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libSBML C++ API
5.20.4
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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 (const Compartment *c) |
| Adds a copy of the given Compartment object to this Model. More... | |
| int | addCompartmentType (const CompartmentType *ct) |
| Adds a copy of the given CompartmentType object to this Model. More... | |
| int | addConstraint (const Constraint *c) |
| Adds a copy of the given Constraint object to this Model. More... | |
| int | addCVTerm (CVTerm *term, bool newBag=false) |
| Adds a copy of the given CVTerm object to this SBML object. More... | |
| int | addEvent (const Event *e) |
| Adds a copy of the given Event object to this Model. More... | |
| int | addFunctionDefinition (const FunctionDefinition *fd) |
| Adds a copy of the given FunctionDefinition object to this Model. More... | |
| int | addInitialAssignment (const InitialAssignment *ia) |
| Adds a copy of the given InitialAssignment object to this Model. More... | |
| int | addModifiedDate (Date *date) |
| Adds a modified date to the ModelHistory of this object. More... | |
| int | addParameter (const Parameter *p) |
| Adds a copy of the given Parameter object to this Model. More... | |
| int | addReaction (const Reaction *r) |
| Adds a copy of the given Reaction object to this Model. More... | |
| int | addRule (const Rule *r) |
| Adds a copy of the given Rule object to this Model. More... | |
| int | addSpecies (const Species *s) |
| Adds a copy of the given Species object to this Model. More... | |
| int | addSpeciesType (const SpeciesType *st) |
| Adds a copy of the given SpeciesType object to this Model. More... | |
| int | addUnitDefinition (const UnitDefinition *ud) |
| Adds a copy of the given UnitDefinition object to this Model. More... | |
| virtual int | appendAnnotation (const std::string &annotation) |
| Appends annotation content to any existing content in the "annotation" subelement of this object. More... | |
| virtual int | appendAnnotation (const XMLNode *annotation) |
| Appends annotation content to any existing content in the "annotation" subelement of this object. More... | |
| virtual int | appendFrom (const Model *model) |
| Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model. More... | |
| int | appendNotes (const std::string ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
| int | appendNotes (const XMLNode *notes) |
Appends the given notes to the "notes" subelement of this object. More... | |
| void | clearAllElementIdList () |
| Clears the internal list of the identifiers of all elements within this Model object. More... | |
| void | clearAllElementMetaIdList () |
| Clears the internal list of the metaids of all elements within this Model object. More... | |
| virtual ModelDefinition * | clone () const |
| Creates and returns a deep copy of this ModelDefinition object. More... | |
| 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 | deleteDisabledPlugins (bool recursive=true) |
| Deletes all information stored in disabled plugins. More... | |
| int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
| Disables the given SBML Level 3 package on this object. More... | |
| int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
| Enables or disables the given SBML Level 3 package on this object. More... | |
| IdList | getAllElementIdList () const |
| Returns the internal list of the identifiers of all elements within this Model object. More... | |
| IdList | getAllElementMetaIdList () const |
| Returns the internal list of the metaids of all elements within this Model object. More... | |
| virtual List * | getAllElements (ElementFilter *filter=NULL) |
| Returns a List of all child objects. More... | |
| virtual List * | getAllElementsFromPlugins (ElementFilter *filter=NULL) |
| Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
| SBase * | getAncestorOfType (int type, const std::string &pkgName="core") |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
| Returns the first ancestor object that has the given SBML type code from the given package. More... | |
| XMLNode * | getAnnotation () |
| Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
| XMLNode * | getAnnotation () const |
| Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
| std::string | getAnnotationString () |
| Returns the content of the "annotation" subelement of this object as a character string. More... | |
| std::string | getAnnotationString () const |
| Returns the content of the "annotation" subelement of this object as a character string. More... | |
| const std::string & | getAreaUnits () const |
| Returns the value of the "areaUnits" attribute of this Model. More... | |
| AssignmentRule * | getAssignmentRule (const std::string &variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| const AssignmentRule * | getAssignmentRule (const std::string &variable) const |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| AssignmentRule * | getAssignmentRuleByVariable (const std::string &variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| const AssignmentRule * | getAssignmentRuleByVariable (const std::string &variable) const |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| unsigned int | getColumn () const |
| Returns the column number where this object first appears in the XML representation of the SBML document. More... | |
| Compartment * | getCompartment (const std::string &sid) |
| Get a Compartment object based on its identifier. More... | |
| const Compartment * | getCompartment (const std::string &sid) const |
| Get a Compartment object based on its identifier. More... | |
| Compartment * | getCompartment (unsigned int n) |
| Get the nth Compartment object in this Model. More... | |
| const Compartment * | getCompartment (unsigned int n) const |
| Get the nth Compartment object in this Model. More... | |
| CompartmentType * | getCompartmentType (const std::string &sid) |
| Get a CompartmentType object based on its identifier. More... | |
| const CompartmentType * | getCompartmentType (const std::string &sid) const |
| Get a CompartmentType object based on its identifier. More... | |
| CompartmentType * | getCompartmentType (unsigned int n) |
| Get the nth CompartmentType object in this Model. More... | |
| const CompartmentType * | getCompartmentType (unsigned int n) const |
| Get the nth CompartmentType object in this Model. More... | |
| Constraint * | getConstraint (unsigned int n) |
| Get the nth Constraint object in this Model. More... | |
| const Constraint * | getConstraint (unsigned int n) const |
| Get the nth Constraint object in this Model. More... | |
| const std::string & | getConversionFactor () const |
| Returns the value of the "conversionFactor" attribute of this Model. More... | |
| Date * | getCreatedDate () |
| Returns the "creation date" portion of the ModelHistory of this object. More... | |
| Date * | getCreatedDate () const |
| Returns the "creation date" portion of the ModelHistory of this object. More... | |
| CVTerm * | getCVTerm (unsigned int n) |
| Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
| List * | getCVTerms () |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| List * | getCVTerms () const |
| Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
| SBasePlugin * | getDisabledPlugin (unsigned int n) |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| const SBasePlugin * | getDisabledPlugin (unsigned int n) const |
| Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| virtual SBase * | getElementByMetaId (const std::string &metaid) |
Returns the first child element it can find with the given metaid. More... | |
| const SBase * | getElementByMetaId (const std::string &metaid) const |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found. More... | |
| virtual SBase * | getElementBySId (const std::string &id) |
Returns the first child element found that has the given id. More... | |
| virtual const SBase * | getElementBySId (const std::string &id) const |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More... | |
| virtual const std::string & | getElementName () const |
| Returns the XML element name of this object. More... | |
| Event * | getEvent (const std::string &sid) |
| Get an Event object based on its identifier. More... | |
| const Event * | getEvent (const std::string &sid) const |
| Get an Event object based on its identifier. More... | |
| Event * | getEvent (unsigned int n) |
| Get the nth Event object in this Model. More... | |
| const Event * | getEvent (unsigned int n) const |
| Get the nth Event object in this Model. More... | |
| const std::string & | getExtentUnits () const |
| Returns the value of the "extentUnits" attribute of this Model. More... | |
| FunctionDefinition * | getFunctionDefinition (const std::string &sid) |
| Get a FunctionDefinition object based on its identifier. More... | |
| const FunctionDefinition * | getFunctionDefinition (const std::string &sid) const |
| Get a FunctionDefinition object based on its identifier. More... | |
| FunctionDefinition * | getFunctionDefinition (unsigned int n) |
| Get the nth FunctionDefinitions object in this Model. More... | |
| const FunctionDefinition * | getFunctionDefinition (unsigned int n) const |
| Get the nth FunctionDefinitions object in this Model. More... | |
| virtual const std::string & | getId () const |
| Returns the value of the "id" attribute of this Model. More... | |
| const std::string & | getIdAttribute () const |
| Returns the value of the "id" attribute of this SBML object. More... | |
| InitialAssignment * | getInitialAssignment (const std::string &symbol) |
| Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
| const InitialAssignment * | getInitialAssignment (const std::string &symbol) const |
| Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
| InitialAssignment * | getInitialAssignment (unsigned int n) |
| Get the nth InitialAssignment object in this Model. More... | |
| const InitialAssignment * | getInitialAssignment (unsigned int n) const |
| Get the nth InitialAssignment object in this Model. More... | |
| InitialAssignment * | getInitialAssignmentBySymbol (const std::string &symbol) |
| Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
| const InitialAssignment * | getInitialAssignmentBySymbol (const std::string &symbol) const |
| Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
| const std::string & | getLengthUnits () const |
| Returns the value of the "lengthUnits" attribute of this Model. More... | |
| unsigned int | getLevel () const |
| Returns the SBML Level of the SBMLDocument object containing this object. More... | |
| unsigned int | getLine () const |
| Returns the line number where this object first appears in the XML representation of the SBML document. More... | |
| ListOfCompartments * | getListOfCompartments () |
| Get the ListOfCompartments object in this Model. More... | |
| const ListOfCompartments * | getListOfCompartments () const |
| Get the ListOfCompartments object in this Model. More... | |
| ListOfCompartmentTypes * | getListOfCompartmentTypes () |
| Get the ListOfCompartmentTypes object in this Model. More... | |
| const ListOfCompartmentTypes * | getListOfCompartmentTypes () const |
| Get the ListOfCompartmentTypes object in this Model. More... | |
| ListOfConstraints * | getListOfConstraints () |
| Get the ListOfConstraints object in this Model. More... | |
| const ListOfConstraints * | getListOfConstraints () const |
| Get the ListOfConstraints object in this Model. More... | |
| ListOfEvents * | getListOfEvents () |
| Get the ListOfEvents object in this Model. More... | |
| const ListOfEvents * | getListOfEvents () const |
| Get the ListOfEvents object in this Model. More... | |
| ListOfFunctionDefinitions * | getListOfFunctionDefinitions () |
| Get the ListOfFunctionDefinitions object in this Model. More... | |
| const ListOfFunctionDefinitions * | getListOfFunctionDefinitions () const |
| Get the ListOfFunctionDefinitions object in this Model. More... | |
| ListOfInitialAssignments * | getListOfInitialAssignments () |
| Get the ListOfInitialAssignments object in this Model. More... | |
| const ListOfInitialAssignments * | getListOfInitialAssignments () const |
| Get the ListOfInitialAssignments object in this Model. More... | |
| ListOfParameters * | getListOfParameters () |
| Get the ListOfParameters object in this Model. More... | |
| const ListOfParameters * | getListOfParameters () const |
| Get the ListOfParameters object in this Model. More... | |
| ListOfReactions * | getListOfReactions () |
| Get the ListOfReactions object in this Model. More... | |
| const ListOfReactions * | getListOfReactions () const |
| Get the ListOfReactions object in this Model. More... | |
| ListOfRules * | getListOfRules () |
| Get the ListOfRules object in this Model. More... | |
| const ListOfRules * | getListOfRules () const |
| Get the ListOfRules object in this Model. More... | |
| ListOfSpecies * | getListOfSpecies () |
| Get the ListOfSpecies object in this Model. More... | |
| const ListOfSpecies * | getListOfSpecies () const |
| Get the ListOfSpecies object in this Model. More... | |
| ListOfSpeciesTypes * | getListOfSpeciesTypes () |
| Get the ListOfSpeciesTypes object in this Model. More... | |
| const ListOfSpeciesTypes * | getListOfSpeciesTypes () const |
| Get the ListOfSpeciesTypes object in this Model. More... | |
| ListOfUnitDefinitions * | getListOfUnitDefinitions () |
| Get the ListOfUnitDefinitions object in this Model. More... | |
| const ListOfUnitDefinitions * | getListOfUnitDefinitions () const |
| Get the ListOfUnitDefinitions object in this Model. More... | |
| std::string & | getMetaId () |
| Returns the value of the "metaid" attribute of this SBML object. More... | |
| const std::string & | getMetaId () const |
| Returns the value of the "metaid" attribute of this SBML object. More... | |
| const Model * | getModel () const |
| 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... | |
| ModelHistory * | getModelHistory () const |
| Returns the ModelHistory object, if any, attached to this object. More... | |
| Date * | getModifiedDate (unsigned int n) |
| Get the nth Date object in the list of "modified date" values stored in the ModelHistory of this object. More... | |
| ModifierSpeciesReference * | getModifierSpeciesReference (const std::string &sid) |
| Get a ModifierSpeciesReference object based on its identifier. More... | |
| const ModifierSpeciesReference * | getModifierSpeciesReference (const std::string &sid) const |
| Get a ModifierSpeciesReference object based on its identifier. More... | |
| virtual const std::string & | getName () const |
| Returns the value of the "name" attribute of this Model object. More... | |
| virtual XMLNamespaces * | getNamespaces () const |
| 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... | |
| XMLNode * | getNotes () const |
| Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
| std::string | getNotesString () |
| Returns the content of the "notes" subelement of this object as a string. More... | |
| std::string | getNotesString () const |
| Returns the content of the "notes" subelement of this object as a string. More... | |
| unsigned int | getNumCompartments () const |
| Get the number of Compartment objects in this Model. More... | |
| unsigned int | getNumCompartmentTypes () const |
| Get the number of CompartmentType objects in this Model. More... | |
| unsigned int | getNumConstraints () const |
| Get the number of Constraint objects in this Model. More... | |
| unsigned int | getNumCVTerms () const |
| Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
| unsigned int | getNumDisabledPlugins () const |
| Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More... | |
| unsigned int | getNumEvents () const |
| Get the number of Event objects in this Model. More... | |
| unsigned int | getNumFunctionDefinitions () const |
| Get the number of FunctionDefinition objects in this Model. More... | |
| unsigned int | getNumInitialAssignments () const |
| Get the number of InitialAssignment objects in this Model. More... | |
| unsigned int | getNumModifiedDates () |
| Get the number of Date objects in the ModelHistory of this Iobject's list of "modified dates". More... | |
| unsigned int | getNumParameters () const |
| Get the number of Parameter objects in this Model. More... | |
| unsigned int | getNumPlugins () const |
| Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
| unsigned int | getNumReactions () const |
| Get the number of Reaction objects in this Model. More... | |
| unsigned int | getNumRules () const |
| Get the number of Rule objects in this Model. More... | |
| unsigned int | getNumSpecies () const |
| Get the number of Species objects in this Model. More... | |
| unsigned int | getNumSpeciesTypes () const |
| Get the number of SpeciesType objects in this Model. More... | |
| unsigned int | getNumSpeciesWithBoundaryCondition () const |
Get the number of Species in this Model having their "boundaryCondition" attribute value set to true. More... | |
| unsigned int | getNumUnitDefinitions () const |
| Get the number of UnitDefinition objects in this Model. More... | |
| unsigned int | getPackageCoreVersion () const |
| Returns the SBML Core Version within the SBML Level of the actual object. More... | |
| const std::string & | getPackageName () const |
| Returns the name of the SBML Level 3 package in which this element is defined. More... | |
| unsigned int | getPackageVersion () const |
| Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
| Parameter * | getParameter (const std::string &sid) |
| Get a Parameter object based on its identifier. More... | |
| const Parameter * | getParameter (const std::string &sid) const |
| Get a Parameter object based on its identifier. More... | |
| Parameter * | getParameter (unsigned int n) |
| Get the nth Parameter object in this Model. More... | |
| const Parameter * | getParameter (unsigned int n) const |
| Get the nth Parameter object in this Model. More... | |
| SBase * | getParentSBMLObject () |
| Returns the parent SBML object containing this object. More... | |
| const SBase * | getParentSBMLObject () const |
| Returns the parent SBML object containing this object. More... | |
| SBasePlugin * | getPlugin (const std::string &package) |
| Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
| const SBasePlugin * | getPlugin (const std::string &package) const |
| Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
| SBasePlugin * | getPlugin (unsigned int n) |
| Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| const SBasePlugin * | getPlugin (unsigned int n) const |
| Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
| std::string | getPrefix () const |
| Returns the XML namespace prefix of this element. More... | |
| RateRule * | getRateRule (const std::string &variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| const RateRule * | getRateRule (const std::string &variable) const |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| RateRule * | getRateRuleByVariable (const std::string &variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| const RateRule * | getRateRuleByVariable (const std::string &variable) const |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| Reaction * | getReaction (const std::string &sid) |
| Get a Reaction object based on its identifier. More... | |
| const Reaction * | getReaction (const std::string &sid) const |
| Get a Reaction object based on its identifier. More... | |
| Reaction * | getReaction (unsigned int n) |
| Get the nth Reaction object in this Model. More... | |
| const Reaction * | getReaction (unsigned int n) const |
| Get the nth Reaction object in this Model. More... | |
| BiolQualifierType_t | getResourceBiologicalQualifier (std::string resource) const |
| Returns the MIRIAM biological qualifier associated with the given resource. More... | |
| ModelQualifierType_t | getResourceModelQualifier (std::string resource) const |
| Returns the MIRIAM model qualifier associated with the given resource. More... | |
| Rule * | getRule (const std::string &variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| const Rule * | getRule (const std::string &variable) const |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| Rule * | getRule (unsigned int n) |
| Get the nth Rule object in this Model. More... | |
| const Rule * | getRule (unsigned int n) const |
| Get the nth Rule object in this Model. More... | |
| Rule * | getRuleByVariable (const std::string &variable) |
| Get a Rule object based on the variable to which it assigns a value. More... | |
| const Rule * | getRuleByVariable (const std::string &variable) const |
| 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... | |
| const SBMLDocument * | getSBMLDocument () const |
| Returns the SBMLDocument object containing this object instance. More... | |
| int | getSBOTerm () const |
| Returns the integer portion of the value of the "sboTerm" attribute of this object. More... | |
| std::string | getSBOTermAsURL () const |
| Returns the URL representation of the "sboTerm" attribute of this object. More... | |
| std::string | getSBOTermID () const |
| Returns the string representation of the "sboTerm" attribute of this object. More... | |
| Species * | getSpecies (const std::string &sid) |
| Get a Species object based on its identifier. More... | |
| const Species * | getSpecies (const std::string &sid) const |
| Get a Species object based on its identifier. More... | |
| Species * | getSpecies (unsigned int n) |
| Get the nth Species object in this Model. More... | |
| const Species * | getSpecies (unsigned int n) const |
| Get the nth Species object in this Model. More... | |
| SpeciesReference * | getSpeciesReference (const std::string &sid) |
| Get a SpeciesReference object based on its identifier. More... | |
| const SpeciesReference * | getSpeciesReference (const std::string &sid) const |
| Get a SpeciesReference object based on its identifier. More... | |
| SpeciesType * | getSpeciesType (const std::string &sid) |
| Get a SpeciesType object based on its identifier. More... | |
| const SpeciesType * | getSpeciesType (const std::string &sid) const |
| Get a SpeciesType object based on its identifier. More... | |
| SpeciesType * | getSpeciesType (unsigned int n) |
| Get the nth SpeciesType object in this Model. More... | |
| const SpeciesType * | getSpeciesType (unsigned int n) const |
| Get the nth SpeciesType object in this Model. More... | |
| const std::string & | getSubstanceUnits () const |
| Returns the value of the "substanceUnits" attribute of this Model. More... | |
| const std::string & | getTimeUnits () const |
| Returns the value of the "timeUnits" attribute of this Model. More... | |
| virtual int | getTypeCode () const |
| Returns the libSBML type code of this object instance. More... | |
| UnitDefinition * | getUnitDefinition (const std::string &sid) |
| Get a UnitDefinition based on its identifier. More... | |
| const UnitDefinition * | getUnitDefinition (const std::string &sid) const |
| Get a UnitDefinition based on its identifier. More... | |
| UnitDefinition * | getUnitDefinition (unsigned int n) |
| Get the nth UnitDefinition object in this Model. More... | |
| const UnitDefinition * | getUnitDefinition (unsigned int n) const |
| Get the nth UnitDefinition object in this Model. More... | |
| std::string | getURI () const |
| Returns the namespace URI to which this element belongs to. More... | |
| void * | getUserData () const |
| Returns the user data that has been previously set via setUserData(). More... | |
| unsigned int | getVersion () const |
| Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
| const std::string & | getVolumeUnits () const |
| Returns the value of the "volumeUnits" attribute of this Model. More... | |
| virtual bool | hasRequiredElements () const |
Predicate returning true if all the required elements for this Model object have been set. More... | |
| bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
| bool | isPackageEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPackageURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isPkgEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
| bool | isPkgURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
| bool | isPopulatedAllElementIdList () const |
Predicate returning true if libSBML has a list of the ids of all components of this model. More... | |
| bool | isPopulatedAllElementMetaIdList () const |
Predicate returning true if libSBML has a list of the metaids of all components of this model. More... | |
| bool | isPopulatedListFormulaUnitsData () |
Predicate returning true if libSBML has derived units for the components of this model. More... | |
| bool | isSetAnnotation () const |
Predicate returning true if this object's "annotation" subelement exists and has content. More... | |
| bool | isSetAreaUnits () const |
Predicate returning true if this Model's "areaUnits" attribute is set. More... | |
| bool | isSetConversionFactor () const |
Predicate returning true if this Model's "conversionFactor" attribute is set. More... | |
| bool | isSetCreatedDate () const |
Predicate returning true if this object has a ModelHistory object attached to it and the created date is set. More... | |
| bool | isSetExtentUnits () const |
Predicate returning true if this Model's "extentUnits" attribute is set. More... | |
| virtual bool | isSetId () const |
Predicate returning true if this Model's "id" attribute is set. More... | |
| bool | isSetIdAttribute () const |
Predicate returning true if this object's "id" attribute is set. More... | |
| bool | isSetLengthUnits () const |
Predicate returning true if this Model's "lengthUnits" attribute is set. More... | |
| bool | isSetMetaId () const |
Predicate returning true if this object's "metaid" attribute is set. More... | |
| bool | isSetModelHistory () const |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
| bool | isSetModifiedDate () const |
Predicate returning true or false depending on whether the ModelHistory's "modified date" of this object is set. More... | |
| virtual bool | isSetName () const |
Predicate returning true if this Model's "name" attribute is set. More... | |
| bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
| bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
| bool | isSetSubstanceUnits () const |
Predicate returning true if this Model's "substanceUnits" attribute is set. More... | |
| bool | isSetTimeUnits () const |
Predicate returning true if this Model's "timeUnits" attribute is set. More... | |
| bool | isSetUserData () const |
| Predicate returning true or false depending on whether the user data of this element has been set. More... | |
| bool | isSetVolumeUnits () const |
Predicate returning true if this Model's "volumeUnits" attribute is set. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (const SBase *sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| bool | matchesSBMLNamespaces (const SBase *sb) const |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
| ModelDefinition (CompPkgNamespaces *compns) | |
| Creates a new ModelDefinition with the given CompPkgNamespaces object. More... | |
| ModelDefinition (const Model &source) | |
| Copy constructor from base Model object. More... | |
| ModelDefinition (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion()) | |
| Creates a new ModelDefinition with the given level, version, and package version. More... | |
| ModelDefinition & | operator= (const Model &source) |
| Assignment operator. More... | |
| void | populateAllElementIdList () |
| Populates the internal list of the identifiers of all elements within this Model object. More... | |
| void | populateAllElementMetaIdList () |
| Populates the internal list of the metaids of all elements within this Model object. More... | |
| void | populateListFormulaUnitsData () |
| Populates the internal list of derived units for this Model object. More... | |
| void | read (const XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED) |
| Reads (initializes) this SBML object by reading from the given XMLNode. More... | |
| Compartment * | removeCompartment (const std::string &sid) |
| Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More... | |
| Compartment * | removeCompartment (unsigned int n) |
| Removes the nth Compartment object from this Model object and returns a pointer to it. More... | |
| CompartmentType * | removeCompartmentType (const std::string &sid) |
| Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More... | |
| CompartmentType * | removeCompartmentType (unsigned int n) |
| Removes the nth CompartmentType object from this Model object and returns a pointer to it. More... | |
| Constraint * | removeConstraint (unsigned int n) |
| Removes the nth Constraint object from this Model object and returns a pointer to it. More... | |
| Event * | removeEvent (const std::string &sid) |
| Removes the Event object with the given identifier from this Model object and returns a pointer to it. More... | |
| Event * | removeEvent (unsigned int n) |
| Removes the nth Event object from this Model object and returns a pointer to it. More... | |
| virtual int | removeFromParentAndDelete () |
| Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself. More... | |
| FunctionDefinition * | removeFunctionDefinition (const std::string &sid) |
| Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
| FunctionDefinition * | removeFunctionDefinition (unsigned int n) |
| Removes the nth FunctionDefinition object from this Model object and returns a pointer to it. More... | |
| InitialAssignment * | removeInitialAssignment (const std::string &symbol) |
| Removes the InitialAssignment object with the given "symbol" attribute from this Model object and returns a pointer to it. More... | |
| InitialAssignment * | removeInitialAssignment (unsigned int n) |
| Removes the nth InitialAssignment object from this Model object and returns a pointer to it. More... | |
| Parameter * | removeParameter (const std::string &sid) |
| Removes the Parameter object with the given identifier from this Model object and returns a pointer to it. More... | |
| Parameter * | removeParameter (unsigned int n) |
| Removes the nth Parameter object from this Model object and returns a pointer to it. More... | |
| Reaction * | removeReaction (const std::string &sid) |
| Removes the Reaction object with the given identifier from this Model object and returns a pointer to it. More... | |
| Reaction * | removeReaction (unsigned int n) |
| Removes the nth Reaction object from this Model object and returns a pointer to it. More... | |
| Rule * | removeRule (const std::string &variable) |
| Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it. More... | |
| Rule * | removeRule (unsigned int n) |
| Removes the nth Rule object from this Model object and returns a pointer to it. More... | |
| Rule * | removeRuleByVariable (const std::string &variable) |
| Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it. More... | |
| Species * | removeSpecies (const std::string &sid) |
| Removes the Species object with the given identifier from this Model object and returns a pointer to it. More... | |
| Species * | removeSpecies (unsigned int n) |
| Removes the nth Species object from this Model object and returns a pointer to it. More... | |
| SpeciesType * | removeSpeciesType (const std::string &sid) |
| Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More... | |
| SpeciesType * | removeSpeciesType (unsigned int n) |
| Removes the nth SpeciesType object from this Model object and returns a pointer to it. More... | |
| int | removeTopLevelAnnotationElement (const std::string &elementName, const std::string elementURI="", bool removeEmpty=true) |
| Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
| UnitDefinition * | removeUnitDefinition (const std::string &sid) |
| Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
| UnitDefinition * | removeUnitDefinition (unsigned int n) |
| Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More... | |
| virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
| virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
| virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
| int | replaceTopLevelAnnotationElement (const std::string &annotation) |
| Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
| int | replaceTopLevelAnnotationElement (const XMLNode *annotation) |
| Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
| virtual int | setAnnotation (const std::string &annotation) |
Sets the value of the "annotation" subelement of this SBML object to a copy of annotation. More... | |
| virtual int | setAnnotation (const XMLNode *annotation) |
Sets the value of the "annotation" subelement of this SBML object to a copy of annotation. More... | |
| int | setAreaUnits (const std::string &units) |
| Sets the value of the "areaUnits" attribute of this Model. More... | |
| int | setConversionFactor (const std::string &units) |
| Sets the value of the "conversionFactor" attribute of this Model. More... | |
| int | setCreatedDate (Date *date) |
| Sets the creation date of the ModelHistory of this object. More... | |
| int | setExtentUnits (const std::string &units) |
| Sets the value of the "extentUnits" attribute of this Model. More... | |
| virtual int | setId (const std::string &sid) |
| Sets the value of the "id" attribute of this Model. More... | |
| virtual int | setIdAttribute (const std::string &sid) |
| Sets the value of the "id" attribute of this SBML object. More... | |
| int | setLengthUnits (const std::string &units) |
| Sets the value of the "lengthUnits" attribute of this Model. More... | |
| int | setMetaId (const std::string &metaid) |
| Sets the value of the meta-identifier attribute of this SBML object. More... | |
| int | setModelHistory (ModelHistory *history) |
| Sets the ModelHistory of this object. More... | |
| virtual int | setName (const std::string &name) |
| Sets the value of the "name" attribute of this Model. More... | |
| int | setNamespaces (XMLNamespaces *xmlns) |
| Sets the namespaces relevant of this SBML object. More... | |
| int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes. More... | |
| int | setNotes (const XMLNode *notes) |
| Sets the value of the "notes" subelement of this SBML object. More... | |
| virtual int | setSBOTerm (const std::string &sboid) |
| Sets the value of the "sboTerm" attribute by string. More... | |
| virtual int | setSBOTerm (int value) |
| Sets the value of the "sboTerm" attribute. More... | |
| int | setSubstanceUnits (const std::string &units) |
| Sets the value of the "substanceUnits" attribute of this Model. More... | |
| int | setTimeUnits (const std::string &units) |
| Sets the value of the "timeUnits" attribute of this Model. More... | |
| int | setUserData (void *userData) |
| Sets the user data of this element. More... | |
| int | setVolumeUnits (const std::string &units) |
| Sets the value of the "volumeUnits" attribute of this Model. More... | |
| char * | toSBML () |
| Returns a string consisting of a partial SBML corresponding to just this object. More... | |
| 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 | unsetCreatedDate () |
| Unsets the created date of the ModelHistory object attached to this object. More... | |
| int | unsetCVTerms () |
| Clears the list of CVTerm objects attached to this SBML object. More... | |
| int | unsetExtentUnits () |
| Unsets the value of the "extentUnits" attribute of this Model. More... | |
| virtual int | unsetId () |
| Unsets the value of the "id" attribute of this Model. More... | |
| int | unsetIdAttribute () |
| Unsets the value of the "id" attribute of this SBML object. More... | |
| int | unsetLengthUnits () |
| Unsets the value of the "lengthUnits" attribute of this Model. More... | |
| int | unsetMetaId () |
| Unsets the value of the "metaid" attribute of this SBML object. More... | |
| int | unsetModelHistory () |
| Unsets the ModelHistory object attached to this object. More... | |
| int | unsetModifiedDates () |
| Unsets the modified dates of the ModelHistory object attached to this object. More... | |
| virtual int | unsetName () |
| Unsets the value of the "name" attribute of this Model. More... | |
| int | unsetNotes () |
| Unsets the value of the "notes" subelement of this SBML object. More... | |
| int | unsetSBOTerm () |
| Unsets the value of the "sboTerm" attribute of this SBML object. More... | |
| int | unsetSubstanceUnits () |
| Unsets the value of the "substanceUnits" attribute of this Model. More... | |
| int | unsetTimeUnits () |
| Unsets the value of the "timeUnits" attribute of this Model. More... | |
| int | unsetUserData () |
| Unsets the user data of this element. More... | |
| int | unsetVolumeUnits () |
| Unsets the value of the "volumeUnits" attribute of this Model. More... | |
| virtual | ~ModelDefinition () |
| Destructor. More... | |
Protected Member Functions | |
| virtual void | setElementText (const std::string &text) |
| When overridden allows SBase elements to use the text included in between the elements tags. More... | |
| ModelDefinition::ModelDefinition | ( | unsigned int | level = CompExtension::getDefaultLevel(), |
| unsigned int | version = CompExtension::getDefaultVersion(), |
||
| unsigned int | pkgVersion = CompExtension::getDefaultPackageVersion() |
||
| ) |
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. |
| ModelDefinition::ModelDefinition | ( | CompPkgNamespaces * | compns | ) |
Creates a new ModelDefinition with the given CompPkgNamespaces object.
| compns | the CompPkgNamespaces object. |
| ModelDefinition::ModelDefinition | ( | const Model & | source | ) |
Copy constructor from base Model object.
| source | the instance to copy. |
|
virtual |
Destructor.
|
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 |
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 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 |
Adds a modified date to the ModelHistory of this object.
| date | a Date object representing the date to which the "modified date" portion of this ModelHistory should be set. |
|
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.
|
virtualinherited |
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. |
Reimplemented from SBase.
|
virtualinherited |
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. |
Reimplemented from SBase.
|
virtualinherited |
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.
| model | the Model to merge with this one. |
|
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 |
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 |
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.
|
virtual |
Creates and returns a deep copy of this ModelDefinition object.
Reimplemented from Model.
|
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 |
Deletes all information stored in disabled plugins.
If the plugin is re-enabled later, it will then not have any previously-stored information.
| 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. |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).
| pkgURI | the URI of the package. |
| pkgPrefix | the XML prefix of the package. |
| flag | whether to enable (true) or disable (false) the package. |
|
inherited |
Returns the internal list of the identifiers of all elements within this Model object.
|
inherited |
Returns the internal list of the metaids of all elements within this Model object.
|
virtualinherited |
Returns a List of all child objects.
This returns all child objects nested to an arbitrary depth. If an optional element filter is provided, only those objects for which the filter's filter() method returns true will be added to the list.
| filter | a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects. |
Reimplemented from SBase.
|
virtualinherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.
| filter | a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects. |
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.
| 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.
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. The set of possible type codes is defined in the enumeration SBMLTypeCode_t. The names of the type codes all begin with the characters SBML_.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.
| 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.
|
inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
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.
|
inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
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.
|
inherited |
Returns the content of the "annotation" subelement of this object as a character string.
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.
|
inherited |
Returns the content of the "annotation" subelement of this object as a character string.
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.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns the column number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
Get a Compartment object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such Compartment exists.
|
inherited |
Get a Compartment object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such Compartment exists.
|
inherited |
Get the nth Compartment object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth Compartment object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get a CompartmentType object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such CompartmentType exists.
|
inherited |
Get a CompartmentType object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such CompartmentType exists.
|
inherited |
Get the nth CompartmentType object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth CompartmentType object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth Constraint object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth Constraint object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
|
inherited |
Returns the "creation date" portion of the ModelHistory of this object.
|
inherited |
Returns the "creation date" portion of the ModelHistory of this object.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
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.
| n | the index of the disabled plug-in to return. |
n is invalid, NULL is returned.
|
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.
| n | the index of the disabled plug-in to return. |
n is invalid, NULL is returned.
|
virtualinherited |
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. Reimplemented from SBase.
|
inherited |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL if no such object is found.
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.| metaid | string representing the "metaid" attribute value of the object to find. |
|
virtualinherited |
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. Reimplemented from SBase.
|
virtualinherited |
Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.
| id | string representing the "id" attribute value of the object to find. |
|
virtual |
Returns the XML element name of this object.
The only difference between a Model and a ModelDefinition is the element name ('modelDefinition').
Reimplemented from Model.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get a FunctionDefinition object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such FunctionDefinition exists.
|
inherited |
Get a FunctionDefinition object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such FunctionDefinition exists.
|
inherited |
Get the nth FunctionDefinitions object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth FunctionDefinitions object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
virtualinherited |
Returns the value of the "id" attribute of this Model.
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.
Reimplemented from SBase.
|
inherited |
Returns the value of the "id" attribute of this SBML object.
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 |
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.
|
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.
|
inherited |
Get the nth InitialAssignment object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth InitialAssignment object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
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.
|
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.
|
inherited |
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number where this object first appears in the XML representation of the SBML document.
0.
|
inherited |
Get the ListOfCompartments object in this Model.
|
inherited |
Get the ListOfCompartments object in this Model.
|
inherited |
Get the ListOfCompartmentTypes object in this Model.
|
inherited |
Get the ListOfCompartmentTypes object in this Model.
|
inherited |
Get the ListOfConstraints object in this Model.
|
inherited |
Get the ListOfConstraints object in this Model.
|
inherited |
Get the ListOfEvents object in this Model.
|
inherited |
Get the ListOfEvents object in this Model.
|
inherited |
Get the ListOfFunctionDefinitions object in this Model.
|
inherited |
Get the ListOfFunctionDefinitions object in this Model.
|
inherited |
Get the ListOfInitialAssignments object in this Model.
|
inherited |
Get the ListOfInitialAssignments object in this Model.
|
inherited |
Get the ListOfParameters object in this Model.
|
inherited |
Get the ListOfParameters object in this Model.
|
inherited |
Get the ListOfReactions object in this Model.
|
inherited |
Get the ListOfReactions object in this Model.
|
inherited |
Get the ListOfRules object in this Model.
|
inherited |
Get the ListOfRules object in this Model.
|
inherited |
Get the ListOfSpecies object in this Model.
|
inherited |
Get the ListOfSpecies object in this Model.
|
inherited |
Get the ListOfSpeciesTypes object in this Model.
|
inherited |
Get the ListOfSpeciesTypes object in this Model.
|
inherited |
Get the ListOfUnitDefinitions object in this Model.
|
inherited |
Get the ListOfUnitDefinitions object in this Model.
|
inherited |
Returns the value of the "metaid" attribute of this SBML object.
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 |
Returns the value of the "metaid" attribute of this SBML object.
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 |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL if none exist.
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL if none exist.
|
inherited |
Get the nth Date object in the list of "modified date" values stored in the ModelHistory of this object.
In the MIRIAM format for annotations, there can be multiple modification dates. The libSBML ModelHistory class supports this by storing a list of "modified date" values.
NULL if no such object exists.
|
inherited |
Get a ModifierSpeciesReference object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such ModifierSpeciesReference exists.
|
inherited |
Get a ModifierSpeciesReference object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such ModifierSpeciesReference exists.
|
virtualinherited |
Returns the value of the "name" attribute of this Model object.
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.
Reimplemented from SBase.
|
virtualinherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
NULL in certain very usual circumstances where a namespace is not set.Reimplemented in SBMLDocument.
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
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().
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
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().
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
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.
|
inherited |
Returns the content of the "notes" subelement of this object as a string.
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.
|
inherited |
Get the number of Compartment objects in this Model.
|
inherited |
Get the number of CompartmentType objects in this Model.
|
inherited |
Get the number of Constraint objects in this Model.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
|
inherited |
|
inherited |
Get the number of FunctionDefinition objects in this Model.
|
inherited |
Get the number of InitialAssignment objects in this Model.
|
inherited |
Get the number of Date objects in the ModelHistory of this Iobject's list of "modified dates".
In the MIRIAM format for annotations, there can be multiple modification dates. The libSBML ModelHistory class supports this by storing a list of "modified date" values.
|
inherited |
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get the number of SpeciesType objects in this Model.
|
inherited |
|
inherited |
Get the number of UnitDefinition objects in this Model.
|
inherited |
Returns the SBML Core Version within the SBML Level of the actual object.
|
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.
|
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.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get the nth Parameter object in this Model.
| n | the index of the object to return. |
|
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.
|
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.
|
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.
| package | the name or URI of the package. |
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
The returned plug-in will be the appropriate type of plugin requested: calling Model::getPlugin("fbc") will return an FbcModelPlugin; calling Parameter::getPlugin("comp") will return CompSBasePlugin, etc.
If no such plugin exists, NULL is returned.
| package | the name or URI of the package. |
|
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.
| n | the index of the plug-in to return. |
n is invalid, NULL is returned.
|
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.
| n | the index of the plug-in to return. |
n is invalid, NULL is returned.
|
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.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values from the enumeration type BiolQualifierType_t.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value from the enumeration type BiolQualifierType_t.
| resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892". |
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is "isDerivedFrom", to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values from the enumeration type ModelQualifierType_t.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value from the enumeration type ModelQualifierType_t.
| resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892". |
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inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the integer portion of the value of the "sboTerm" attribute of this object.
int, and SBO identifiers are stored simply as integers. -1 if the value is not set.
|
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".
|
inherited |
Returns the string representation of the "sboTerm" attribute of this object.
int, and SBO identifiers are stored simply as integers.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get a SpeciesReference object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such SpeciesReference exists.
|
inherited |
Get a SpeciesReference object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such SpeciesReference exists.
|
inherited |
Get a SpeciesType object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such SpeciesType exists.
|
inherited |
Get a SpeciesType object based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such SpeciesType exists.
|
inherited |
Get the nth SpeciesType object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth SpeciesType object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
|
inherited |
|
virtual |
Returns the libSBML type code of this object instance.
SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase::getPackageName() method on the object.The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
Reimplemented from Model.
|
inherited |
Get a UnitDefinition based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such UnitDefinition exists.
|
inherited |
Get a UnitDefinition based on its identifier.
| sid | the identifier to search for. |
sid or NULL if no such UnitDefinition exists.
|
inherited |
Get the nth UnitDefinition object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Get the nth UnitDefinition object in this Model.
| n | the index of the object to return. |
n is invalid, NULL is returned.
|
inherited |
Returns 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.
|
inherited |
Returns the user data that has been previously set via setUserData().
NULL if no user data has been set.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
inherited |
|
virtualinherited |
Predicate returning true if all the required elements for this Model object have been set.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
inherited |
|
inherited |
|
inherited |
Predicate returning true if this object has a ModelHistory object attached to it and the created date is set.
true if the CreatedDate of the ModelHistory of this object is set, false otherwise.
|
inherited |
|
virtualinherited |
Predicate returning true if this Model's "id" attribute is set.
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.Reimplemented from SBase.
|
inherited |
Predicate returning true if this object's "id" attribute is set.
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.
|
inherited |
|
inherited |
Predicate returning true if this object's "metaid" attribute is set.
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.
|
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.
|
inherited |
Predicate returning true or false depending on whether the ModelHistory's "modified date" of this object is set.
true if the modification date value of this ModelHistory object is set, false otherwise.
|
virtualinherited |
Predicate returning true if this Model's "name" attribute is set.
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.Reimplemented from SBase.
|
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.
|
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.
|
inherited |
|
inherited |
|
inherited |
Predicate returning true or false depending on whether the user data of this element has been set.
true if this object's user data has been set, false otherwise.
|
inherited |
|
inherited |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
| 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.
|
inherited |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
| 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.
|
inherited |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
| 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.
|
inherited |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
| 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. | ModelDefinition & ModelDefinition::operator= | ( | const Model & | source | ) |
Assignment operator.
| source | the object whose values are used as the basis of the assignment. |
|
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().
|
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().
|
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.
|
inherited |
Reads (initializes) this SBML object by reading from the given XMLNode.
| node | the XMLNode to read from. |
| flag | an optional flag that determines how how errors are logged during the reading process. |
|
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.
|
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.
|
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.
|
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.
|
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.
|
inherited |
|
inherited |
|
virtual |
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.
Reimplemented from Model.
|
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.
|
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.
|
inherited |
Removes the InitialAssignment object with the given "symbol" attribute from this Model object and returns a pointer to it.
Removes the InitialAssignment object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| symbol | the "symbol" attribute of the InitialAssignment object to remove. |
NULL if no InitialAssignment object with the "symbol" attribute exists in this Model object.
|
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.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it.
Removes the Rule object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| variable | the "variable" attribute of the Rule object to remove. |
|
inherited |
|
inherited |
Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it.
Removes the Rule object with the given variable from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
| variable | the "variable" attribute of the Rule object to remove. |
|
inherited |
|
inherited |
|
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.
|
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.
|
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). |
|
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.
|
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.
|
virtualinherited |
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. |
Reimplemented in GraphicalObject, and Port.
|
virtualinherited |
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. |
Reimplemented from SBase.
|
virtualinherited |
UnitSIdRef type attribute value with another value.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. |
Reimplemented from SBase.
|
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. |
|
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. |
|
virtualinherited |
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. |
Reimplemented from SBase.
|
virtualinherited |
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. |
Reimplemented from SBase.
|
inherited |
Sets the value of the "areaUnits" attribute of this Model.
The string in units is copied.
| units | the new areaUnits for the Model. |
|
inherited |
Sets the value of the "conversionFactor" attribute of this Model.
The string in units is copied.
| units | the new conversionFactor for the Model. |
|
inherited |
Sets the creation date of the ModelHistory of this object.
| date | a Date object representing the date to which the "created date" portion of this ModelHistory should be set. |
|
protectedvirtualinherited |
When overridden allows SBase elements to use the text included in between the elements tags.
The default implementation does nothing.
| text | the text string found between the element tags. |
|
inherited |
Sets the value of the "extentUnits" attribute of this Model.
The string in units is copied.
| units | the new extentUnits for the Model. |
|
virtualinherited |
Sets the value of the "id" attribute of this Model.
sid is copied.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. |
Reimplemented from SBase.
|
virtualinherited |
Sets the value of the "id" attribute of this SBML object.
sid is copied.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. |
|
inherited |
Sets the value of the "lengthUnits" attribute of this Model.
The string in units is copied.
| units | the new lengthUnits for the Model. |
|
inherited |
Sets the value of the meta-identifier attribute of this SBML object.
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. |
|
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. |
|
virtualinherited |
Sets the value of the "name" attribute of this Model.
The string in name is copied.
| name | the new name for the SBML object. |
Reimplemented from SBase.
|
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. |
|
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. |
|
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. |
|
virtualinherited |
Sets the value of the "sboTerm" attribute by string.
int, and SBO identifiers are stored simply as integers. | sboid | the SBO identifier string of the form "SBO:NNNNNNN". |
|
virtualinherited |
Sets the value of the "sboTerm" attribute.
int, and SBO identifiers are stored simply as integers. | value | the NNNNNNN integer portion of the SBO identifier. |
|
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 user data of this element.
| userData | specifies the new user data. |
|
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 |
Unsets the value of the "areaUnits" attribute of this Model.
|
inherited |
Unsets the value of the "conversionFactor" attribute of this Model.
|
inherited |
Unsets the created date of the ModelHistory object attached to this object.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
inherited |
Unsets the value of the "extentUnits" attribute of this Model.
|
virtualinherited |
Unsets the value of the "id" attribute of this Model.
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.
Reimplemented from SBase.
|
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 |
Unsets the value of the "lengthUnits" attribute of this Model.
|
inherited |
Unsets the value of the "metaid" attribute of this SBML object.
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 modified dates of the ModelHistory object attached to this object.
|
virtualinherited |
Unsets the value of the "name" attribute of this Model.
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.
Reimplemented from SBase.
|
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.
|
inherited |
Unsets the value of the "substanceUnits" attribute of this Model.
|
inherited |
Unsets the value of the "timeUnits" attribute of this Model.
|
inherited |
Unsets the user data of this element.
|
inherited |
Unsets the value of the "volumeUnits" attribute of this Model.