libSBML C# API  libSBML 5.8.0 C# API
 All Classes Namespaces Files Functions Variables Properties Pages
libsbmlcs.ModelDefinition Class Reference
Inheritance diagram for libsbmlcs.ModelDefinition:
[legend]

Public Member Functions

virtual bool acceptComp (SWIGTYPE_p_CompVisitor v)
 
int addCompartment (Compartment c)
 Adds a copy of the given Compartment object to this Model. More...
 
int addCompartmentType (CompartmentType ct)
 Adds a copy of the given CompartmentType object to this Model. More...
 
void addConstantAttribute ()
 Predicate returning true if the given ASTNode is a bool. More...
 
int addConstraint (Constraint c)
 Adds a copy of the given Constraint object to this Model. More...
 
int addCVTerm (CVTerm term, bool newBag)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
int addCVTerm (CVTerm term)
 Adds a copy of the given CVTerm object to this SBML object. More...
 
void addDefinitionsForDefaultUnits ()
 Predicate returning true if the given ASTNode is a bool. More...
 
int addEvent (Event e)
 Adds a copy of the given Event object to this Model. More...
 
int addFunctionDefinition (FunctionDefinition fd)
 Adds a copy of the given FunctionDefinition object to this Model. More...
 
int addInitialAssignment (InitialAssignment ia)
 Adds a copy of the given InitialAssignment object to this Model. More...
 
void addModifiers ()
 Predicate returning true if the given ASTNode is a bool. More...
 
int addParameter (Parameter p)
 Adds a copy of the given Parameter object to this Model. More...
 
int addReaction (Reaction r)
 Adds a copy of the given Reaction object to this Model. More...
 
int addRule (Rule r)
 Adds a copy of the given Rule object to this Model. More...
 
int addSpecies (Species s)
 Adds a copy of the given Species object to this Model. More...
 
int addSpeciesType (SpeciesType st)
 Adds a copy of the given SpeciesType object to this Model. More...
 
int addUnitDefinition (UnitDefinition ud)
 Adds a copy of the given UnitDefinition object to this Model. More...
 
new int appendAnnotation (XMLNode annotation)
 Appends annotation content to any existing content in the 'annotation' subelement of this object. More...
 
new int appendAnnotation (string annotation)
 Appends annotation content to any existing content in the 'annotation' subelement of this object. More...
 
int appendFrom (Model model)
 Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model. More...
 
int appendNotes (XMLNode notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
int appendNotes (string notes)
 Appends the given notes to the 'notes' subelement of this object. More...
 
void assignRequiredValues ()
 Predicate returning true if the given ASTNode is a bool. More...
 
int checkCompatibility (SBase arg0)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
string checkMathMLNamespace (XMLToken elem)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
new SBase clone ()
 Creates and returns a deep copy of this Model object. More...
 
void connectToParent (SBase parent)
 Sets the parent SBML object of this SBML object. More...
 
void convertL1ToL2 ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL1ToL3 ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL2ToL1 (bool strict)
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL2ToL1 ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL2ToL3 ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL3ToL1 ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL3ToL2 (bool strict)
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertL3ToL2 ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertParametersToLocals (long level, long version)
 Predicate returning true if the given ASTNode is a bool. More...
 
void convertStoichiometryMath ()
 Predicate returning true if the given ASTNode is a bool. 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 dealWithEvents (bool strict)
 Predicate returning true if the given ASTNode is a bool. More...
 
void dealWithModelUnits ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void dealWithStoichiometry ()
 Predicate returning true if the given ASTNode is a bool. More...
 
int disablePackage (string pkgURI, string pkgPrefix)
 Disables the given SBML Level 3 package. More...
 
override void Dispose ()
 
void divideAssignmentsToSIdByFunction (string id, ASTNode function)
 If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...
 
int enablePackage (string pkgURI, string pkgPrefix, bool flag)
 Enables or disables the given SBML Level 3 package. More...
 
override bool Equals (Object sb)
 
SBase getAncestorOfType (int type, string pkgName)
 Returns the first ancestor object that has the given SBML type code. More...
 
SBase getAncestorOfType (int type)
 Returns the first ancestor object that has the given SBML type code. More...
 
XMLNode getAnnotation ()
 Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...
 
string getAnnotationString ()
 Returns the content of the 'annotation' subelement of this object as a character string. More...
 
string getAreaUnits ()
 Returns the value of the 'areaUnits' attribute of this Model. More...
 
long getColumn ()
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
Compartment getCompartment (long n)
 Get the nth Compartment object in this Model. More...
 
Compartment getCompartment (string sid)
 Get a Compartment object based on its identifier. More...
 
CompartmentType getCompartmentType (long n)
 Get the nth CompartmentType object in this Model. More...
 
CompartmentType getCompartmentType (string sid)
 Get a CompartmentType object based on its identifier. More...
 
Constraint getConstraint (long n)
 Get the nth Constraint object in this Model. More...
 
string getConversionFactor ()
 Returns the value of the 'conversionFactor' attribute of this Model. More...
 
CVTerm getCVTerm (long n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
CVTermList getCVTerms ()
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
SBase getElementByMetaId (string metaid)
 Returns the first child element it can find with the given metaid, or null if no such object is found. More...
 
SBase getElementBySId (string id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found. More...
 
SBase getElementFromPluginsByMetaId (string metaid)
 Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More...
 
SBase getElementFromPluginsBySId (string id)
 Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More...
 
new string getElementName ()
 Returns the XML element name of this object, which for Model, is always 'model'. More...
 
Event getEvent (long n)
 Get the nth Event object in this Model. More...
 
Event getEvent (string sid)
 Get an Event object based on its identifier. More...
 
string getExtentUnits ()
 Returns the value of the 'extentUnits' attribute of this Model. More...
 
FunctionDefinition getFunctionDefinition (long n)
 Get the nth FunctionDefinitions object in this Model. More...
 
FunctionDefinition getFunctionDefinition (string sid)
 Get a FunctionDefinition object based on its identifier. More...
 
override int GetHashCode ()
 
new string getId ()
 Returns the value of the 'id' attribute of this Model. More...
 
InitialAssignment getInitialAssignment (long n)
 Get the nth InitialAssignment object in this Model. More...
 
InitialAssignment getInitialAssignment (string symbol)
 Get an InitialAssignment object based on the symbol to which it assigns a value. More...
 
string getLengthUnits ()
 Returns the value of the 'lengthUnits' attribute of this Model. More...
 
long getLevel ()
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
long getLine ()
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
SBaseList getListOfAllElements ()
 
SBaseList getListOfAllElementsFromPlugins ()
 
ListOfCompartments getListOfCompartments ()
 Get the ListOfCompartments object in this Model. More...
 
ListOfCompartmentTypes getListOfCompartmentTypes ()
 Get the ListOfCompartmentTypes object in this Model. More...
 
ListOfConstraints getListOfConstraints ()
 Get the ListOfConstraints object in this Model. More...
 
ListOfEvents getListOfEvents ()
 Get the ListOfEvents object in this Model. More...
 
ListOfFunctionDefinitions getListOfFunctionDefinitions ()
 Get the ListOfFunctionDefinitions object in this Model. More...
 
ListOfInitialAssignments getListOfInitialAssignments ()
 Get the ListOfInitialAssignments object in this Model. More...
 
ListOfParameters getListOfParameters ()
 Get the ListOfParameters object in this Model. More...
 
ListOfReactions getListOfReactions ()
 Get the ListOfReactions object in this Model. More...
 
ListOfRules getListOfRules ()
 Get the ListOfRules object in this Model. More...
 
