

inherited

void libsbmlcs.Model.setSpeciesReferenceConstantValueAndStoichiometry ( )

inherited

int libsbmlcs.Model.setSubstanceUnits ( string units )

inherited

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 )

inherited

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 )

inherited

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.transformIdentifiers ( IdentifierTransformer idTransformer )

inherited

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. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

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

int libsbmlcs.Model.unsetAreaUnits ( )

inherited

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 ( )

inherited

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 ( )

inherited

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 ( )

inherited

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

Returns

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

int libsbmlcs.Model.unsetLengthUnits ( )

inherited

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 ( )

inherited

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

Returns

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

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. The possible values returned by this function are:

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 ( )

inherited

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 ( )

inherited

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.Model.unsetVolumeUnits ( )

inherited

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.

void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream stream )

inherited

Writes out contained SBML objects of package extensions (if any) as XML elements.

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation