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libSBML C# API
5.18.0
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libSBML C# API
5.18.0
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The Hierarchical Model Composition (“comp”) package 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... | |
| new int | appendFrom (Model model) |
| Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model. More... | |
| int | appendNotes (XMLNode notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
| int | appendNotes (string notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
| void | assignRequiredValues () |
| int | checkCompatibility (SBase arg0) |
| string | checkMathMLNamespace (XMLToken elem) |
| void | clearAllElementIdList () |
| Clears the internal list of the identifiers of all elements within this Model object. More... | |
| void | clearAllElementMetaIdList () |
| Clears the internal list of the metaids of all elements within this Model object. More... | |
| new SBase | clone () |
| Creates and returns a deep copy of this ModelDefinition object. More... | |
| override void | connectToChild () |
| void | convertFromL3V2 (bool strict) |
| void | convertFromL3V2 () |
| void | convertL1ToL2 () |
| void | convertL1ToL3 (bool addDefaultUnits) |
| void | convertL1ToL3 () |
| void | convertL2ToL1 (bool strict) |
| void | convertL2ToL1 () |
| void | convertL2ToL3 (bool strict, bool addDefaultUnits) |
| void | convertL2ToL3 (bool strict) |
| void | convertL2ToL3 () |
| void | convertL3ToL1 (bool strict) |
| void | convertL3ToL1 () |
| void | convertL3ToL2 (bool strict) |
| void | convertL3ToL2 () |
| void | convertParametersToLocals (long level, long version) |
| void | convertStoichiometryMath () |
| AlgebraicRule | createAlgebraicRule () |
| Creates a new AlgebraicRule inside this Model and returns it. More... | |
| AssignmentRule | createAssignmentRule () |
| Creates a new AssignmentRule inside this Model and returns it. More... | |
| Compartment | createCompartment () |
| Creates a new Compartment inside this Model and returns it. More... | |
| CompartmentType | createCompartmentType () |
| Creates a new CompartmentType inside this Model and returns it. More... | |
| Constraint | createConstraint () |
| Creates a new Constraint inside this Model and returns it. More... | |
| Delay | createDelay () |
| Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it. More... | |
| Event | createEvent () |
| Creates a new Event inside this Model and returns it. More... | |
| EventAssignment | createEventAssignment () |
| Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it. More... | |
| FunctionDefinition | createFunctionDefinition () |
| Creates a new FunctionDefinition inside this Model and returns it. More... | |
| InitialAssignment | createInitialAssignment () |
| Creates a new InitialAssignment inside this Model and returns it. More... | |
| KineticLaw | createKineticLaw () |
| Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it. More... | |
| LocalParameter | createKineticLawLocalParameter () |
| Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More... | |
| Parameter | createKineticLawParameter () |
| Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More... | |
| ModifierSpeciesReference | createModifier () |
| Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it. More... | |
| Parameter | createParameter () |
| Creates a new Parameter inside this Model and returns it. More... | |
| SpeciesReference | createProduct () |
| Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it. More... | |
| RateRule | createRateRule () |
| Creates a new RateRule inside this Model and returns it. More... | |
| SpeciesReference | createReactant () |
| Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it. More... | |
| Reaction | createReaction () |
| Creates a new Reaction inside this Model and returns it. More... | |
| Species | createSpecies () |
| Creates a new Species inside this Model and returns it. More... | |
| SpeciesType | createSpeciesType () |
| Creates a new SpeciesType inside this Model and returns it. More... | |
| Trigger | createTrigger () |
| Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it. More... | |
| Unit | createUnit () |
| Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it. More... | |
| UnitDefinition | createUnitDefinition () |
| Creates a new UnitDefinition inside this Model and returns it. More... | |
| void | dealWithDefaultValues () |
| void | dealWithEvents (bool strict) |
| void | dealWithFast () |
| void | dealWithL3Fast (long targetVersion) |
| void | dealWithModelUnits (bool strict) |
| void | dealWithModelUnits () |
| void | dealWithStoichiometry () |
| void | deleteDisabledPlugins (bool recursive) |
| Deletes all information stored in disabled plugins. More... | |
| void | deleteDisabledPlugins () |
| Deletes all information stored in disabled plugins. More... | |
| int | disablePackage (string pkgURI, string pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| override void | Dispose () |
| int | enablePackage (string pkgURI, string pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| override bool | Equals (Object sb) |
| IdList | getAllElementIdList () |
| Returns the internal list of the identifiers of all elements within this Model object. More... | |
| IdList | getAllElementMetaIdList () |
| Returns the internal list of the metaids of all elements within this Model object. More... | |
| SBase | getAncestorOfType (int type, string pkgName) |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| SBase | getAncestorOfType (int type) |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| XMLNode | getAnnotation () |
| Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
| string | getAnnotationString () |
| Returns the content of the 'annotation' subelement of this object as a character string. More... | |
| string | getAreaUnits () |
| Returns the value of the 'areaUnits' attribute of this Model. More... | |
| AssignmentRule | getAssignmentRule (string variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| AssignmentRule | getAssignmentRuleByVariable (string variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| long | getColumn () |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| Compartment | getCompartment (long n) |
| Get the nth Compartment object in this Model. More... | |
| Compartment | getCompartment (string sid) |
| Get a Compartment object based on its identifier. More... | |
| CompartmentType | getCompartmentType (long n) |
| Get the nth CompartmentType object in this Model. More... | |
| CompartmentType | getCompartmentType (string sid) |
| Get a CompartmentType object based on its identifier. More... | |
| Constraint | getConstraint (long n) |
| Get the nth Constraint object in this Model. More... | |
| string | getConversionFactor () |
| Returns the value of the 'conversionFactor' attribute of this Model. More... | |
| CVTerm | getCVTerm (long n) |
| Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
| CVTermList | getCVTerms () |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| SBasePlugin | getDisabledPlugin (long n) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| new SBase | getElementByMetaId (string metaid) |
Returns the first child element it can find with the given metaid. More... | |
| new SBase | getElementBySId (string id) |
Returns the first child element found that has the given id. More... | |
| new string | getElementName () |
| Returns the XML element name of this object. More... | |
| Event | getEvent (long n) |
| Get the nth Event object in this Model. More... | |
| Event | getEvent (string sid) |
| Get an Event object based on its identifier. More... | |
| string | getExtentUnits () |
| Returns the value of the 'extentUnits' attribute of this Model. More... | |
| SWIGTYPE_p_FormulaUnitsData | getFormulaUnitsDataForAssignment (string sid) |
| SWIGTYPE_p_FormulaUnitsData | getFormulaUnitsDataForVariable (string sid) |
| FunctionDefinition | getFunctionDefinition (long n) |
| Get the nth FunctionDefinitions object in this Model. More... | |
| FunctionDefinition | getFunctionDefinition (string sid) |
| Get a FunctionDefinition object based on its identifier. More... | |
| override int | GetHashCode () |
| new string | getId () |
| Returns the value of the 'id' attribute of this Model. More... | |
| string | getIdAttribute () |
| Returns the value of the 'id' attribute of this SBML object. More... | |
| InitialAssignment | getInitialAssignment (long n) |
| Get the nth InitialAssignment object in this Model. More... | |
| InitialAssignment | getInitialAssignment (string symbol) |
| Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
| InitialAssignment | getInitialAssignmentBySymbol (string symbol) |
| Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
| string | getLengthUnits () |
| Returns the value of the 'lengthUnits' attribute of this Model. More... | |
| long | getLevel () |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| long | getLine () |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| SBaseList | getListOfAllElements (ElementFilter filter) |
| SBaseList | getListOfAllElements () |
| SBaseList | getListOfAllElementsFromPlugins (ElementFilter filter) |
| SBaseList | getListOfAllElementsFromPlugins () |
| ListOfCompartments | getListOfCompartments () |
| Get the ListOfCompartments object in this Model. More... | |
| ListOfCompartmentTypes | getListOfCompartmentTypes () |
| Get the ListOfCompartmentTypes object in this Model. More... | |
| ListOfConstraints | getListOfConstraints () |
| Get the ListOfConstraints object in this Model. More... | |
| ListOfEvents | getListOfEvents () |
| Get the ListOfEvents object in this Model. More... | |
| ListOfFunctionDefinitions | getListOfFunctionDefinitions () |
| Get the ListOfFunctionDefinitions object in this Model. More... | |
| ListOfInitialAssignments | getListOfInitialAssignments () |
| Get the ListOfInitialAssignments object in this Model. More... | |
| ListOfParameters | getListOfParameters () |
| Get the ListOfParameters object in this Model. More... | |
| ListOfReactions | getListOfReactions () |
| Get the ListOfReactions object in this Model. More... | |
| ListOfRules | getListOfRules () |
| Get the ListOfRules object in this Model. More... | |
| ListOfSpecies | getListOfSpecies () |
| Get the ListOfSpecies object in this Model. More... | |
| ListOfSpeciesTypes | getListOfSpeciesTypes () |
| Get the ListOfSpeciesTypes object in this Model. More... | |
| ListOfUnitDefinitions | getListOfUnitDefinitions () |
| Get the ListOfUnitDefinitions object in this Model. More... | |
| string | getMetaId () |
| Returns the value of the 'metaid' attribute of this SBML object. More... | |
| Model | getModel () |
| Returns the Model object for the SBML Document in which the current object is located. More... | |
| ModelHistory | getModelHistory () |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| ModifierSpeciesReference | getModifierSpeciesReference (string sid) |
| Get a ModifierSpeciesReference object based on its identifier. More... | |
| new string | getName () |
| Returns the value of the 'name' attribute of this Model object. More... | |
| new XMLNamespaces | getNamespaces () |
| Returns a list of the XML Namespaces declared on the SBML document owning this object. More... | |
| XMLNode | getNotes () |
| Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
| string | getNotesString () |
| Returns the content of the 'notes' subelement of this object as a string. More... | |
| long | getNumCompartments () |
| Get the number of Compartment objects in this Model. More... | |
| long | getNumCompartmentTypes () |
| Get the number of CompartmentType objects in this Model. More... | |
| long | getNumConstraints () |
| Get the number of Constraint objects in this Model. More... | |
| long | getNumCVTerms () |
| Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
| long | getNumDisabledPlugins () |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More... | |
| long | getNumEvents () |
| Get the number of Event objects in this Model. More... | |
| long | getNumFunctionDefinitions () |
| Get the number of FunctionDefinition objects in this Model. More... | |
| long | getNumInitialAssignments () |
| Get the number of InitialAssignment objects in this Model. More... | |
| long | getNumParameters () |
| Get the number of Parameter objects in this Model. More... | |
| long | getNumPlugins () |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| long | getNumReactions () |
| Get the number of Reaction objects in this Model. More... | |
| long | getNumRules () |
| Get the number of Rule objects in this Model. More... | |
| long | getNumSpecies () |
| Get the number of Species objects in this Model. More... | |
| long | getNumSpeciesTypes () |
| Get the number of SpeciesType objects in this Model. More... | |
| long | getNumSpeciesWithBoundaryCondition () |
Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true. More... | |
| long | getNumUnitDefinitions () |
| Get the number of UnitDefinition objects in this Model. More... | |
| long | getPackageCoreVersion () |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| string | getPackageName () |
| Returns the name of the SBML Level 3 package in which this element is defined. More... | |
| long | getPackageVersion () |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| Parameter | getParameter (long n) |
| Get the nth Parameter object in this Model. More... | |
| Parameter | getParameter (string sid) |
| Get a Parameter object based on its identifier. More... | |
| SBase | getParentSBMLObject () |
| Returns the parent SBML object containing this object. More... | |
| SBasePlugin | getPlugin (string package) |
| Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
| SBasePlugin | getPlugin (long n) |
| Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| string | getPrefix () |
| Returns the XML namespace prefix of this element. More... | |
| RateRule | getRateRule (string variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| RateRule | getRateRuleByVariable (string variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| Reaction | getReaction (long n) |
| Get the nth Reaction object in this Model. More... | |
| Reaction | getReaction (string sid) |
| Get a Reaction object based on its identifier. More... | |
| int | getResourceBiologicalQualifier (string resource) |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| int | getResourceModelQualifier (string resource) |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| Rule | getRule (long n) |
| Get the nth Rule object in this Model. More... | |
| Rule | getRule (string variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| Rule | getRuleByVariable (string variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| SBMLDocument | getSBMLDocument () |
| Returns the SBMLDocument object containing this object instance. More... | |
| int | getSBOTerm () |
| Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
| string | getSBOTermAsURL () |
| Returns the URL representation of the 'sboTerm' attribute of this object. More... | |
| string | getSBOTermID () |
| Returns the string representation of the 'sboTerm' attribute of this object. More... | |
| Species | getSpecies (long n) |
| Get the nth Species object in this Model. More... | |
| Species | getSpecies (string sid) |
| Get a Species object based on its identifier. More... | |
| SpeciesReference | getSpeciesReference (string sid) |
| Get a SpeciesReference object based on its identifier. More... | |
| SpeciesType | getSpeciesType (long n) |
| Get the nth SpeciesType object in this Model. More... | |
| SpeciesType | getSpeciesType (string sid) |
| Get a SpeciesType object based on its identifier. More... | |
| string | getSubstanceUnits () |
| Returns the value of the 'substanceUnits' attribute of this Model. More... | |
| string | getTimeUnits () |
| Returns the value of the 'timeUnits' attribute of this Model. More... | |
| new int | getTypeCode () |
| Returns the libSBML type code 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... | |
| new bool | hasRequiredElements () |
Predicate returning true if all the required elements for this Model object have been set. More... | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| bool | isPackageEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPackageURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isPkgEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPkgURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isPopulatedAllElementIdList () |
Predicate returning true if libSBML has a list of the ids of all components of this model. More... | |
| bool | isPopulatedAllElementMetaIdList () |
Predicate returning true if libSBML has a list of the metaids of all components of this model. More... | |
| bool | isPopulatedListFormulaUnitsData () |
Predicate returning true if libSBML has derived units for the components of this model. More... | |
| bool | isSetAnnotation () |
Predicate returning true if this object's 'annotation' subelement exists and has content. More... | |
| bool | isSetAreaUnits () |
Predicate returning true if this Model's 'areaUnits' attribute is set. More... | |
| bool | isSetConversionFactor () |
Predicate returning true if this Model's 'conversionFactor' attribute is set. More... | |
| bool | isSetExtentUnits () |
Predicate returning true if this Model's 'extentUnits' attribute is set. More... | |
| new bool | isSetId () |
Predicate returning true if this Model's 'id' attribute is set. More... | |
| bool | isSetIdAttribute () |
Predicate returning true if this object's 'id' attribute is set. More... | |
| bool | isSetLengthUnits () |
Predicate returning true if this Model's 'lengthUnits' attribute is set. More... | |
| bool | isSetMetaId () |
Predicate returning true if this object's 'metaid' attribute is set. More... | |
| bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
| new bool | isSetName () |
Predicate returning true if this Model's 'name' attribute is set. More... | |
| bool | isSetNotes () |
Predicate returning true if this object's 'notes' subelement exists and has content. More... | |
| bool | isSetSBOTerm () |
Predicate returning true if this object's 'sboTerm' attribute is set. More... | |
| bool | isSetSubstanceUnits () |
Predicate returning true if this Model's 'substanceUnits' attribute is set. More... | |
| bool | isSetTimeUnits () |
Predicate returning true if this Model's 'timeUnits' attribute is set. More... | |
| bool | isSetUserData () |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| bool | isSetVolumeUnits () |
Predicate returning true if this Model's 'volumeUnits' attribute is set. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (SBase sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (SBase sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| 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 | populateAllElementIdList () |
| Populates the internal list of the identifiers of all elements within this Model object. More... | |
| void | populateAllElementMetaIdList () |
| Populates the internal list of the metaids of all elements within this Model object. More... | |
| void | populateListFormulaUnitsData () |
| Populates the internal list of derived units for this Model object. More... | |
| Compartment | removeCompartment (long n) |
| Removes the nth Compartment object from this Model object and returns a pointer to it. More... | |
| Compartment | removeCompartment (string sid) |
| Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More... | |
| CompartmentType | removeCompartmentType (long n) |
| Removes the nth CompartmentType object from this Model object and returns a pointer to it. More... | |
| CompartmentType | removeCompartmentType (string sid) |
| Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More... | |
| void | removeCompartmentTypes () |
| Constraint | removeConstraint (long n) |
| Removes the nth Constraint object from this Model object and returns a pointer to it. More... | |
| Event | removeEvent (long n) |
| Removes the nth Event object from this Model object and returns a pointer to it. More... | |
| Event | removeEvent (string sid) |
| Removes the Event object with the given identifier from this Model object and returns a pointer to it. More... | |
| new int | removeFromParentAndDelete () |
| 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... | |
| Rule | removeRuleByVariable (string variable) |
| Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it. More... | |
| Species | removeSpecies (long n) |
| Removes the nth Species object from this Model object and returns a pointer to it. More... | |
| Species | removeSpecies (string sid) |
| Removes the Species object with the given identifier from this Model object and returns a pointer to it. More... | |
| SpeciesType | removeSpeciesType (long n) |
| Removes the nth SpeciesType object from this Model object and returns a pointer to it. More... | |
| SpeciesType | removeSpeciesType (string sid) |
| Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More... | |
| void | removeSpeciesTypes () |
| int | removeTopLevelAnnotationElement (string elementName, string elementURI, bool removeEmpty) |
| Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
| int | removeTopLevelAnnotationElement (string elementName, string elementURI) |
| Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
| int | removeTopLevelAnnotationElement (string elementName) |
| Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
| UnitDefinition | removeUnitDefinition (long n) |
| Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More... | |
| UnitDefinition | removeUnitDefinition (string sid) |
| Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
| void | renameIDs (SBaseList elements, IdentifierTransformer idTransformer) |
| new void | renameMetaIdRefs (string oldid, string newid) |
| Replaces all uses of a given meta identifier attribute value with another value. More... | |
| new void | renameSIdRefs (string oldid, string newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
| new void | renameUnitSIdRefs (string oldid, string newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
| int | replaceTopLevelAnnotationElement (XMLNode annotation) |
| Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
| int | replaceTopLevelAnnotationElement (string annotation) |
| Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
| new int | setAnnotation (XMLNode annotation) |
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation. More... | |
| new int | setAnnotation (string annotation) |
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation. More... | |
| int | setAreaUnits (string units) |
| Sets the value of the 'areaUnits' attribute of this Model. More... | |
| int | setConversionFactor (string units) |
| Sets the value of the 'conversionFactor' attribute of this Model. More... | |
| int | setExtentUnits (string units) |
| Sets the value of the 'extentUnits' attribute of this Model. More... | |
| new int | setId (string sid) |
| Sets the value of the 'id' attribute of this Model. More... | |
| new int | setIdAttribute (string sid) |
| Sets the value of the 'id' attribute of this SBML object. More... | |
| int | setLengthUnits (string units) |
| Sets the value of the 'lengthUnits' attribute of this Model. More... | |
| int | setMetaId (string metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| int | setModelHistory (ModelHistory history) |
| Sets the ModelHistory of this object. More... | |
| new int | setName (string name) |
| Sets the value of the 'name' attribute of this Model. More... | |
| int | setNamespaces (XMLNamespaces xmlns) |
| Sets the namespaces relevant of this SBML object. More... | |
| int | setNotes (XMLNode notes) |
| Sets the value of the 'notes' subelement of this SBML object. More... | |
| int | setNotes (string notes, bool addXHTMLMarkup) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More... | |
| int | setNotes (string notes) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More... | |
| void | setSBMLNamespacesAndOwn (SBMLNamespaces disownedNs) |
| new int | setSBOTerm (int value) |
| Sets the value of the 'sboTerm' attribute. More... | |
| new int | setSBOTerm (string sboid) |
| Sets the value of the 'sboTerm' attribute by string. More... | |
| void | setSpatialDimensions (double dims) |
| void | setSpatialDimensions () |
| void | setSpeciesReferenceConstantValueAndStoichiometry () |
| int | setSubstanceUnits (string units) |
| Sets the value of the 'substanceUnits' attribute of this Model. More... | |
| int | setTimeUnits (string units) |
| Sets the value of the 'timeUnits' attribute of this Model. More... | |
| int | setVolumeUnits (string units) |
| Sets the value of the 'volumeUnits' attribute of this Model. More... | |
| string | toSBML () |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| XMLNode | toXMLNode () |
| Returns this element as an XMLNode. More... | |
| int | unsetAnnotation () |
| Unsets the value of the 'annotation' subelement of this SBML object. More... | |
| int | unsetAreaUnits () |
| Unsets the value of the 'areaUnits' attribute of this Model. More... | |
| int | unsetConversionFactor () |
| Unsets the value of the 'conversionFactor' attribute of this Model. More... | |
| int | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| int | unsetExtentUnits () |
| Unsets the value of the 'extentUnits' attribute of this Model. More... | |
| new int | unsetId () |
| Unsets the value of the 'id' attribute of this Model. More... | |
| int | unsetIdAttribute () |
| Unsets the value of the 'id' attribute of this SBML object. More... | |
| int | unsetLengthUnits () |
| Unsets the value of the 'lengthUnits' attribute of this Model. More... | |
| int | unsetMetaId () |
| Unsets the value of the 'metaid' attribute of this SBML object. More... | |
| int | unsetModelHistory () |
| Unsets the ModelHistory object attached to this object. More... | |
| new int | unsetName () |
| Unsets the value of the 'name' attribute of this Model. More... | |
| int | unsetNotes () |
| Unsets the value of the 'notes' subelement of this SBML object. More... | |
| int | unsetSBOTerm () |
| Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
| int | unsetSubstanceUnits () |
| Unsets the value of the 'substanceUnits' attribute of this Model. More... | |
| int | unsetTimeUnits () |
| Unsets the value of the 'timeUnits' attribute of this Model. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
| int | unsetVolumeUnits () |
| Unsets the value of the 'volumeUnits' attribute of this Model. More... | |
Static Public Member Functions | |
| static bool | operator!= (SBase lhs, SBase rhs) |
| static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
| bool | swigCMemOwn |
| libsbmlcs.ModelDefinition.ModelDefinition | ( | long | level, |
| long | version, | ||
| long | pkgVersion | ||
| ) |
Creates a new ModelDefinition with the given level, version, and package version.
| 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.
| 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.
| 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.
| 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.
The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
| compns | the CompPkgNamespaces object. |
| libsbmlcs.ModelDefinition.ModelDefinition | ( | Model | source | ) |
Copy constructor from base Model object.
| source | the instance to copy. |
|
inherited |
Adds a copy of the given Compartment object to this Model.
| c | the Compartment object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given CompartmentType object to this Model.
| ct | the CompartmentType object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
|
inherited |
Adds a copy of the given Constraint object to this Model.
| c | the Constraint object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| 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. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
| 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. |
create) for alternatives that do not lead to these issues.
|
inherited |
|
inherited |
Adds a copy of the given Event object to this Model.
| e | the Event object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given FunctionDefinition object to this Model.
| fd | the FunctionDefinition to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given InitialAssignment object to this Model.
| ia | the InitialAssignment object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
|
inherited |
Adds a copy of the given Parameter object to this Model.
| p | the Parameter object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given Reaction object to this Model.
| r | the Reaction object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given Rule object to this Model.
| r | the Rule object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given Species object to this Model.
| s | the Species object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given SpeciesType object to this Model.
| st | the SpeciesType object to add. |
create) for alternatives that do not lead to these issues.
|
inherited |
Adds a copy of the given UnitDefinition object to this Model.
| ud | the UnitDefinition object to add. |
create) for alternatives that do not lead to these issues.
|
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.
| annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object. |
|
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.
| annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object. |
|
inherited |
Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model.
This method also calls the appendFrom method on all libSBML plug-in objects.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| model | the Model to merge with this one. |
|
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.
| notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object. |
|
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.
| notes | an XML string that is to appended to the content of the 'notes' subelement of this object. |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Clears the internal list of the identifiers of all elements within this Model object.
|
inherited |
Clears the internal list of the metaids of all elements within this Model object.
| new SBase libsbmlcs.ModelDefinition.clone | ( | ) |
Creates and returns a deep copy of this ModelDefinition object.
|
virtualinherited |
Reimplemented from libsbmlcs.SBase.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
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.
|
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.
|
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.
|
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.
|
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.
|
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 EventAssignment is not created and null is returned instead.
|
inherited |
|
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.
|
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.
|
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.
|
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, a new SpeciesReference is not created and null is returned instead.
null is returned.
|
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.
null is returned.
|
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.
null is returned.
|
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 SpeciesReference is not created and null is returned instead.
null is returned.
|
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.
|
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.
null is returned.
|
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.
|
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.
null is returned.
|
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.
|
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.
|
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.
|
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 EventAssignment is not created and null is returned instead.
|
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.
|
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.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
inherited |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
| recursive | if true, the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
inherited |
Disables the given SBML Level 3 package on this object.
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
|
virtual |
Reimplemented from libsbmlcs.Model.
|
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).
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (true) or disable (false) the package. |
|
inherited |
|
inherited |
|
inherited |
|
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.
| 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. |
null if no ancestor exists.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.
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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.
| 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. |
null if no ancestor exists.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.
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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.
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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.
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inherited |
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inherited |
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inherited |
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inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.
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inherited |
Get the nth Compartment object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
Get a Compartment object based on its identifier.
| sid | the identifier to search for. |
sid or null if no such Compartment exists.
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inherited |
Get the nth CompartmentType object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
Get a CompartmentType object based on its identifier.
| sid | the identifier to search for. |
sid or null if no such CompartmentType exists.
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inherited |
Get the nth Constraint object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
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inherited |
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inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
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inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
If no such plugin exists, null is returned.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
| n | the index of the disabled plug-in to return. |
n is invalid, null is returned.
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inherited |
Returns the first child element it can find with the given metaid.
| metaid | string representing the meta-identifier of the object to find. |
metaid, or null if no such object is found.
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inherited |
Returns the first child element found that has the given id.
This operation searches the model-wide SId identifier type namespace
| id | string representing the id of the object to find. |
id, or null if no such object is found. | new string libsbmlcs.ModelDefinition.getElementName | ( | ) |
Returns the XML element name of this object.
The only difference between a Model and a ModelDefinition is the element name ('modelDefinition').
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inherited |
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inherited |
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inherited |
|
inherited |
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inherited |
Get the nth FunctionDefinitions object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
Get a FunctionDefinition object based on its identifier.
| sid | the identifier to search for. |
sid or null if no such FunctionDefinition exists.
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inherited |
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inherited |
Returns the value of the 'id' attribute of this Model.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
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inherited |
Returns the value of the 'id' attribute of this SBML object.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
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inherited |
Get the nth InitialAssignment object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
Get an InitialAssignment object based on the symbol to which it assigns a value.
| symbol | the symbol to search for. |
null if no such InitialAssignment exists.
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inherited |
Get an InitialAssignment object based on the symbol to which it assigns a value.
| symbol | the symbol to search for. |
null if no such InitialAssignment exists.
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inherited |
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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.)
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Returns the line number where this object first appears in the XML representation of the SBML document.
0.
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
Get the ListOfCompartments object in this Model.
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inherited |
Get the ListOfCompartmentTypes object in this Model.
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inherited |
Get the ListOfConstraints object in this Model.
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inherited |
Get the ListOfEvents object in this Model.
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inherited |
Get the ListOfFunctionDefinitions object in this Model.
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inherited |
Get the ListOfInitialAssignments object in this Model.
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inherited |
Get the ListOfParameters object in this Model.
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inherited |
Get the ListOfReactions object in this Model.
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inherited |
Get the ListOfRules object in this Model.
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inherited |
Get the ListOfSpecies object in this Model.
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inherited |
Get the ListOfSpeciesTypes object in this Model.
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inherited |
Get the ListOfUnitDefinitions object in this Model.
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inherited |
Returns the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
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inherited |
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inherited |
Returns the ModelHistory object, if any, attached to this object.
null if none exist.
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inherited |
Get a ModifierSpeciesReference object based on its identifier.
| sid | the identifier to search for. |
sid or null if no such ModifierSpeciesReference exists.
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inherited |
Returns the value of the 'name' attribute of this Model object.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
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inherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
null in certain very usual circumstances where a namespace is not set.
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inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
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inherited |
Returns the content of the 'notes' subelement of this object as a string.
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
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inherited |
Get the number of Compartment objects in this Model.
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inherited |
Get the number of CompartmentType objects in this Model.
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inherited |
Get the number of Constraint objects in this Model.
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inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
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inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
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inherited |
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inherited |
Get the number of FunctionDefinition objects in this Model.
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inherited |
Get the number of InitialAssignment objects in this Model.
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inherited |
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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.
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inherited |
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inherited |
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inherited |
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inherited |
Get the number of SpeciesType objects in this Model.
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inherited |
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inherited |
Get the number of UnitDefinition objects in this Model.
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inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
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inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"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.
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inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0 will be returned if this element belongs to the SBML Level 3 Core package.
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inherited |
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inherited |
|
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.
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inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin('fbc') will return an FbcModelPlugin; calling Parameter::getPlugin('comp') will return CompSBasePlugin, etc.
If no such plugin exists, null is returned.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| package | the name or URI of the package. |
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inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin('fbc') will return an FbcModelPlugin; calling Parameter::getPlugin('comp') will return CompSBasePlugin, etc.
If no such plugin exists, null is returned.
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
| n | the index of the plug-in to return. |
n is invalid, null is returned.
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inherited |
Returns the XML namespace prefix of this element.
This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.
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inherited |
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inherited |
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inherited |
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inherited |
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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.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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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.
| resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'. |
BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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inherited |
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inherited |
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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.
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inherited |
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
-1 if the value is not set.
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inherited |
Returns the URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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inherited |
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inherited |
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inherited |
Get a SpeciesReference object based on its identifier.
| sid | the identifier to search for. |
sid or null if no such SpeciesReference exists.
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inherited |
Get the nth SpeciesType object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
Get a SpeciesType object based on its identifier.
| sid | the identifier to search for. |
sid or null if no such SpeciesType exists.
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inherited |
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inherited |
| new 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 SBase::getPackageName() method on the object.
The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
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inherited |
Get the nth UnitDefinition object in this Model.
| n | the index of the object to return. |
n is invalid, null is returned.
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inherited |
Get a UnitDefinition based on its identifier.
| sid | the identifier to search for. |
sid or null if no such UnitDefinition exists.
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inherited |
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.
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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.)
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inherited |
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inherited |
Predicate returning true if all the required elements for this Model object have been set.
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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:
http://www.sbml.org/sbml/level1" http://www.sbml.org/sbml/level2" http://www.sbml.org/sbml/level2/version2" http://www.sbml.org/sbml/level2/version3" http://www.sbml.org/sbml/level2/version4" http://www.sbml.org/sbml/level2/version5" http://www.sbml.org/sbml/level3/version1/core" http://www.sbml.org/sbml/level3/version2/core" true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
| pkgName | the name of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
| pkgURI | the URI of the package. |
true if the given package is enabled within this object, false otherwise.
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inherited |
Predicate returning true if libSBML has a list of the ids of all components of this model.
true if the id list has already been populated, false otherwise.
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inherited |
Predicate returning true if libSBML has a list of the metaids of all components of this model.
true if the metaid list has already been populated, false otherwise.
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inherited |
Predicate returning true if libSBML has derived units for the components of this model.
LibSBML can infer the units of measurement associated with different elements of a model. When libSBML does that, it builds a complex internal structure during a resource-intensive operation. This is done automatically only when callers invoke validation (via SBMLDocument::checkConsistency()) and have not turned off the unit validation option.
Callers can force units to be recalculated by calling populateListFormulaUnitsData(). To avoid calling that method unnecessarily, calling programs may first want to invoke this method (isPopulatedListFormulaUnitsData()) to determine whether it is even necessary.
true if the units have already been computed, false otherwise.
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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.
true if a 'annotation' subelement exists, false otherwise.
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inherited |
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inherited |
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inherited |
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inherited |
Predicate returning true if this Model's 'id' attribute is set.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
true if the 'id' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object's 'id' attribute is set.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
true if the 'id' attribute of this SBML object is set, false otherwise.
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inherited |
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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.
true if the 'metaid' attribute of this SBML object is set, false otherwise.
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inherited |
Predicate returning true if this object has a ModelHistory object attached to it.
true if the ModelHistory of this object is set, false otherwise.
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inherited |
Predicate returning true if this Model's 'name' attribute is set.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
true if the 'name' attribute of this SBML object is set, false otherwise.
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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.
true if a 'notes' subelement exists, false otherwise.
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inherited |
Predicate returning true if this object's 'sboTerm' attribute is set.
true if the 'sboTerm' attribute of this SBML object is set, false otherwise.
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inherited |
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inherited |
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inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
true if this object's user data has been set, false otherwise.
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inherited |
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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.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is a subset of sb's, false otherwise.
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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.
| sb | an object to compare with respect to namespaces. |
true if this object's collection of namespaces is the same as sb's, false otherwise.
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inherited |
Populates the internal list of the identifiers of all elements within this Model object.
This method tells libSBML to retrieve the identifiers of all elements of the enclosing Model object. The result is stored in an internal list of ids. Users can access the resulting data by calling the method getAllElementIdList().
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inherited |
Populates the internal list of the metaids of all elements within this Model object.
This method tells libSBML to retrieve the identifiers of all elements of the enclosing Model object. The result is stored in an internal list of metaids. Users can access the resulting data by calling the method getAllElementMetaIdList().
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inherited |
Populates the internal list of derived units for this Model object.
This method tells libSBML to (re)calculate all units for all components of the enclosing Model object. The result is stored in an internal list of unit data. Users can access the resulting data by calling the method SBase::getDerivedUnitDefinition() available on most objects. (The name 'formula units data' is drawn from the name of the internal objects libSBML uses to store the data; note that these internal objects are not exposed to callers, because callers can interact with the results using the ordinary SBML unit objects.)
This method is used by libSBML itself in the validator concerned with unit consistency. The unit consistency validator (like all other validators in libSBML) is invoked by using SBMLDocument::checkConsistency(), with the consistency checks for the category LIBSBML_CAT_UNITS_CONSISTENCY turned on. The method populateListFormulaUnitsData() does not need to be called prior to invoking the validator if unit consistency checking has not been turned off. This method is only provided for cases when callers have a special need to force the unit data to be recalculated. For instance, during construction of a model, a caller may want to interrogate libSBML's inferred units without invoking full-blown model validation; this is a scenario in which calling populateListFormulaUnitsData() may be useful.
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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.
| n | the index of the Compartment object to remove. |
null if the given index is out of range.
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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.
| sid | the identifier of the Compartment object to remove. |
null if no Compartment object with the identifier exists in this Model object.
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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.
| n | the index of the CompartmentType object to remove. |
null if the given index is out of range.
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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.
| sid | the identifier of the object to remove. |
null if no CompartmentType object with the identifier exists in this Model object.
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inherited |
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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.
| n | the index of the Constraint object to remove. |
null if the given index is out of range.
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inherited |
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inherited |
| new 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.
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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.
| n | the index of the FunctionDefinition object to remove. |
null if the given index is out of range.
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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.
| sid | the identifier of the FunctionDefinition object to remove. |
null if no FunctionDefinition object with the identifier exists in this Model object.
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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.
| n | the index of the InitialAssignment object to remove. |
null if the given index is out of range.
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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.
| symbol | the 'symbol' attribute of the InitialAssignment object to remove. |
null if no InitialAssignment object with the 'symbol' attribute exists in this Model object.
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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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.
| n | the index of the SpeciesType object to remove. |
null if the given index is out of range.
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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.
| sid | the identifier of the SpeciesType object to remove. |
null if no SpeciesType object with the identifier exists in this Model object.
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inherited |
|
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.
| 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). |
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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.
| 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). |
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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.
| 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). |
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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.
| n | the index of the UnitDefinition object to remove. |
null if the given index is out of range.
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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.
| sid | the identifier of the UnitDefinition object to remove. |
null if no UnitDefinition object with the identifier exists in this Model object.
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inherited |
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.
This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
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inherited |
Replaces all uses of a given SIdRef type attribute value with another value.
In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
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inherited |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
| oldid | the old identifier. |
| newid | the new identifier. |
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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.
| annotation | XMLNode representing the replacement top level annotation. |
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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.
| annotation | string representing the replacement top level annotation. |
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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().
| annotation | an XML structure that is to be used as the content of the 'annotation' subelement of this object. |
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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().
| annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object. |
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inherited |
Sets the value of the 'areaUnits' attribute of this Model.
The string in units is copied.
| units | the new areaUnits for the Model. |
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inherited |
Sets the value of the 'conversionFactor' attribute of this Model.
The string in units is copied.
| units | the new conversionFactor for the Model. |
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inherited |
Sets the value of the 'extentUnits' attribute of this Model.
The string in units is copied.
| units | the new extentUnits for the Model. |
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inherited |
Sets the value of the 'id' attribute of this Model.
The string sid is copied.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
| sid | the string to use as the identifier of this object. |
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inherited |
Sets the value of the 'id' attribute of this SBML object.
The string sid is copied.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
| sid | the string to use as the identifier of this object. |
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inherited |
Sets the value of the 'lengthUnits' attribute of this Model.
The string in units is copied.
| units | the new lengthUnits for the Model. |
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inherited |
Sets the value of the meta-identifier attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
The string metaid is copied.
| metaid | the identifier string to use as the value of the 'metaid' attribute. |
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inherited |
Sets the ModelHistory of this object.
The content of history is copied, and this object's existing model history content is deleted.
| history | ModelHistory of this object. |
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inherited |
Sets the value of the 'name' attribute of this Model.
The string in name is copied.
| name | the new name for the SBML object. |
|
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.
| xmlns | the namespaces to set. |
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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.
| notes | an XML structure that is to be used as the content of the 'notes' subelement of this object. |
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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.
| notes | an XML string that is to be used as the content of the 'notes' subelement of this object. |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
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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.
| notes | an XML string that is to be used as the content of the 'notes' subelement of this object. |
| addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
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inherited |
|
inherited |
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
| value | the NNNNNNN integer portion of the SBO identifier. |
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inherited |
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 2, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Sets the value of the 'substanceUnits' attribute of this Model.
The string in units is copied.
| units | the new substanceUnits for the Model. |
|
inherited |
Sets the value of the 'timeUnits' attribute of this Model.
The string in units is copied.
| units | the new timeUnits for the Model. |
|
inherited |
Sets the value of the 'volumeUnits' attribute of this Model.
The string in units is copied.
| units | the new volumeUnits for the Model. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
|
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.
|
inherited |
|
inherited |
Unsets the value of the 'conversionFactor' attribute of this Model.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
inherited |
|
inherited |
Unsets the value of the 'id' attribute of this Model.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
|
inherited |
Unsets the value of the 'id' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.
|
inherited |
|
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.
|
inherited |
Unsets the ModelHistory object attached to this object.
|
inherited |
Unsets the value of the 'name' attribute of this Model.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
|
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.
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
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inherited |
|
inherited |
|
inherited |
Unsets the user data of this element.
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
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inherited |
|
protectedinherited |