ListOfSpecies getListOfSpecies ()
 Get the ListOfSpecies object in this Model. More...
 
ListOfSpeciesTypes getListOfSpeciesTypes ()
 Get the ListOfSpeciesTypes object in this Model. More...
 
ListOfUnitDefinitions getListOfUnitDefinitions ()
 Get the ListOfUnitDefinitions object in this Model. More...
 
string getMetaId ()
 Returns the value of the 'metaid' attribute of this object. More...
 
Model getModel ()
 Returns the Model object in which the current object is located. More...
 
ModelHistory getModelHistory ()
 Returns the ModelHistory object, if any, attached to this object. More...
 
new string getName ()
 Returns the value of the 'name' attribute of this Model. More...
 
XMLNamespaces getNamespaces ()
 Returns a list of the XML Namespaces declared on this SBML document. More...
 
XMLNode getNotes ()
 Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...
 
string getNotesString ()
 Returns the content of the 'notes' subelement of this object as a string. More...
 
long getNumCompartments ()
 Get the number of Compartment objects in this Model. More...
 
long getNumCompartmentTypes ()
 Get the number of CompartmentType objects in this Model. More...
 
long getNumConstraints ()
 Get the number of Constraint objects in this Model. More...
 
long getNumCVTerms ()
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
long getNumEvents ()
 Get the number of Event objects in this Model. More...
 
long getNumFunctionDefinitions ()
 Get the number of FunctionDefinition objects in this Model. More...
 
long getNumInitialAssignments ()
 Get the number of InitialAssignment objects in this Model. More...
 
long getNumParameters ()
 Get the number of Parameter objects in this Model. More...
 
long getNumPlugins ()
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
long getNumReactions ()
 Get the number of Reaction objects in this Model. More...
 
long getNumRules ()
 Get the number of Rule objects in this Model. More...
 
long getNumSpecies ()
 Get the number of Specie objects in this Model. More...
 
long getNumSpeciesTypes ()
 Get the number of SpeciesType objects in this Model. More...
 
long getNumSpeciesWithBoundaryCondition ()
 Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true. More...
 
long getNumUnitDefinitions ()
 Get the number of UnitDefinition objects in this Model. More...
 
string getPackageName ()
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
long getPackageVersion ()
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
Parameter getParameter (long n)
 Get the nth Parameter object in this Model. More...
 
Parameter getParameter (string sid)
 Get a Parameter object based on its identifier. More...
 
SBase getParentSBMLObject ()
 Returns the parent SBML object containing this object. More...
 
SBasePlugin getPlugin (string package)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...
 
SBasePlugin getPlugin (long n)
 Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
Reaction getReaction (long n)
 Get the nth Reaction object in this Model. More...
 
Reaction getReaction (string sid)
 Get a Reaction object based on its identifier. More...
 
int getResourceBiologicalQualifier (string resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
int getResourceModelQualifier (string resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
Rule getRule (long n)
 Get the nth Rule object in this Model. More...
 
Rule getRule (string variable)
 Get a Rule object based on the variable to which it assigns a value. More...
 
SBMLDocument getSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
SBMLNamespaces getSBMLNamespaces ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int getSBOTerm ()
 Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...
 
string getSBOTermAsURL ()
 Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More...
 
string getSBOTermID ()
 Returns the string representation of the 'sboTerm' attribute of this object. More...
 
Species getSpecies (long n)
 Get the nth Species object in this Model. More...
 
Species getSpecies (string sid)
 Get a Species object based on its identifier. More...
 
SpeciesReference getSpeciesReference (string sid)
 Get a SpeciesReference object based on its identifier. More...
 
SpeciesType getSpeciesType (long n)
 Get the nth SpeciesType object in this Model. More...
 
SpeciesType getSpeciesType (string sid)
 Get a SpeciesType object based on its identifier. More...
 
string getSubstanceUnits ()
 Returns the value of the 'substanceUnits' attribute of this Model. More...
 
string getTimeUnits ()
 Returns the value of the 'timeUnits' attribute of this Model. More...
 
new int getTypeCode ()
 Returns the libSBML type code for this SBML object. More...
 
UnitDefinition getUnitDefinition (long n)
 Get the nth UnitDefinition object in this Model. More...
 
UnitDefinition getUnitDefinition (string sid)
 Get a UnitDefinition based on its identifier. More...
 
long getVersion ()
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
string getVolumeUnits ()
 Returns the value of the 'volumeUnits' attribute of this Model. More...
 
bool hasNonstandardIdentifierBeginningWith (string prefix)
 Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More...
 
bool hasRequiredAttributes ()
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
new bool hasRequiredElements ()
 Predicate returning true if all the required elements for this Model object have been set. More...
 
bool hasValidLevelVersionNamespaceCombination ()
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
bool isPackageEnabled (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPackageURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPkgEnabled (string pkgName)
 Predicate returning true if the given SBML Level 3 package is enabled with this object. More...
 
bool isPkgURIEnabled (string pkgURI)
 Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More...
 
bool isPopulatedListFormulaUnitsData ()
 Predicate returning true if the list of FormulaUnitsData is populated. More...
 
bool isSetAnnotation ()
 Predicate returning true if this object's 'annotation' subelement exists and has content. More...
 
bool isSetAreaUnits ()
 Predicate returning true if this Model's 'areaUnits' attribute is set. More...
 
bool isSetConversionFactor ()
 Predicate returning true if this Model's 'conversionFactor' attribute is set. More...
 
bool isSetExtentUnits ()
 Predicate returning true if this Model's 'extentUnits' attribute is set. More...
 
new bool isSetId ()
 Predicate returning true if this Model's 'id' attribute is set. More...
 
bool isSetLengthUnits ()
 Predicate returning true if this Model's 'lengthUnits' attribute is set. More...
 
bool isSetMetaId ()
 Predicate returning true if this object's 'metaid' attribute is set. More...
 
bool isSetModelHistory ()
 Predicate returning true if this object has a ModelHistory object attached to it. More...
 
new bool isSetName ()
 Predicate returning true if this Model's 'name' attribute is set. More...
 
bool isSetNotes ()
 Predicate returning true if this object's 'notes' subelement exists and has content. More...
 
bool isSetSBOTerm ()
 Predicate returning true if this object's 'sboTerm' attribute is set. More...
 
bool isSetSubstanceUnits ()
 Predicate returning true if this Model's 'substanceUnits' attribute is set. More...
 
bool isSetTimeUnits ()
 Predicate returning true if this Model's 'timeUnits' attribute is set. More...
 
bool isSetVolumeUnits ()
 Predicate returning true if this Model's 'volumeUnits' attribute is set. More...
 
bool matchesRequiredSBMLNamespacesForAddition (SBase sb)
 Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
bool matchesSBMLNamespaces (SBase sb)
 Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
 ModelDefinition (long level, long version, long pkgVersion)
 
 ModelDefinition (long level, long version)
 
 ModelDefinition (long level)
 
 ModelDefinition ()
 
 ModelDefinition (CompPkgNamespaces compns)
 
 ModelDefinition (Model source)
 
void multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
 If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...
 
void populateListFormulaUnitsData ()
 Populates the list of FormulaDataUnits with the units derived for the model. More...
 
int prependStringToAllIdentifiers (string prefix)
 Add the given string to all identifiers in the object. More...
 
Compartment removeCompartment (long n)
 Removes the nth Compartment object from this Model object and returns a pointer to it. More...
 
Compartment removeCompartment (string sid)
 Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More...
 
CompartmentType removeCompartmentType (long n)
 Removes the nth CompartmentType object from this Model object and returns a pointer to it. More...
 
CompartmentType removeCompartmentType (string sid)
 Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More...
 
Constraint removeConstraint (long n)
 Removes the nth Constraint object from this Model object and returns a pointer to it. More...
 
Event removeEvent (long n)
 Removes the nth Event object from this Model object and returns a pointer to it. More...
 
Event removeEvent (string sid)
 Removes the Event object with the given identifier from this Model object and returns a pointer to it. More...
 
new int removeFromParentAndDelete ()
 
FunctionDefinition removeFunctionDefinition (long n)
 Removes the nth FunctionDefinition object from this Model object and returns a pointer to it. More...
 
FunctionDefinition removeFunctionDefinition (string sid)
 Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it. More...
 
InitialAssignment removeInitialAssignment (long n)
 Removes the nth InitialAssignment object from this Model object and returns a pointer to it. More...
 
InitialAssignment removeInitialAssignment (string symbol)
 Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it. More...
 
Parameter removeParameter (long n)
 Removes the nth Parameter object from this Model object and returns a pointer to it. More...
 
Parameter removeParameter (string sid)
 Removes the Parameter object with the given identifier from this Model object and returns a pointer to it. More...
 
void removeParameterRuleUnits (bool strict)
 Predicate returning true if the given ASTNode is a bool. More...
 
Reaction removeReaction (long n)
 Removes the nth Reaction object from this Model object and returns a pointer to it. More...
 
Reaction removeReaction (string sid)
 Removes the Reaction object with the given identifier from this Model object and returns a pointer to it. More...
 
Rule removeRule (long n)
 Removes the nth Rule object from this Model object and returns a pointer to it. More...
 
Rule removeRule (string variable)
 Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it. More...
 
Species removeSpecies (long n)
 Removes the nth Species object from this Model object and returns a pointer to it. More...
 
Species removeSpecies (string sid)
 Removes the Species object with the given identifier from this Model object and returns a pointer to it. More...
 
SpeciesType removeSpeciesType (long n)
 Removes the nth SpeciesType object from this Model object and returns a pointer to it. More...
 
SpeciesType removeSpeciesType (string sid)
 Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More...
 
int removeTopLevelAnnotationElement (string elementName, string elementURI)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
int removeTopLevelAnnotationElement (string elementName)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
UnitDefinition removeUnitDefinition (long n)
 Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More...
 
UnitDefinition removeUnitDefinition (string sid)
 Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More...
 
void renameMetaIdRefs (string oldid, string newid)
 Renames all the MetaIdRef attributes on this element. More...
 
void renameSIdRefs (string oldid, string newid)
 Renames all the SIdRef attributes on this element, including any found in MathML. More...
 
void renameUnitSIdRefs (string oldid, string newid)
 Renames all the UnitSIdRef attributes on this element. More...
 
void replaceSIDWithFunction (string id, ASTNode function)
 If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...
 
int replaceTopLevelAnnotationElement (XMLNode annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
int replaceTopLevelAnnotationElement (string annotation)
 Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More...
 
new int setAnnotation (XMLNode annotation)
 Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation. More...
 
new int setAnnotation (string annotation)
 Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation. More...
 
int setAreaUnits (string units)
 Sets the value of the 'areaUnits' attribute of this Model. More...
 
int setConversionFactor (string units)
 Sets the value of the 'conversionFactor' attribute of this Model. More...
 
int setExtentUnits (string units)
 Sets the value of the 'extentUnits' attribute of this Model. More...
 
new int setId (string sid)
 Sets the value of the 'id' attribute of this Model. More...
 
int setLengthUnits (string units)
 Sets the value of the 'lengthUnits' attribute of this Model. More...
 
int setMetaId (string metaid)
 Sets the value of the 'metaid' attribute of this object. More...
 
int setModelHistory (ModelHistory history)
 Sets the ModelHistory of this object. More...
 
new int setName (string name)
 Sets the value of the 'name' attribute of this Model. More...
 
int setNamespaces (XMLNamespaces xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
int setNotes (XMLNode notes)
 Sets the value of the 'notes' subelement of this SBML object. More...
 
int setNotes (string notes, bool addXHTMLMarkup)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
int setNotes (string notes)
 Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes. More...
 
void setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns)
 Subclasses should override this method to write out their contained SBML objects as XML elements. More...
 
int setSBOTerm (int value)
 Sets the value of the 'sboTerm' attribute. More...
 
int setSBOTerm (string sboid)
 Sets the value of the 'sboTerm' attribute by string. More...
 
void setSpatialDimensions (double dims)
 Predicate returning true if the given ASTNode is a bool. More...
 
void setSpatialDimensions ()
 Predicate returning true if the given ASTNode is a bool. More...
 
void setSpeciesReferenceConstantValueAndStoichiometry ()
 Predicate returning true if the given ASTNode is a bool. More...
 
int setSubstanceUnits (string units)
 Sets the value of the 'substanceUnits' attribute of this Model. More...
 
int setTimeUnits (string units)
 Sets the value of the 'timeUnits' attribute of this Model. More...
 
int setVolumeUnits (string units)
 Sets the value of the 'volumeUnits' attribute of this Model. More...
 
string toSBML ()
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
int unsetAnnotation ()
 Unsets the value of the 'annotation' subelement of this SBML object. More...
 
int unsetAreaUnits ()
 Unsets the value of the 'areaUnits' attribute of this Model. More...
 
int unsetConversionFactor ()
 Unsets the value of the 'conversionFactor' attribute of this Model. More...
 
int unsetCVTerms ()
 Clears the list of CVTerm objects attached to this SBML object. More...
 
int unsetExtentUnits ()
 Unsets the value of the 'extentUnits' attribute of this Model. More...
 
new int unsetId ()
 Unsets the value of the 'id' attribute of this Model. More...
 
int unsetLengthUnits ()
 Unsets the value of the 'lengthUnits' attribute of this Model. More...
 
int unsetMetaId ()
 Unsets the value of the 'metaid' attribute of this SBML object. More...
 
int unsetModelHistory ()
 Unsets the ModelHistory object attached to this object. More...
 
new int unsetName ()
 Unsets the value of the 'name' attribute of this Model. More...
 
int unsetNotes ()
 Unsets the value of the 'notes' subelement of this SBML object. More...
 
int unsetSBOTerm ()
 Unsets the value of the 'sboTerm' attribute of this SBML object. More...
 
int unsetSubstanceUnits ()
 Unsets the value of the 'substanceUnits' attribute of this Model. More...
 
int unsetTimeUnits ()
 Unsets the value of the 'timeUnits' attribute of this Model. More...
 
int unsetVolumeUnits ()
 Unsets the value of the 'volumeUnits' attribute of this Model. More...
 
void writeExtensionElements (XMLOutputStream stream)
 Writes out contained SBML objects of package extensions (if any) as XML elements. More...
 

Static Public Member Functions

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

Protected Attributes

bool swigCMemOwn
 

Constructor & Destructor Documentation

libsbmlcs.ModelDefinition.ModelDefinition ( long  level,
long  version,
long  pkgVersion 
)
libsbmlcs.ModelDefinition.ModelDefinition ( long  level,
long  version 
)
libsbmlcs.ModelDefinition.ModelDefinition ( long  level)
libsbmlcs.ModelDefinition.ModelDefinition ( )
libsbmlcs.ModelDefinition.ModelDefinition ( CompPkgNamespaces  compns)
libsbmlcs.ModelDefinition.ModelDefinition ( Model  source)

Member Function Documentation

virtual bool libsbmlcs.ModelDefinition.acceptComp ( SWIGTYPE_p_CompVisitor  v)
virtual
int libsbmlcs.Model.addCompartment ( Compartment  c)
inherited

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

Parameters
cthe Compartment object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createCompartment() for a method that does not lead to these issues.
See Also
createCompartment()
int libsbmlcs.Model.addCompartmentType ( CompartmentType  ct)
inherited

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

Parameters
ctthe CompartmentType object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createCompartmentType() for a method that does not lead to these issues.
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See Also
createCompartmentType()
void libsbmlcs.Model.addConstantAttribute ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
int libsbmlcs.Model.addConstraint ( Constraint  c)
inherited

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

Parameters
cthe Constraint object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createConstraint() for a method that does not lead to these issues.
See Also
createConstraint()
int libsbmlcs.SBase.addCVTerm ( CVTerm  term,
bool  newBag 
)
inherited

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

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
int libsbmlcs.SBase.addCVTerm ( CVTerm  term)
inherited

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

Parameters
termthe CVTerm to assign.
newBagif true, creates a new RDF bag with the same identifier as a previous bag, and if false, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
void libsbmlcs.Model.addDefinitionsForDefaultUnits ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
int libsbmlcs.Model.addEvent ( Event  e)
inherited

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

Parameters
ethe Event object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createEvent() for a method that does not lead to these issues.
See Also
createEvent()
int libsbmlcs.Model.addFunctionDefinition ( FunctionDefinition  fd)
inherited

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

Parameters
fdthe FunctionDefinition to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createFunctionDefinition() for a method that does not lead to these issues.
See Also
createFunctionDefinition()
int libsbmlcs.Model.addInitialAssignment ( InitialAssignment  ia)
inherited

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

Parameters
iathe InitialAssignment object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createInitialAssignment() for a method that does not lead to these issues.
See Also
createInitialAssignment()
void libsbmlcs.Model.addModifiers ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
int libsbmlcs.Model.addParameter ( Parameter  p)
inherited

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

Parameters
pthe Parameter object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createParameter() for a method that does not lead to these issues.
See Also
createParameter()
int libsbmlcs.Model.addReaction ( Reaction  r)
inherited

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

Parameters
rthe Reaction object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createReaction() for a method that does not lead to these issues.
See Also
createReaction()
int libsbmlcs.Model.addRule ( Rule  r)
inherited

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

Parameters
rthe Rule object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see the methods Model::createAlgebraicRule(), Model::createAssignmentRule() and Model::createRateRule() for methods that do not lead to these issues.
See Also
createAlgebraicRule()
createAssignmentRule()
createRateRule()
int libsbmlcs.Model.addSpecies ( Species  s)
inherited

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

Parameters
sthe Species object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createSpecies() for a method that does not lead to these issues.
See Also
createSpecies()
int libsbmlcs.Model.addSpeciesType ( SpeciesType  st)
inherited

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

Parameters
stthe SpeciesType object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createSpeciesType() for a method that does not lead to these issues.
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See Also
createSpeciesType()
int libsbmlcs.Model.addUnitDefinition ( UnitDefinition  ud)
inherited

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

Parameters
udthe UnitDefinition object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model::createUnitDefinition() for a method that does not lead to these issues.
See Also
createUnitDefinition()
new int libsbmlcs.Model.appendAnnotation ( XMLNode  annotation)
inherited

Appends annotation content to any existing content in the 'annotation' subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setAnnotation(XMLNode annotation)
new int libsbmlcs.Model.appendAnnotation ( string  annotation)
inherited

Appends annotation content to any existing content in the 'annotation' subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setAnnotation(string annotation)
int libsbmlcs.Model.appendFrom ( Model  model)
inherited

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

Also calls 'appendFrom' on all plugin objects.

Parameters
modelthe Model to merge with this one.
int libsbmlcs.SBase.appendNotes ( XMLNode  notes)
inherited

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.appendNotes ( string  notes)
inherited

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
void libsbmlcs.Model.assignRequiredValues ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
int libsbmlcs.SBase.checkCompatibility ( SBase  arg0)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

string libsbmlcs.SBase.checkMathMLNamespace ( XMLToken  elem)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

new SBase libsbmlcs.ModelDefinition.clone ( )

Creates and returns a deep copy of this Model object.

Returns
a (deep) copy of this Model.
void libsbmlcs.SBase.connectToParent ( SBase  parent)
inherited

Sets the parent SBML object of this SBML object.

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

Parameters
parentthe SBML object to use
void libsbmlcs.Model.convertL1ToL2 ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL1ToL3 ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL2ToL1 ( bool  strict)
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL2ToL1 ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL2ToL3 ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL3ToL1 ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL3ToL2 ( bool  strict)
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertL3ToL2 ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertParametersToLocals ( long  level,
long  version 
)
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.convertStoichiometryMath ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
AlgebraicRule libsbmlcs.Model.createAlgebraicRule ( )
inherited

Creates a new AlgebraicRule inside this Model and returns it.

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

Returns
the AlgebraicRule object created
See Also
addRule(Rule r)
AssignmentRule libsbmlcs.Model.createAssignmentRule ( )
inherited

Creates a new AssignmentRule inside this Model and returns it.

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

Returns
the AssignmentRule object created
See Also
addRule(Rule r)
Compartment libsbmlcs.Model.createCompartment ( )
inherited

Creates a new Compartment inside this Model and returns it.

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

Returns
the Compartment object created
See Also
addCompartment(Compartment c)
CompartmentType libsbmlcs.Model.createCompartmentType ( )
inherited

Creates a new CompartmentType inside this Model and returns it.

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

Returns
the CompartmentType object created
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See Also
addCompartmentType(CompartmentType ct)
Constraint libsbmlcs.Model.createConstraint ( )
inherited

Creates a new Constraint inside this Model and returns it.

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

Returns
the Constraint object created
See Also
addConstraint(Constraint c)
Delay libsbmlcs.Model.createDelay ( )
inherited

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

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

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

Returns
the Delay object created
Event libsbmlcs.Model.createEvent ( )
inherited

Creates a new Event inside this Model and returns it.

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

Returns
the Event object created
EventAssignment libsbmlcs.Model.createEventAssignment ( )
inherited

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

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

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

Returns
the EventAssignment object created
FunctionDefinition libsbmlcs.Model.createFunctionDefinition ( )
inherited

Creates a new FunctionDefinition inside this Model and returns it.

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

Returns
the FunctionDefinition object created
See Also
addFunctionDefinition(FunctionDefinition fd)
InitialAssignment libsbmlcs.Model.createInitialAssignment ( )
inherited

Creates a new InitialAssignment inside this Model and returns it.

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

Returns
the InitialAssignment object created
See Also
addInitialAssignment(InitialAssignment ia)
KineticLaw libsbmlcs.Model.createKineticLaw ( )
inherited

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

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

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

Returns
the KineticLaw object created
LocalParameter libsbmlcs.Model.createKineticLawLocalParameter ( )
inherited

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

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

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

Returns
the Parameter object created
Parameter libsbmlcs.Model.createKineticLawParameter ( )
inherited

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

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

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

Returns
the Parameter object created
ModifierSpeciesReference libsbmlcs.Model.createModifier ( )
inherited

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

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

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

Returns
the SpeciesReference object created
Parameter libsbmlcs.Model.createParameter ( )
inherited

Creates a new Parameter inside this Model and returns it.

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

Returns
the Parameter object created
See Also
addParameter(Parameter p)
SpeciesReference libsbmlcs.Model.createProduct ( )
inherited

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

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

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

Returns
the SpeciesReference object created
RateRule libsbmlcs.Model.createRateRule ( )
inherited

Creates a new RateRule inside this Model and returns it.

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

Returns
the RateRule object created
See Also
addRule(Rule r)
SpeciesReference libsbmlcs.Model.createReactant ( )
inherited

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

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

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

Returns
the SpeciesReference object created
Reaction libsbmlcs.Model.createReaction ( )
inherited

Creates a new Reaction inside this Model and returns it.

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

Returns
the Reaction object created
See Also
addReaction(Reaction r)
Species libsbmlcs.Model.createSpecies ( )
inherited

Creates a new Species inside this Model and returns it.

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

Returns
the Species object created
See Also
addSpecies(Species s)
SpeciesType libsbmlcs.Model.createSpeciesType ( )
inherited

Creates a new SpeciesType inside this Model and returns it.

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

Returns
the SpeciesType object created
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See Also
addSpeciesType(SpeciesType st)
Trigger libsbmlcs.Model.createTrigger ( )
inherited

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

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

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

Returns
the Trigger object created
Unit libsbmlcs.Model.createUnit ( )
inherited

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

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

The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and null is returned instead.

Returns
the Unit object created
See Also
addUnitDefinition(UnitDefinition ud)
UnitDefinition libsbmlcs.Model.createUnitDefinition ( )
inherited

Creates a new UnitDefinition inside this Model and returns it.

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

Returns
the UnitDefinition object created
See Also
addUnitDefinition(UnitDefinition ud)
void libsbmlcs.Model.dealWithEvents ( bool  strict)
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.dealWithModelUnits ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.dealWithStoichiometry ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
int libsbmlcs.SBase.disablePackage ( string  pkgURI,
string  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package.

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

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override void libsbmlcs.ModelDefinition.Dispose ( )
virtual

Reimplemented from libsbmlcs.Model.

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

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

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.enablePackage ( string  pkgURI,
string  pkgPrefix,
bool  flag 
)
inherited

Enables or disables the given SBML Level 3 package.

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

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether to enable (true) or disable (false) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
override bool libsbmlcs.SBase.Equals ( Object  sb)
inherited
SBase libsbmlcs.SBase.getAncestorOfType ( int  type,
string  pkgName 
)
inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
SBase libsbmlcs.SBase.getAncestorOfType ( int  type)
inherited

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

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.
XMLNode libsbmlcs.SBase.getAnnotation ( )
inherited

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

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

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

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
string libsbmlcs.SBase.getAnnotationString ( )
inherited

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

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

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

The annotations returned by this method will be in string form.

Returns
the annotation of this SBML object as a character string.
See Also
getAnnotation()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
string libsbmlcs.Model.getAreaUnits ( )
inherited

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

Returns
the areaUnits of this Model.
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
long libsbmlcs.SBase.getColumn ( )
inherited

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

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

Get the nth Compartment object in this Model.

Returns
the nth Compartment of this Model.
Compartment libsbmlcs.Model.getCompartment ( string  sid)
inherited

Get a Compartment object based on its identifier.

Returns
the Compartment in this Model with the identifier sid or null if no such Compartment exists.
CompartmentType libsbmlcs.Model.getCompartmentType ( long  n)
inherited

Get the nth CompartmentType object in this Model.

Returns
the nth CompartmentType of this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
CompartmentType libsbmlcs.Model.getCompartmentType ( string  sid)
inherited

Get a CompartmentType object based on its identifier.

Returns
the CompartmentType in this Model with the identifier sid or null if no such CompartmentType exists.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
Constraint libsbmlcs.Model.getConstraint ( long  n)
inherited

Get the nth Constraint object in this Model.

Returns
the nth Constraint of this Model.
string libsbmlcs.Model.getConversionFactor ( )
inherited

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

Returns
the conversionFactor of this Model.
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
CVTerm libsbmlcs.SBase.getCVTerm ( long  n)
inherited

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

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
CVTermList libsbmlcs.SBase.getCVTerms ( )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns
the list of CVTerms for this SBML object.
SBase libsbmlcs.Model.getElementByMetaId ( string  metaid)
inherited

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

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.Model.getElementBySId ( string  id)
inherited

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

Parameters
idstring representing the id of objects to find.
Returns
pointer to the first element found with the given id.
SBase libsbmlcs.SBase.getElementFromPluginsByMetaId ( string  metaid)
inherited

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

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
SBase libsbmlcs.SBase.getElementFromPluginsBySId ( string  id)
inherited

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

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
new string libsbmlcs.ModelDefinition.getElementName ( )

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

Returns
the name of this element, i.e., 'model'.
Event libsbmlcs.Model.getEvent ( long  n)
inherited

Get the nth Event object in this Model.

Returns
the nth Event of this Model.
Event libsbmlcs.Model.getEvent ( string  sid)
inherited

Get an Event object based on its identifier.

Returns
the Event in this Model with the identifier sid or null if no such Event exists.
string libsbmlcs.Model.getExtentUnits ( )
inherited

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

Returns
the extentUnits of this Model.
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
FunctionDefinition libsbmlcs.Model.getFunctionDefinition ( long  n)
inherited

Get the nth FunctionDefinitions object in this Model.

Returns
the nth FunctionDefinition of this Model.
FunctionDefinition libsbmlcs.Model.getFunctionDefinition ( string  sid)
inherited

Get a FunctionDefinition object based on its identifier.

Returns
the FunctionDefinition in this Model with the identifier sid or null if no such FunctionDefinition exists.
override int libsbmlcs.SBase.GetHashCode ( )
inherited
new string libsbmlcs.Model.getId ( )
inherited

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

Returns
the id of this Model.
InitialAssignment libsbmlcs.Model.getInitialAssignment ( long  n)
inherited

Get the nth InitialAssignment object in this Model.

Returns
the nth InitialAssignment of this Model.
InitialAssignment libsbmlcs.Model.getInitialAssignment ( string  symbol)
inherited

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

Returns
the InitialAssignment in this Model with the given 'symbol' attribute value or null if no such InitialAssignment exists.
string libsbmlcs.Model.getLengthUnits ( )
inherited

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

Returns
the lengthUnits of this Model.
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
long libsbmlcs.SBase.getLevel ( )
inherited

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

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
long libsbmlcs.SBase.getLine ( )
inherited

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

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

Get the ListOfCompartments object in this Model.

Returns
the list of Compartments for this Model.
ListOfCompartmentTypes libsbmlcs.Model.getListOfCompartmentTypes ( )
inherited

Get the ListOfCompartmentTypes object in this Model.

Returns
the list of CompartmentTypes for this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
ListOfConstraints libsbmlcs.Model.getListOfConstraints ( )
inherited

Get the ListOfConstraints object in this Model.

Returns
the list of Constraints for this Model.
ListOfEvents libsbmlcs.Model.getListOfEvents ( )
inherited

Get the ListOfEvents object in this Model.

Returns
the list of Events for this Model.
ListOfFunctionDefinitions libsbmlcs.Model.getListOfFunctionDefinitions ( )
inherited

Get the ListOfFunctionDefinitions object in this Model.

Returns
the list of FunctionDefinitions for this Model.
ListOfInitialAssignments libsbmlcs.Model.getListOfInitialAssignments ( )
inherited

Get the ListOfInitialAssignments object in this Model.

Returns
the list of InitialAssignments for this Model.
ListOfParameters libsbmlcs.Model.getListOfParameters ( )
inherited

Get the ListOfParameters object in this Model.

Returns
the list of Parameters for this Model.
ListOfReactions libsbmlcs.Model.getListOfReactions ( )
inherited

Get the ListOfReactions object in this Model.

Returns
the list of Reactions for this Model.
ListOfRules libsbmlcs.Model.getListOfRules ( )
inherited

Get the ListOfRules object in this Model.

Returns
the list of Rules for this Model.
ListOfSpecies libsbmlcs.Model.getListOfSpecies ( )
inherited

Get the ListOfSpecies object in this Model.

Returns
the list of Species for this Model.
ListOfSpeciesTypes libsbmlcs.Model.getListOfSpeciesTypes ( )
inherited

Get the ListOfSpeciesTypes object in this Model.

Returns
the list of SpeciesTypes for this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
ListOfUnitDefinitions libsbmlcs.Model.getListOfUnitDefinitions ( )
inherited

Get the ListOfUnitDefinitions object in this Model.

Returns
the list of UnitDefinitions for this Model.
string libsbmlcs.SBase.getMetaId ( )
inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
the meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId(string metaid)
Model libsbmlcs.SBase.getModel ( )
inherited

Returns the Model object in which the current object is located.

Returns
the parent Model of this SBML object.
See Also
getParentSBMLObject()
getSBMLDocument()
ModelHistory libsbmlcs.SBase.getModelHistory ( )
inherited

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

Returns
the ModelHistory object attached to this object, or null if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new string libsbmlcs.Model.getName ( )
inherited

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

Returns
the name of this Model.
XMLNamespaces libsbmlcs.SBase.getNamespaces ( )
inherited

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

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

Returns
the XML Namespaces associated with this SBML object
See Also
getLevel()
getVersion()
XMLNode libsbmlcs.SBase.getNotes ( )
inherited

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

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

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

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
string libsbmlcs.SBase.getNotesString ( )
inherited

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

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

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

Returns
the content of the 'notes' subelement of this SBML object as a string.
See Also
getNotes()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
long libsbmlcs.Model.getNumCompartments ( )
inherited

Get the number of Compartment objects in this Model.

Returns
the number of Compartments in this Model.
long libsbmlcs.Model.getNumCompartmentTypes ( )
inherited

Get the number of CompartmentType objects in this Model.

Returns
the number of CompartmentTypes in this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
long libsbmlcs.Model.getNumConstraints ( )
inherited

Get the number of Constraint objects in this Model.

Returns
the number of Constraints in this Model.
long libsbmlcs.SBase.getNumCVTerms ( )
inherited

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
long libsbmlcs.Model.getNumEvents ( )
inherited

Get the number of Event objects in this Model.

Returns
the number of Events in this Model.
long libsbmlcs.Model.getNumFunctionDefinitions ( )
inherited

Get the number of FunctionDefinition objects in this Model.

Returns
the number of FunctionDefinitions in this Model.
long libsbmlcs.Model.getNumInitialAssignments ( )
inherited

Get the number of InitialAssignment objects in this Model.

Returns
the number of InitialAssignments in this Model.
long libsbmlcs.Model.getNumParameters ( )
inherited

Get the number of Parameter objects in this Model.

Returns
the number of Parameters in this Model. Parameters defined in KineticLaws are not included.
long libsbmlcs.SBase.getNumPlugins ( )
inherited

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

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
long libsbmlcs.Model.getNumReactions ( )
inherited

Get the number of Reaction objects in this Model.

Returns
the number of Reactions in this Model.
long libsbmlcs.Model.getNumRules ( )
inherited

Get the number of Rule objects in this Model.

Returns
the number of Rules in this Model.
long libsbmlcs.Model.getNumSpecies ( )
inherited

Get the number of Specie objects in this Model.

Returns
the number of Species in this Model.
long libsbmlcs.Model.getNumSpeciesTypes ( )
inherited

Get the number of SpeciesType objects in this Model.

Returns
the number of SpeciesTypes in this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
long libsbmlcs.Model.getNumSpeciesWithBoundaryCondition ( )
inherited

Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true.

Returns
the number of Species in this Model with boundaryCondition set to true.
long libsbmlcs.Model.getNumUnitDefinitions ( )
inherited

Get the number of UnitDefinition objects in this Model.

Returns
the number of UnitDefinitions in this Model.
string libsbmlcs.SBase.getPackageName ( )
inherited

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
long libsbmlcs.SBase.getPackageVersion ( )
inherited

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See Also
getLevel()
getVersion()
Parameter libsbmlcs.Model.getParameter ( long  n)
inherited

Get the nth Parameter object in this Model.

Returns
the nth Parameter of this Model.
Parameter libsbmlcs.Model.getParameter ( string  sid)
inherited

Get a Parameter object based on its identifier.

Returns
the Parameter in this Model with the identifier sid or null if no such Parameter exists.
SBase libsbmlcs.SBase.getParentSBMLObject ( )
inherited

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See Also
getSBMLDocument()
getModel()
SBasePlugin libsbmlcs.SBase.getPlugin ( string  package)
inherited

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

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
SBasePlugin libsbmlcs.SBase.getPlugin ( long  n)
inherited

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

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
Reaction libsbmlcs.Model.getReaction ( long  n)
inherited

Get the nth Reaction object in this Model.

Returns
the nth Reaction of this Model.
Reaction libsbmlcs.Model.getReaction ( string  sid)
inherited

Get a Reaction object based on its identifier.

Returns
the Reaction in this Model with the identifier sid or null if no such Reaction exists.
int libsbmlcs.SBase.getResourceBiologicalQualifier ( string  resource)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
int libsbmlcs.SBase.getResourceModelQualifier ( string  resource)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_ in the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
Rule libsbmlcs.Model.getRule ( long  n)
inherited

Get the nth Rule object in this Model.

Returns
the nth Rule of this Model.
Rule libsbmlcs.Model.getRule ( string  variable)
inherited

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

Returns
the Rule in this Model with the given 'variable' attribute value or null if no such Rule exists.
SBMLDocument libsbmlcs.SBase.getSBMLDocument ( )
inherited

Returns the SBMLDocument object containing this object instance.

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

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See Also
getParentSBMLObject()
getModel()
SBMLNamespaces libsbmlcs.SBase.getSBMLNamespaces ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.getSBOTerm ( )
inherited

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

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

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

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

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

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

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

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

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

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

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

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

Get the nth Species object in this Model.

Returns
the nth Species of this Model.
Species libsbmlcs.Model.getSpecies ( string  sid)
inherited

Get a Species object based on its identifier.

Returns
the Species in this Model with the identifier sid or null if no such Species exists.
SpeciesReference libsbmlcs.Model.getSpeciesReference ( string  sid)
inherited

Get a SpeciesReference object based on its identifier.

Returns
the SpeciesReference in this Model with the identifier sid or null if no such SpeciesReference exists.
SpeciesType libsbmlcs.Model.getSpeciesType ( long  n)
inherited

Get the nth SpeciesType object in this Model.

Returns
the nth SpeciesType of this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
SpeciesType libsbmlcs.Model.getSpeciesType ( string  sid)
inherited

Get a SpeciesType object based on its identifier.

Returns
the SpeciesType in this Model with the identifier sid or null if no such SpeciesType exists.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
string libsbmlcs.Model.getSubstanceUnits ( )
inherited

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

Returns
the substanceUnits of this Model.
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
string libsbmlcs.Model.getTimeUnits ( )
inherited

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

Returns
the timeUnits of this Model.
Note
The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
new int libsbmlcs.ModelDefinition.getTypeCode ( )

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_.

Returns
the SBML type code for this object, or SBML_UNKNOWN (default).
See Also
getElementName()
UnitDefinition libsbmlcs.Model.getUnitDefinition ( long  n)
inherited

Get the nth UnitDefinition object in this Model.

Returns
the nth UnitDefinition of this Model.
UnitDefinition libsbmlcs.Model.getUnitDefinition ( string  sid)
inherited

Get a UnitDefinition based on its identifier.

Returns
the UnitDefinition in this Model with the identifier sid or null if no such UnitDefinition exists.
long libsbmlcs.SBase.getVersion ( )
inherited

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

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
string libsbmlcs.Model.getVolumeUnits ( )
inherited

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

Returns
the volumeUnits of this Model.
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.SBase.hasNonstandardIdentifierBeginningWith ( string  prefix)
inherited

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

bool libsbmlcs.SBase.hasRequiredAttributes ( )
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

new bool libsbmlcs.Model.hasRequiredElements ( )
inherited

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

Note
The required elements for a Model object are: listOfCompartments (L1 only); listOfSpecies (L1V1 only); listOfReactions(L1V1 only)
Returns
a bool value indicating whether all the required elements for this object have been defined.
bool libsbmlcs.SBase.hasValidLevelVersionNamespaceCombination ( )
inherited

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

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

Returns
true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.
bool libsbmlcs.SBase.isPackageEnabled ( string  pkgName)
inherited

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

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageURIEnabled()
bool libsbmlcs.SBase.isPackageURIEnabled ( string  pkgURI)
inherited

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

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPackageEnabled()
bool libsbmlcs.SBase.isPkgEnabled ( string  pkgName)
inherited

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

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgURIEnabled()
bool libsbmlcs.SBase.isPkgURIEnabled ( string  pkgURI)
inherited

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

Parameters
pkgURIthe URI of the package
Returns
true if the given package is enabled within this object, false otherwise.
See Also
isPkgEnabled()
bool libsbmlcs.Model.isPopulatedListFormulaUnitsData ( )
inherited

Predicate returning true if the list of FormulaUnitsData is populated.

Returns
true if the list of FormulaUnitsData is populated, false otherwise.
bool libsbmlcs.SBase.isSetAnnotation ( )
inherited

Predicate returning true if this object's 'annotation' subelement exists and has content.

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

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

Returns
true if a 'annotation' subelement exists, false otherwise.
See Also
getAnnotation()
getAnnotationString()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
unsetAnnotation()
bool libsbmlcs.Model.isSetAreaUnits ( )
inherited

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

Returns
true if the 'areaUnits' attribute of this Model is set, false otherwise.
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.Model.isSetConversionFactor ( )
inherited

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

Returns
true if the 'conversionFactor' attribute of this Model is set, false otherwise.
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.Model.isSetExtentUnits ( )
inherited

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

Returns
true if the 'extentUnits' attribute of this Model is set, false otherwise.
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
new bool libsbmlcs.Model.isSetId ( )
inherited

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

Returns
true if the 'id' attribute of this Model is set, false otherwise.
bool libsbmlcs.Model.isSetLengthUnits ( )
inherited

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

Returns
true if the 'lengthUnits' attribute of this Model is set, false otherwise.
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.SBase.isSetMetaId ( )
inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also
getMetaId()
setMetaId(string metaid)
bool libsbmlcs.SBase.isSetModelHistory ( )
inherited

Predicate returning true if this object has a ModelHistory object attached to it.

Returns
true if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new bool libsbmlcs.Model.isSetName ( )
inherited

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

Returns
true if the 'name' attribute of this Model is set, false otherwise.
bool libsbmlcs.SBase.isSetNotes ( )
inherited

Predicate returning true if this object's 'notes' subelement exists and has content.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
true if a 'notes' subelement exists, false otherwise.
See Also
getNotes()
getNotesString()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
bool libsbmlcs.SBase.isSetSBOTerm ( )
inherited

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

Returns
true if the 'sboTerm' attribute of this SBML object is set, false otherwise.
bool libsbmlcs.Model.isSetSubstanceUnits ( )
inherited

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

Returns
true if the 'substanceUnits' attribute of this Model is set, false otherwise.
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.Model.isSetTimeUnits ( )
inherited

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

Returns
true if the 'timeUnits' attribute of this Model is set, false otherwise.
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.Model.isSetVolumeUnits ( )
inherited

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

Returns
true if the 'volumeUnits' attribute of this Model is set, false otherwise.
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
bool libsbmlcs.SBase.matchesRequiredSBMLNamespacesForAddition ( SBase  sb)
inherited

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

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is a subset of sb's, false otherwise.
bool libsbmlcs.SBase.matchesSBMLNamespaces ( SBase  sb)
inherited

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

Parameters
sban object to compare with respect to namespaces
Returns
bool, true if this object's collection of namespaces is the same as sb's, false otherwise.
void libsbmlcs.SBase.multiplyAssignmentsToSIdByFunction ( string  id,
ASTNode  function 
)
inherited

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

static bool libsbmlcs.SBase.operator!= ( SBase  lhs,
SBase  rhs 
)
staticinherited
static bool libsbmlcs.SBase.operator== ( SBase  lhs,
SBase  rhs 
)
staticinherited
void libsbmlcs.Model.populateListFormulaUnitsData ( )
inherited

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

The list contains elements of class FormulaUnitsData.

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

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

The next elements record the units of any parameters.

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

Note
This function is utilised by the Unit Consistency Validator. The list is populated prior to running the validation and thus the consistency of units can be checked by accessing the members of the list and comparing the appropriate data.
int libsbmlcs.SBase.prependStringToAllIdentifiers ( string  prefix)
inherited

Add the given string to all identifiers in the object.

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

Compartment libsbmlcs.Model.removeCompartment ( long  n)
inherited

Removes the nth Compartment object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Compartment object to remove
Returns
the Compartment object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Compartment libsbmlcs.Model.removeCompartment ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the Compartment object to remove
Returns
the Compartment object removed. As mentioned above, the caller owns the returned object. null is returned if no Compartment object with the identifier exists in this Model object.
CompartmentType libsbmlcs.Model.removeCompartmentType ( long  n)
inherited

Removes the nth CompartmentType object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the CompartmentType object to remove
Returns
the ComapartmentType object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
CompartmentType libsbmlcs.Model.removeCompartmentType ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the object to remove
Returns
the CompartmentType object removed. As mentioned above, the caller owns the returned object. null is returned if no CompartmentType object with the identifier exists in this Model object.
Constraint libsbmlcs.Model.removeConstraint ( long  n)
inherited

Removes the nth Constraint object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Constraint object to remove
Returns
the Constraint object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Event libsbmlcs.Model.removeEvent ( long  n)
inherited

Removes the nth Event object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Event object to remove
Returns
the Event object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Event libsbmlcs.Model.removeEvent ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the Event object to remove
Returns
the Event object removed. As mentioned above, the caller owns the returned object. null is returned if no Event object with the identifier exists in this Model object.
new int libsbmlcs.ModelDefinition.removeFromParentAndDelete ( )
FunctionDefinition libsbmlcs.Model.removeFunctionDefinition ( long  n)
inherited

Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the FunctionDefinition object to remove
Returns
the FunctionDefinition object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
FunctionDefinition libsbmlcs.Model.removeFunctionDefinition ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the FunctionDefinition object to remove
Returns
the FunctionDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if no FunctionDefinition object with the identifier exists in this Model object.
InitialAssignment libsbmlcs.Model.removeInitialAssignment ( long  n)
inherited

Removes the nth InitialAssignment object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the InitialAssignment object to remove
Returns
the InitialAssignment object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
InitialAssignment libsbmlcs.Model.removeInitialAssignment ( string  symbol)
inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the InitialAssignment objects in this Model object have the 'symbol' attribute symbol, then null is returned.

Parameters
symbolthe 'symbol' attribute of the InitialAssignment object to remove
Returns
the InitialAssignment object removed. As mentioned above, the caller owns the returned object. null is returned if no InitialAssignment object with the 'symbol' attribute exists in this Model object.
Parameter libsbmlcs.Model.removeParameter ( long  n)
inherited

Removes the nth Parameter object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Parameter object to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Parameter libsbmlcs.Model.removeParameter ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the Parameter object to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned object. null is returned if no Parameter object with the identifier exists in this Model object.
void libsbmlcs.Model.removeParameterRuleUnits ( bool  strict)
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
Reaction libsbmlcs.Model.removeReaction ( long  n)
inherited

Removes the nth Reaction object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Reaction object to remove
Returns
the Reaction object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Reaction libsbmlcs.Model.removeReaction ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the Reaction object to remove
Returns
the Reaction object removed. As mentioned above, the caller owns the returned object. null is returned if no Reaction object with the identifier exists in this Model object.
Rule libsbmlcs.Model.removeRule ( long  n)
inherited

Removes the nth Rule object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Rule object to remove
Returns
the Rule object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Rule libsbmlcs.Model.removeRule ( string  variable)
inherited

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

The caller owns the returned object and is responsible for deleting it. If none of the Rule objects in this Model object have the 'variable' attribute variable, then null is returned.

Parameters
variablethe 'variable' attribute of the Rule object to remove
Returns
the Rule object removed. As mentioned above, the caller owns the returned object. null is returned if no Rule object with the 'variable' attribute exists in this Model object.
Species libsbmlcs.Model.removeSpecies ( long  n)
inherited

Removes the nth Species object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the Species object to remove
Returns
the Species object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
Species libsbmlcs.Model.removeSpecies ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the Species object to remove
Returns
the Species object removed. As mentioned above, the caller owns the returned object. null is returned if no Species object with the identifier exists in this Model object.
SpeciesType libsbmlcs.Model.removeSpeciesType ( long  n)
inherited

Removes the nth SpeciesType object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the SpeciesType object to remove
Returns
the SpeciesType object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
SpeciesType libsbmlcs.Model.removeSpeciesType ( string  sid)
inherited

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

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

Parameters
sidthe identifier of the SpeciesType object to remove
Returns
the SpeciesType object removed. As mentioned above, the caller owns the returned object. null is returned if no SpeciesType object with the identifier exists in this Model object.
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName,
string  elementURI 
)
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

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

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.removeTopLevelAnnotationElement ( string  elementName)
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

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

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement(XMLNode )
replaceTopLevelAnnotationElement(string)
UnitDefinition libsbmlcs.Model.removeUnitDefinition ( long  n)
inherited

Removes the nth UnitDefinition object from this Model object and returns a pointer to it.

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

Parameters
nthe index of the UnitDefinition object to remove
Returns
the UnitDefinition object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
UnitDefinition libsbmlcs.Model.removeUnitDefinition ( string  sid)
inherited

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

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

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

Renames all the MetaIdRef attributes on this element.

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

Parameters
oldidthe old identifier
newidthe new identifier
void libsbmlcs.Model.renameSIdRefs ( string  oldid,
string  newid 
)
inherited

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

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

Renames all the UnitSIdRef attributes on this element.

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

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

Note
This function does nothing itself—subclasses with ASTNode subelements must override this function.
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( XMLNode  annotation)
inherited

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

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

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

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(string)
int libsbmlcs.SBase.replaceTopLevelAnnotationElement ( string  annotation)
inherited

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

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

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

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
removeTopLevelAnnotationElement(string elementName, string elementURI)
replaceTopLevelAnnotationElement(XMLNode)
new int libsbmlcs.Model.setAnnotation ( XMLNode  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.

Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters
annotationan XML structure that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
appendAnnotation(XMLNode annotation)
new int libsbmlcs.Model.setAnnotation ( string  annotation)
inherited

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.

Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
appendAnnotation(string annotation)
int libsbmlcs.Model.setAreaUnits ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new areaUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.setConversionFactor ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new conversionFactor for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.setExtentUnits ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new extentUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
new int libsbmlcs.Model.setId ( string  sid)
inherited

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

The string sid is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:

letter ::= 'a'..'z','A'..'Z'
digit  ::= '0'..'9'
idChar ::= letter | digit | '_'
SId    ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

Parameters
sidthe string to use as the identifier of this Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Model.setLengthUnits ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new lengthUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.SBase.setMetaId ( string  metaid)
inherited

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
int libsbmlcs.SBase.setModelHistory ( ModelHistory  history)
inherited

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new int libsbmlcs.Model.setName ( string  name)
inherited

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

The string in name is copied.

Parameters
namethe new name for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNamespaces ( XMLNamespaces  xmlns)
inherited

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

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

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.setNotes ( XMLNode  notes)
inherited

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes,
bool  addXHTMLMarkup 
)
inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.setNotes ( string  notes)
inherited

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">

here is my note

</body>');

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
unsetNotes()
SyntaxChecker::hasExpectedXHTMLSyntax()
void libsbmlcs.SBase.setSBMLNamespacesAndOwn ( SBMLNamespaces  sbmlns)
inherited

Subclasses should override this method to write out their contained SBML objects as XML elements.

Be sure to call your parents implementation of this method as well. For example:

int libsbmlcs.SBase.setSBOTerm ( int  value)
inherited

Sets the value of the 'sboTerm' attribute.

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

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

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

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

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

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

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm(int value)
void libsbmlcs.Model.setSpatialDimensions ( double  dims)
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.setSpatialDimensions ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
void libsbmlcs.Model.setSpeciesReferenceConstantValueAndStoichiometry ( )
inherited

Predicate returning true if the given ASTNode is a bool.

Often times, this question can be answered with the ASTNode's own isBoolean() method, but if the AST is an expression that calls a function defined in the Model's ListOfFunctionDefinitions, the model is needed for lookup context.

Returns
true if the given ASTNode is a bool.
int libsbmlcs.Model.setSubstanceUnits ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new substanceUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.setTimeUnits ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new timeUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.setVolumeUnits ( string  units)
inherited

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

The string in units is copied.

Parameters
unitsthe new volumeUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
string libsbmlcs.SBase.toSBML ( )
inherited

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

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
int libsbmlcs.SBase.unsetAnnotation ( )
inherited

Unsets the value of the 'annotation' subelement of this SBML object.

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation(XMLNode annotation)
setAnnotation(string annotation)
appendAnnotation(XMLNode annotation)
appendAnnotation(string annotation)
int libsbmlcs.Model.unsetAreaUnits ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.unsetConversionFactor ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.SBase.unsetCVTerms ( )
inherited

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Model.unsetExtentUnits ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
new int libsbmlcs.Model.unsetId ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Model.unsetLengthUnits ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.SBase.unsetMetaId ( )
inherited

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

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetModelHistory ( )
inherited

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
new int libsbmlcs.Model.unsetName ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.SBase.unsetNotes ( )
inherited

Unsets the value of the 'notes' subelement of this SBML object.

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

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes(XMLNode notes)
setNotes(string notes)
appendNotes(XMLNode notes)
appendNotes(string notes)
SyntaxChecker::hasExpectedXHTMLSyntax()
int libsbmlcs.SBase.unsetSBOTerm ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int libsbmlcs.Model.unsetSubstanceUnits ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.unsetTimeUnits ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
int libsbmlcs.Model.unsetVolumeUnits ( )
inherited

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
void libsbmlcs.SBase.writeExtensionElements ( XMLOutputStream  stream)
inherited

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

Member Data Documentation

bool libsbmlcs.SBase.swigCMemOwn
protectedinherited