libSBML Perl API
libSBML 5.8.0 Perl API
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The Hierarchical Model Composition package ('comp') allows multiple Model objects to be defined in a single SBMLDocument. While these new Model objects are not new SBML classes, they are given a new name, <modelDefinition>
, and reside in ListOfModelDefinition objects. In libSBML, this class inherits from the Model class, changing only the expected parent of the object, and the XML name.
An additional restriction is placed on the "id" attribute of ModelDefinition objects: not only must it be unique across all such attributes of type SId within the ModelDefintion, it must also be unique across all Model, ModelDefinition, and ExternalModelDefinition objects in the same SBMLDocument.
Public Member Functions | |
virtual bool | accept (SBMLVisitor &v) const |
Accepts the given SBMLVisitor for this instance of Constraint. More... | |
int | addCompartment (const Compartment *c) |
Adds a copy of the given Compartment object to this Model. More... | |
int | addCompartmentType (const CompartmentType *ct) |
Adds a copy of the given CompartmentType object to this Model. More... | |
int | addConstraint (const Constraint *c) |
Adds a copy of the given Constraint object to this Model. More... | |
int | addCVTerm (CVTerm *term, bool newBag=false) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | addEvent (const Event *e) |
Adds a copy of the given Event object to this Model. More... | |
int | addFunctionDefinition (const FunctionDefinition *fd) |
Adds a copy of the given FunctionDefinition object to this Model. More... | |
int | addInitialAssignment (const InitialAssignment *ia) |
Adds a copy of the given InitialAssignment object to this Model. More... | |
int | addParameter (const Parameter *p) |
Adds a copy of the given Parameter object to this Model. More... | |
int | addReaction (const Reaction *r) |
Adds a copy of the given Reaction object to this Model. More... | |
int | addRule (const Rule *r) |
Adds a copy of the given Rule object to this Model. More... | |
int | addSpecies (const Species *s) |
Adds a copy of the given Species object to this Model. More... | |
int | addSpeciesType (const SpeciesType *st) |
Adds a copy of the given SpeciesType object to this Model. More... | |
int | addUnitDefinition (const UnitDefinition *ud) |
Adds a copy of the given UnitDefinition object to this Model. More... | |
virtual int | appendAnnotation (const XMLNode *annotation) |
Appends annotation content to any existing content in the "annotation" subelement of this object. More... | |
virtual int | appendAnnotation (const std::string &annotation) |
Appends annotation content to any existing content in the "annotation" subelement of this object. More... | |
virtual int | appendFrom (const 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 (const XMLNode *notes) |
Appends the given notes to the "notes" subelement of this object. More... | |
int | appendNotes (const std::string ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
virtual ModelDefinition * | clone () const |
Creates and returns a deep copy of this ModelDefinition object. More... | |
AlgebraicRule * | createAlgebraicRule () |
Creates a new AlgebraicRule inside this Model and returns it. More... | |
AssignmentRule * | createAssignmentRule () |
Creates a new AssignmentRule inside this Model and returns it. More... | |
Compartment * | createCompartment () |
Creates a new Compartment inside this Model and returns it. More... | |
CompartmentType * | createCompartmentType () |
Creates a new CompartmentType inside this Model and returns it. More... | |
Constraint * | createConstraint () |
Creates a new Constraint inside this Model and returns it. More... | |
Delay * | createDelay () |
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it. More... | |
Event * | createEvent () |
Creates a new Event inside this Model and returns it. More... | |
EventAssignment * | createEventAssignment () |
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it. More... | |
FunctionDefinition * | createFunctionDefinition () |
Creates a new FunctionDefinition inside this Model and returns it. More... | |
InitialAssignment * | createInitialAssignment () |
Creates a new InitialAssignment inside this Model and returns it. More... | |
KineticLaw * | createKineticLaw () |
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it. More... | |
LocalParameter * | createKineticLawLocalParameter () |
Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More... | |
Parameter * | createKineticLawParameter () |
Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it. More... | |
ModifierSpeciesReference * | createModifier () |
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it. More... | |
Parameter * | createParameter () |
Creates a new Parameter inside this Model and returns it. More... | |
SpeciesReference * | createProduct () |
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it. More... | |
RateRule * | createRateRule () |
Creates a new RateRule inside this Model and returns it. More... | |
SpeciesReference * | createReactant () |
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it. More... | |
Reaction * | createReaction () |
Creates a new Reaction inside this Model and returns it. More... | |
Species * | createSpecies () |
Creates a new Species inside this Model and returns it. More... | |
SpeciesType * | createSpeciesType () |
Creates a new SpeciesType inside this Model and returns it. More... | |
Trigger * | createTrigger () |
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it. More... | |
Unit * | createUnit () |
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it. More... | |
UnitDefinition * | createUnitDefinition () |
Creates a new UnitDefinition inside this Model and returns it. More... | |
int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
Disables the given SBML Level 3 package. More... | |
int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package. More... | |
virtual List * | getAllElements () |
Returns a List of all child SBase objects, including those nested to an arbitrary depth. More... | |
virtual List * | getAllElementsFromPlugins () |
Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
SBase * | getAncestorOfType (int type, const std::string pkgName="core") |
Returns the first ancestor object that has the given SBML type code. More... | |
const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
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... | |
XMLNode * | getAnnotation () const |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
std::string | getAnnotationString () |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
std::string | getAnnotationString () const |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
const std::string & | getAreaUnits () const |
Returns the value of the "areaUnits" attribute of this Model. More... | |
unsigned int | getColumn () const |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
const Compartment * | getCompartment (unsigned int n) const |
Get the nth Compartment object in this Model. More... | |
Compartment * | getCompartment (unsigned int n) |
Get the nth Compartment object in this Model. More... | |
const Compartment * | getCompartment (const std::string &sid) const |
Get a Compartment object based on its identifier. More... | |
Compartment * | getCompartment (const std::string &sid) |
Get a Compartment object based on its identifier. More... | |
const CompartmentType * | getCompartmentType (unsigned int n) const |
Get the nth CompartmentType object in this Model. More... | |
CompartmentType * | getCompartmentType (unsigned int n) |
Get the nth CompartmentType object in this Model. More... | |
const CompartmentType * | getCompartmentType (const std::string &sid) const |
Get a CompartmentType object based on its identifier. More... | |
CompartmentType * | getCompartmentType (const std::string &sid) |
Get a CompartmentType object based on its identifier. More... | |
const Constraint * | getConstraint (unsigned int n) const |
Get the nth Constraint object in this Model. More... | |
Constraint * | getConstraint (unsigned int n) |
Get the nth Constraint object in this Model. More... | |
const std::string & | getConversionFactor () const |
Returns the value of the "conversionFactor" attribute of this Model. More... | |
CVTerm * | getCVTerm (unsigned int n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
List * | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
List * | getCVTerms () const |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
virtual SBase * | getElementByMetaId (std::string metaid) |
Returns the first child element it can find with the given metaid , or NULL if no such object is found. More... | |
virtual SBase * | getElementBySId (std::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... | |
virtual const std::string & | getElementName () const |
The only difference between a Model and a ModelDefinition is the element name ('modelDefinition') More... | |
const Event * | getEvent (unsigned int n) const |
Get the nth Event object in this Model. More... | |
Event * | getEvent (unsigned int n) |
Get the nth Event object in this Model. More... | |
const Event * | getEvent (const std::string &sid) const |
Get an Event object based on its identifier. More... | |
Event * | getEvent (const std::string &sid) |
Get an Event object based on its identifier. More... | |
const std::string & | getExtentUnits () const |
Returns the value of the "extentUnits" attribute of this Model. More... | |
const FunctionDefinition * | getFunctionDefinition (unsigned int n) const |
Get the nth FunctionDefinitions object in this Model. More... | |
FunctionDefinition * | getFunctionDefinition (unsigned int n) |
Get the nth FunctionDefinitions object in this Model. More... | |
const FunctionDefinition * | getFunctionDefinition (const std::string &sid) const |
Get a FunctionDefinition object based on its identifier. More... | |
FunctionDefinition * | getFunctionDefinition (const std::string &sid) |
Get a FunctionDefinition object based on its identifier. More... | |
virtual const std::string & | getId () const |
Returns the value of the "id" attribute of this Model. More... | |
const InitialAssignment * | getInitialAssignment (unsigned int n) const |
Get the nth InitialAssignment object in this Model. More... | |
InitialAssignment * | getInitialAssignment (unsigned int n) |
Get the nth InitialAssignment object in this Model. More... | |
const InitialAssignment * | getInitialAssignment (const std::string &symbol) const |
Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
InitialAssignment * | getInitialAssignment (const std::string &symbol) |
Get an InitialAssignment object based on the symbol to which it assigns a value. More... | |
const std::string & | getLengthUnits () const |
Returns the value of the "lengthUnits" attribute of this Model. More... | |
unsigned int | getLevel () const |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
unsigned int | getLine () const |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
const ListOfCompartments * | getListOfCompartments () const |
Get the ListOfCompartments object in this Model. More... | |
ListOfCompartments * | getListOfCompartments () |
Get the ListOfCompartments object in this Model. More... | |
const ListOfCompartmentTypes * | getListOfCompartmentTypes () const |
Get the ListOfCompartmentTypes object in this Model. More... | |
ListOfCompartmentTypes * | getListOfCompartmentTypes () |
Get the ListOfCompartmentTypes object in this Model. More... | |
const ListOfConstraints * | getListOfConstraints () const |
Get the ListOfConstraints object in this Model. More... | |
ListOfConstraints * | getListOfConstraints () |
Get the ListOfConstraints object in this Model. More... | |
const ListOfEvents * | getListOfEvents () const |
Get the ListOfEvents object in this Model. More... | |
ListOfEvents * | getListOfEvents () |
Get the ListOfEvents object in this Model. More... | |
const ListOfFunctionDefinitions * | getListOfFunctionDefinitions () const |
Get the ListOfFunctionDefinitions object in this Model. More... | |
ListOfFunctionDefinitions * | getListOfFunctionDefinitions () |
Get the ListOfFunctionDefinitions object in this Model. More... | |
const ListOfInitialAssignments * | getListOfInitialAssignments () const |
Get the ListOfInitialAssignments object in this Model. More... | |
ListOfInitialAssignments * | getListOfInitialAssignments () |
Get the ListOfInitialAssignments object in this Model. More... | |
const ListOfParameters * | getListOfParameters () const |
Get the ListOfParameters object in this Model. More... | |
ListOfParameters * | getListOfParameters () |
Get the ListOfParameters object in this Model. More... | |
const ListOfReactions * | getListOfReactions () const |
Get the ListOfReactions object in this Model. More... | |
ListOfReactions * | getListOfReactions () |
Get the ListOfReactions object in this Model. More... | |
const ListOfRules * | getListOfRules () const |
Get the ListOfRules object in this Model. More... | |
ListOfRules * | getListOfRules () |
Get the ListOfRules object in this Model. More... | |
const ListOfSpecies * | getListOfSpecies () const |
Get the ListOfSpecies object in this Model. More... | |
ListOfSpecies * | getListOfSpecies () |
Get the ListOfSpecies object in this Model. More... | |
const ListOfSpeciesTypes * | getListOfSpeciesTypes () const |
Get the ListOfSpeciesTypes object in this Model. More... | |
ListOfSpeciesTypes * | getListOfSpeciesTypes () |
Get the ListOfSpeciesTypes object in this Model. More... | |
const ListOfUnitDefinitions * | getListOfUnitDefinitions () const |
Get the ListOfUnitDefinitions object in this Model. More... | |
ListOfUnitDefinitions * | getListOfUnitDefinitions () |
Get the ListOfUnitDefinitions object in this Model. More... | |
const std::string & | getMetaId () const |
Returns the value of the "metaid" attribute of this object. More... | |
std::string & | getMetaId () |
Returns the value of the "metaid" attribute of this object. More... | |
const Model * | getModel () const |
Returns the Model object in which the current object is located. More... | |
ModelHistory * | getModelHistory () const |
Returns the ModelHistory object, if any, attached to this object. More... | |
ModelHistory * | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
virtual const std::string & | getName () const |
Returns the value of the "name" attribute of this Model. More... | |
virtual XMLNamespaces * | getNamespaces () const |
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... | |
XMLNode * | getNotes () const |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
std::string | getNotesString () |
Returns the content of the "notes" subelement of this object as a string. More... | |
std::string | getNotesString () const |
Returns the content of the "notes" subelement of this object as a string. More... | |
unsigned int | getNumCompartments () const |
Get the number of Compartment objects in this Model. More... | |
unsigned int | getNumCompartmentTypes () const |
Get the number of CompartmentType objects in this Model. More... | |
unsigned int | getNumConstraints () const |
Get the number of Constraint objects in this Model. More... | |
unsigned int | getNumCVTerms () |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
unsigned int | getNumEvents () const |
Get the number of Event objects in this Model. More... | |
unsigned int | getNumFunctionDefinitions () const |
Get the number of FunctionDefinition objects in this Model. More... | |
unsigned int | getNumInitialAssignments () const |
Get the number of InitialAssignment objects in this Model. More... | |
unsigned int | getNumParameters () const |
Get the number of Parameter objects in this Model. More... | |
unsigned int | getNumPlugins () const |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
unsigned int | getNumReactions () const |
Get the number of Reaction objects in this Model. More... | |
unsigned int | getNumRules () const |
Get the number of Rule objects in this Model. More... | |
unsigned int | getNumSpecies () const |
Get the number of Specie objects in this Model. More... | |
unsigned int | getNumSpeciesTypes () const |
Get the number of SpeciesType objects in this Model. More... | |
unsigned int | getNumSpeciesWithBoundaryCondition () const |
Get the number of Species in this Model having their "boundaryCondition" attribute value set to true . More... | |
unsigned int | getNumUnitDefinitions () const |
Get the number of UnitDefinition objects in this Model. More... | |
const std::string & | getPackageName () const |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
unsigned int | getPackageVersion () const |
Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
const Parameter * | getParameter (unsigned int n) const |
Get the nth Parameter object in this Model. More... | |
Parameter * | getParameter (unsigned int n) |
Get the nth Parameter object in this Model. More... | |
const Parameter * | getParameter (const std::string &sid) const |
Get a Parameter object based on its identifier. More... | |
Parameter * | getParameter (const std::string &sid) |
Get a Parameter object based on its identifier. More... | |
SBase * | getParentSBMLObject () |
Returns the parent SBML object containing this object. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBML object containing this object. More... | |
SBasePlugin * | getPlugin (const std::string &package) |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
const SBasePlugin * | getPlugin (const std::string &package) const |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
SBasePlugin * | getPlugin (unsigned int n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
const SBasePlugin * | getPlugin (unsigned int n) const |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
const Reaction * | getReaction (unsigned int n) const |
Get the nth Reaction object in this Model. More... | |
Reaction * | getReaction (unsigned int n) |
Get the nth Reaction object in this Model. More... | |
const Reaction * | getReaction (const std::string &sid) const |
Get a Reaction object based on its identifier. More... | |
Reaction * | getReaction (const std::string &sid) |
Get a Reaction object based on its identifier. More... | |
BiolQualifierType_t | getResourceBiologicalQualifier (std::string resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
ModelQualifierType_t | getResourceModelQualifier (std::string resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
const Rule * | getRule (unsigned int n) const |
Get the nth Rule object in this Model. More... | |
Rule * | getRule (unsigned int n) |
Get the nth Rule object in this Model. More... | |
const Rule * | getRule (const std::string &variable) const |
Get a Rule object based on the variable to which it assigns a value. More... | |
Rule * | getRule (const std::string &variable) |
Get a Rule object based on the variable to which it assigns a value. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
int | getSBOTerm () const |
Returns the integer portion of the value of the "sboTerm" attribute of this object. More... | |
std::string | getSBOTermAsURL () const |
Returns the identifiers.org URL representation of the "sboTerm" attribute of this object. More... | |
std::string | getSBOTermID () const |
Returns the string representation of the "sboTerm" attribute of this object. More... | |
const Species * | getSpecies (unsigned int n) const |
Get the nth Species object in this Model. More... | |
Species * | getSpecies (unsigned int n) |
Get the nth Species object in this Model. More... | |
const Species * | getSpecies (const std::string &sid) const |
Get a Species object based on its identifier. More... | |
Species * | getSpecies (const std::string &sid) |
Get a Species object based on its identifier. More... | |
SpeciesReference * | getSpeciesReference (const std::string &sid) |
Get a SpeciesReference object based on its identifier. More... | |
const SpeciesReference * | getSpeciesReference (const std::string &sid) const |
Get a SpeciesReference object based on its identifier. More... | |
const SpeciesType * | getSpeciesType (unsigned int n) const |
Get the nth SpeciesType object in this Model. More... | |
SpeciesType * | getSpeciesType (unsigned int n) |
Get the nth SpeciesType object in this Model. More... | |
const SpeciesType * | getSpeciesType (const std::string &sid) const |
Get a SpeciesType object based on its identifier. More... | |
SpeciesType * | getSpeciesType (const std::string &sid) |
Get a SpeciesType object based on its identifier. More... | |
const std::string & | getSubstanceUnits () const |
Returns the value of the "substanceUnits" attribute of this Model. More... | |
const std::string & | getTimeUnits () const |
Returns the value of the "timeUnits" attribute of this Model. More... | |
int | getTypeCode () const |
Returns the libSBML type code for this SBML object. More... | |
const UnitDefinition * | getUnitDefinition (unsigned int n) const |
Get the nth UnitDefinition object in this Model. More... | |
UnitDefinition * | getUnitDefinition (unsigned int n) |
Get the nth UnitDefinition object in this Model. More... | |
const UnitDefinition * | getUnitDefinition (const std::string &sid) const |
Get a UnitDefinition based on its identifier. More... | |
UnitDefinition * | getUnitDefinition (const std::string &sid) |
Get a UnitDefinition based on its identifier. More... | |
void * | getUserData () const |
Returns the user data that has been previously set via setUserData(). More... | |
unsigned int | getVersion () const |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
const std::string & | getVolumeUnits () const |
Returns the value of the "volumeUnits" attribute of this Model. More... | |
virtual bool | hasRequiredElements () const |
Predicate returning true if all the required elements for this Model object have been set. More... | |
bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
bool | isPackageEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPackageURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPkgEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPkgURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPopulatedListFormulaUnitsData () |
Predicate returning true if the list of FormulaUnitsData is populated. More... | |
bool | isSetAnnotation () const |
Predicate returning true if this object's "annotation" subelement exists and has content. More... | |
bool | isSetAreaUnits () const |
Predicate returning true if this Model's "areaUnits" attribute is set. More... | |
bool | isSetConversionFactor () const |
Predicate returning true if this Model's "conversionFactor" attribute is set. More... | |
bool | isSetExtentUnits () const |
Predicate returning true if this Model's "extentUnits" attribute is set. More... | |
virtual bool | isSetId () const |
Predicate returning true if this Model's "id" attribute is set. More... | |
bool | isSetLengthUnits () const |
Predicate returning true if this Model's "lengthUnits" attribute is set. More... | |
bool | isSetMetaId () const |
Predicate returning true if this object's "metaid" attribute is set. More... | |
bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
virtual bool | isSetName () const |
Predicate returning true if this Model's "name" attribute is set. More... | |
bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
bool | isSetSubstanceUnits () const |
Predicate returning true if this Model's "substanceUnits" attribute is set. More... | |
bool | isSetTimeUnits () const |
Predicate returning true if this Model's "timeUnits" attribute is set. More... | |
bool | isSetVolumeUnits () const |
Predicate returning true if this Model's "volumeUnits" attribute is set. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (const SBase *sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (const SBase *sb) const |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
ModelDefinition (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion()) | |
Creates a new ModelDefinition with the given level, version, and package version. More... | |
ModelDefinition (CompPkgNamespaces *compns) | |
Creates a new ModelDefinition with the given CompPkgNamespaces object. More... | |
ModelDefinition (const Model &source) | |
Copy constructor from base Model object. More... | |
ModelDefinition & | operator= (const Model &source) |
Assignment operator. More... | |
void | populateListFormulaUnitsData () |
Populates the list of FormulaDataUnits with the units derived for the model. More... | |
Compartment * | removeCompartment (unsigned int n) |
Removes the nth Compartment object from this Model object and returns a pointer to it. More... | |
Compartment * | removeCompartment (const std::string &sid) |
Removes the Compartment object with the given identifier from this Model object and returns a pointer to it. More... | |
CompartmentType * | removeCompartmentType (unsigned int n) |
Removes the nth CompartmentType object from this Model object and returns a pointer to it. More... | |
CompartmentType * | removeCompartmentType (const std::string &sid) |
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it. More... | |
Constraint * | removeConstraint (unsigned int n) |
Removes the nth Constraint object from this Model object and returns a pointer to it. More... | |
Event * | removeEvent (unsigned int n) |
Removes the nth Event object from this Model object and returns a pointer to it. More... | |
Event * | removeEvent (const std::string &sid) |
Removes the Event object with the given identifier from this Model object and returns a pointer to it. More... | |
virtual int | removeFromParentAndDelete () |
Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself. More... | |
FunctionDefinition * | removeFunctionDefinition (unsigned int n) |
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it. More... | |
FunctionDefinition * | removeFunctionDefinition (const std::string &sid) |
Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
InitialAssignment * | removeInitialAssignment (unsigned int n) |
Removes the nth InitialAssignment object from this Model object and returns a pointer to it. More... | |
InitialAssignment * | removeInitialAssignment (const std::string &symbol) |
Removes the InitialAssignment object with the given "symbol" attribute from this Model object and returns a pointer to it. More... | |
Parameter * | removeParameter (unsigned int n) |
Removes the nth Parameter object from this Model object and returns a pointer to it. More... | |
Parameter * | removeParameter (const std::string &sid) |
Removes the Parameter object with the given identifier from this Model object and returns a pointer to it. More... | |
Reaction * | removeReaction (unsigned int n) |
Removes the nth Reaction object from this Model object and returns a pointer to it. More... | |
Reaction * | removeReaction (const std::string &sid) |
Removes the Reaction object with the given identifier from this Model object and returns a pointer to it. More... | |
Rule * | removeRule (unsigned int n) |
Removes the nth Rule object from this Model object and returns a pointer to it. More... | |
Rule * | removeRule (const std::string &variable) |
Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it. More... | |
Species * | removeSpecies (unsigned int n) |
Removes the nth Species object from this Model object and returns a pointer to it. More... | |
Species * | removeSpecies (const std::string &sid) |
Removes the Species object with the given identifier from this Model object and returns a pointer to it. More... | |
SpeciesType * | removeSpeciesType (unsigned int n) |
Removes the nth SpeciesType object from this Model object and returns a pointer to it. More... | |
SpeciesType * | removeSpeciesType (const std::string &sid) |
Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it. More... | |
int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="") |
Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
UnitDefinition * | removeUnitDefinition (unsigned int n) |
Removes the nth UnitDefinition object from this Model object and returns a pointer to it. More... | |
UnitDefinition * | removeUnitDefinition (const std::string &sid) |
Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it. More... | |
virtual void | renameMetaIdRefs (std::string oldid, std::string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
virtual void | renameSIdRefs (std::string oldid, std::string newid) |
Renames all the SIdRef attributes on this element, including any found in MathML. More... | |
virtual void | renameUnitSIdRefs (std::string oldid, std::string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
int | replaceTopLevelAnnotationElement (const XMLNode *annotation) |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
int | replaceTopLevelAnnotationElement (const std::string &annotation) |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
virtual int | setAnnotation (const XMLNode *annotation) |
Sets the value of the "annotation" subelement of this SBML object to a copy of annotation . More... | |
virtual int | setAnnotation (const std::string &annotation) |
Sets the value of the "annotation" subelement of this SBML object to a copy of annotation . More... | |
int | setAreaUnits (const std::string &units) |
Sets the value of the "areaUnits" attribute of this Model. More... | |
int | setConversionFactor (const std::string &units) |
Sets the value of the "conversionFactor" attribute of this Model. More... | |
int | setExtentUnits (const std::string &units) |
Sets the value of the "extentUnits" attribute of this Model. More... | |
virtual int | setId (const std::string &sid) |
Sets the value of the "id" attribute of this Model. More... | |
int | setLengthUnits (const std::string &units) |
Sets the value of the "lengthUnits" attribute of this Model. More... | |
int | setMetaId (const std::string &metaid) |
Sets the value of the "metaid" attribute of this object. More... | |
int | setModelHistory (ModelHistory *history) |
Sets the ModelHistory of this object. More... | |
virtual int | setName (const std::string &name) |
Sets the value of the "name" attribute of this Model. More... | |
int | setNamespaces (XMLNamespaces *xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
int | setNotes (const XMLNode *notes) |
Sets the value of the "notes" subelement of this SBML object. More... | |
int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes . More... | |
virtual int | setSBOTerm (int value) |
Sets the value of the "sboTerm" attribute. More... | |
virtual int | setSBOTerm (const std::string &sboid) |
Sets the value of the "sboTerm" attribute by string. More... | |
int | setSubstanceUnits (const std::string &units) |
Sets the value of the "substanceUnits" attribute of this Model. More... | |
int | setTimeUnits (const std::string &units) |
Sets the value of the "timeUnits" attribute of this Model. More... | |
int | setUserData (void *userData) |
Sets the user data of this element. More... | |
int | setVolumeUnits (const std::string &units) |
Sets the value of the "volumeUnits" attribute of this Model. More... | |
char * | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
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... | |
virtual 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... | |
virtual int | unsetName () |
Unsets the value of the "name" attribute of this Model. More... | |
int | unsetNotes () |
Unsets the value of the "notes" subelement of this SBML object. More... | |
int | unsetSBOTerm () |
Unsets the value of the "sboTerm" attribute of this SBML object. More... | |
int | unsetSubstanceUnits () |
Unsets the value of the "substanceUnits" attribute of this Model. More... | |
int | unsetTimeUnits () |
Unsets the value of the "timeUnits" attribute of this Model. More... | |
int | unsetVolumeUnits () |
Unsets the value of the "volumeUnits" attribute of this Model. More... | |
virtual | ~ModelDefinition () |
Destructor. More... | |
Protected Member Functions | |
virtual void | setElementText (const std::string &text) |
When overridden allows SBase elements to use the text included in between the elements tags. More... | |
ModelDefinition::ModelDefinition | ( | unsigned int | level = CompExtension::getDefaultLevel() , |
unsigned int | version = CompExtension::getDefaultVersion() , |
||
unsigned int | pkgVersion = CompExtension::getDefaultPackageVersion() |
||
) |
Creates a new ModelDefinition with the given level, version, and package version.
level | the SBML Level |
version | the Version within the SBML Level |
pkgVersion | the version of the package |
ModelDefinition::ModelDefinition | ( | CompPkgNamespaces * | compns | ) |
Creates a new ModelDefinition with the given CompPkgNamespaces object.
compns | the namespace to use |
|
virtual |
Destructor.
|
virtualinherited |
Accepts the given SBMLVisitor for this instance of Constraint.
v | the SBMLVisitor instance to be used. |
v.visit()
. Implements SBase.
|
inherited |
Adds a copy of the given Compartment object to this Model.
c | the Compartment object to add |
|
inherited |
Adds a copy of the given CompartmentType object to this Model.
ct | the CompartmentType object to add |
|
inherited |
Adds a copy of the given Constraint object to this Model.
c | the Constraint object to add |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
|
inherited |
Adds a copy of the given Event object to this Model.
e | the Event object to add |
|
inherited |
Adds a copy of the given FunctionDefinition object to this Model.
fd | the FunctionDefinition to add |
|
inherited |
Adds a copy of the given InitialAssignment object to this Model.
ia | the InitialAssignment object to add |
|
inherited |
Adds a copy of the given Parameter object to this Model.
p | the Parameter object to add |
|
inherited |
Adds a copy of the given Reaction object to this Model.
r | the Reaction object to add |
|
inherited |
Adds a copy of the given Rule object to this Model.
r | the Rule object to add |
|
inherited |
Adds a copy of the given Species object to this Model.
s | the Species object to add |
|
inherited |
Adds a copy of the given SpeciesType object to this Model.
st | the SpeciesType object to add |
|
inherited |
Adds a copy of the given UnitDefinition object to this Model.
ud | the UnitDefinition object to add |
|
virtualinherited |
Appends annotation content to any existing content in the "annotation" subelement of this object.
The content in annotation
is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the "annotation" subelement of this object |
Reimplemented from SBase.
|
virtualinherited |
Appends annotation content to any existing content in the "annotation" subelement of this object.
The content in annotation
is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the "annotation" subelement of this object |
Reimplemented from SBase.
|
virtualinherited |
|
inherited |
Appends the given notes
to the "notes" subelement of this object.
The content of notes
is copied.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
notes | an XML node structure that is to appended to the content of the "notes" subelement of this object |
|
inherited |
Appends the given notes
to the "notes" subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
notes | an XML string that is to appended to the content of the "notes" subelement of this object |
|
virtual |
Creates and returns a deep copy of this ModelDefinition object.
Reimplemented from Model.
|
inherited |
Creates a new AlgebraicRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new AssignmentRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new Compartment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new CompartmentType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new Constraint inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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.
|
inherited |
|
inherited |
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and NULL
is returned instead.
|
inherited |
Creates a new FunctionDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new InitialAssignment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and NULL
is returned instead.
|
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.
|
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.
|
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.
|
inherited |
Creates a new Parameter inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL
is returned instead.
|
inherited |
Creates a new RateRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and NULL
is returned instead.
|
inherited |
Creates a new Reaction inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new Species inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new SpeciesType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Trigger is not created and NULL
is returned instead.
|
inherited |
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and NULL
is returned instead.
|
inherited |
Creates a new UnitDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
|
inherited |
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.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
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.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
|
virtualinherited |
|
virtualinherited |
|
inherited |
Returns the first ancestor object that has the given SBML type code.
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.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
NULL
if no ancestor exists.
|
inherited |
Returns the first ancestor object that has the given SBML type code.
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.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
NULL
if no ancestor exists.
|
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.
|
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.
|
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.
|
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.
|
inherited |
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
|
inherited |
Get the nth Compartment object in this Model.
|
inherited |
Get the nth Compartment object in this Model.
|
inherited |
Get a Compartment object based on its identifier.
sid
or NULL
if no such Compartment exists.
|
inherited |
Get a Compartment object based on its identifier.
sid
or NULL
if no such Compartment exists.
|
inherited |
Get the nth CompartmentType object in this Model.
|
inherited |
Get the nth CompartmentType object in this Model.
|
inherited |
Get a CompartmentType object based on its identifier.
sid
or NULL
if no such CompartmentType exists.
|
inherited |
Get a CompartmentType object based on its identifier.
sid
or NULL
if no such CompartmentType exists.
|
inherited |
Get the nth Constraint object in this Model.
|
inherited |
Get the nth Constraint object in this Model.
|
inherited |
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
virtualinherited |
Returns the first child element it can find with the given metaid
, or NULL if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. Reimplemented from SBase.
|
virtualinherited |
Returns the first child element found that has the given id
in the model-wide SId namespace, or NULL
if no such object is found.
id | string representing the id of objects to find. |
id
. Reimplemented from SBase.
|
virtual |
The only difference between a Model and a ModelDefinition is the element name ('modelDefinition')
Reimplemented from Model.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get the nth FunctionDefinitions object in this Model.
|
inherited |
Get the nth FunctionDefinitions object in this Model.
|
inherited |
Get a FunctionDefinition object based on its identifier.
sid
or NULL
if no such FunctionDefinition exists.
|
inherited |
Get a FunctionDefinition object based on its identifier.
sid
or NULL
if no such FunctionDefinition exists.
|
virtualinherited |
|
inherited |
Get the nth InitialAssignment object in this Model.
|
inherited |
Get the nth InitialAssignment object in this Model.
|
inherited |
Get an InitialAssignment object based on the symbol to which it assigns a value.
NULL
if no such InitialAssignment exists.
|
inherited |
Get an InitialAssignment object based on the symbol to which it assigns a value.
NULL
if no such InitialAssignment exists.
|
inherited |
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
|
inherited |
Get the ListOfCompartments object in this Model.
|
inherited |
Get the ListOfCompartments object in this Model.
|
inherited |
Get the ListOfCompartmentTypes object in this Model.
|
inherited |
Get the ListOfCompartmentTypes object in this Model.
|
inherited |
Get the ListOfConstraints object in this Model.
|
inherited |
Get the ListOfConstraints object in this Model.
|
inherited |
Get the ListOfEvents object in this Model.
|
inherited |
Get the ListOfEvents object in this Model.
|
inherited |
Get the ListOfFunctionDefinitions object in this Model.
|
inherited |
Get the ListOfFunctionDefinitions object in this Model.
|
inherited |
Get the ListOfInitialAssignments object in this Model.
|
inherited |
Get the ListOfInitialAssignments object in this Model.
|
inherited |
Get the ListOfParameters object in this Model.
|
inherited |
Get the ListOfParameters object in this Model.
|
inherited |
Get the ListOfReactions object in this Model.
|
inherited |
Get the ListOfReactions object in this Model.
|
inherited |
Get the ListOfRules object in this Model.
|
inherited |
Get the ListOfRules object in this Model.
|
inherited |
Get the ListOfSpecies object in this Model.
|
inherited |
Get the ListOfSpecies object in this Model.
|
inherited |
Get the ListOfSpeciesTypes object in this Model.
|
inherited |
Get the ListOfSpeciesTypes object in this Model.
|
inherited |
Get the ListOfUnitDefinitions object in this Model.
|
inherited |
Get the ListOfUnitDefinitions object in this Model.
|
inherited |
Returns the value of the "metaid" attribute of this 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.
|
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.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
virtualinherited |
|
virtualinherited |
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.
Reimplemented in SBMLDocument.
|
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().
|
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().
|
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.
|
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.
|
inherited |
Get the number of Compartment objects in this Model.
|
inherited |
Get the number of CompartmentType objects in this Model.
|
inherited |
Get the number of Constraint objects in this Model.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
|
inherited |
Get the number of FunctionDefinition objects in this Model.
|
inherited |
Get the number of InitialAssignment objects in this Model.
|
inherited |
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get the number of SpeciesType objects in this Model.
|
inherited |
|
inherited |
Get the number of UnitDefinition objects in this Model.
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"core"
will be returned if this element is defined in SBML Level 3 Core. The string "unknown"
will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0
will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include "is" and "has part", but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is "isDerivedFrom", to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
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.
|
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.
|
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.
-1
if the value is not set.
|
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.
|
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.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Get a SpeciesReference object based on its identifier.
sid
or NULL
if no such SpeciesReference exists.
|
inherited |
Get a SpeciesReference object based on its identifier.
sid
or NULL
if no such SpeciesReference exists.
|
inherited |
Get the nth SpeciesType object in this Model.
|
inherited |
Get the nth SpeciesType object in this Model.
|
inherited |
Get a SpeciesType object based on its identifier.
sid
or NULL
if no such SpeciesType exists.
|
inherited |
Get a SpeciesType object based on its identifier.
sid
or NULL
if no such SpeciesType exists.
|
inherited |
|
inherited |
|
virtual |
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.
Reimplemented from Model.
|
inherited |
Get the nth UnitDefinition object in this Model.
|
inherited |
Get the nth UnitDefinition object in this Model.
|
inherited |
Get a UnitDefinition based on its identifier.
sid
or NULL
if no such UnitDefinition exists.
|
inherited |
Get a UnitDefinition based on its identifier.
sid
or NULL
if no such UnitDefinition exists.
|
inherited |
Returns the user data that has been previously set via setUserData().
NULL
if no user data has been set.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
inherited |
|
virtualinherited |
Predicate returning true
if all the required elements for this Model object have been set.
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
"http://www.sbml.org/sbml/level1"
"http://www.sbml.org/sbml/level2"
"http://www.sbml.org/sbml/level2/version2"
"http://www.sbml.org/sbml/level2/version3"
"http://www.sbml.org/sbml/level2/version4"
"http://www.sbml.org/sbml/level3/version1/core"
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the list of FormulaUnitsData is populated.
true
if the list of FormulaUnitsData is populated, false
otherwise.
|
inherited |
Predicate returning true
if this object's "annotation" subelement exists and has content.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
true
if a "annotation" subelement exists, false
otherwise.
|
inherited |
|
inherited |
|
inherited |
|
virtualinherited |
|
inherited |
|
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.
true
if the "metaid" attribute of this SBML object is set, false
otherwise.
|
inherited |
Predicate returning true
if this object has a ModelHistory object attached to it.
true
if the ModelHistory of this object is set, false
otherwise.
|
virtualinherited |
|
inherited |
Predicate returning true
if this object's "notes" subelement exists and has content.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
true
if a "notes" subelement exists, false
otherwise.
|
inherited |
Predicate returning true
if this object's "sboTerm" attribute is set.
true
if the "sboTerm" attribute of this SBML object is set, false
otherwise.
|
inherited |
|
inherited |
|
inherited |
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise. ModelDefinition & ModelDefinition::operator= | ( | const Model & | source | ) |
Assignment operator.
|
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.
|
inherited |
Removes the nth Compartment object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Compartment object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the Compartment object to remove |
NULL
is returned if no Compartment object with the identifier exists in this Model object.
|
inherited |
Removes the nth CompartmentType object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the CompartmentType object to remove |
NULL
is returned if the given index is out of range.
|
inherited |
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the CompartmentType objects in this Model object have the identifier sid
, then NULL
is returned.
sid | the identifier of the object to remove |
NULL
is returned if no CompartmentType object with the identifier exists in this Model object.
|
inherited |
Removes the nth Constraint object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Constraint object to remove |
NULL
is returned if the given index is out of range.
|
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.
n | the index of the Event object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the Event object to remove |
|
virtual |
Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself.
This method actually just calls the SBase function, since the Model class overrides it, but that's actually what we want to happen here.
Reimplemented from Model.
|
inherited |
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the FunctionDefinition object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the FunctionDefinition object to remove |
NULL
is returned if no FunctionDefinition object with the identifier exists in this Model object.
|
inherited |
Removes the nth InitialAssignment object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the InitialAssignment object to remove |
NULL
is returned if the given index is out of range.
|
inherited |
Removes the InitialAssignment object with the given "symbol" attribute from this Model object and returns a pointer to it.
Removes the InitialAssignment object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the InitialAssignment objects in this Model object have the "symbol" attribute symbol
, then NULL
is returned.
symbol | the "symbol" attribute of the InitialAssignment object to remove |
NULL
is returned if no InitialAssignment object with the "symbol" attribute exists in this Model object.
|
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.
n | the index of the Parameter object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the Parameter object to remove |
|
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.
n | the index of the Reaction object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the Reaction object to remove |
|
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.
n | the index of the Rule object to remove |
NULL
is returned if the given index is out of range.
|
inherited |
Removes the Rule object with the given "variable" attribute from this Model object and returns a pointer to it.
Removes the Rule object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Rule objects in this Model object have the "variable" attribute variable
, then NULL
is returned.
variable | the "variable" attribute of the Rule object to remove |
|
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.
n | the index of the Species object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the Species object to remove |
|
inherited |
Removes the nth SpeciesType object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the SpeciesType object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the SpeciesType object to remove |
NULL
is returned if no SpeciesType object with the identifier exists in this Model object.
|
inherited |
Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
inherited |
Removes the nth UnitDefinition object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the UnitDefinition object to remove |
NULL
is returned if the given index is out of range.
|
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.
sid | the identifier of the UnitDefinition object to remove |
NULL
is returned if no UnitDefinition object with the identifier exists in this Model object.
|
virtualinherited |
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.
oldid | the old identifier |
newid | the new identifier |
Reimplemented in Port.
|
virtualinherited |
Renames all the SIdRef attributes on this element, including any found in MathML.
Reimplemented from SBase.
|
virtualinherited |
Renames all the UnitSIdRef attributes on this element.
Reimplemented from SBase.
|
inherited |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
|
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.
annotation | string representing the replacement top level annotation |
|
virtualinherited |
Sets the value of the "annotation" subelement of this SBML object to a copy of annotation
.
Any existing content of the "annotation" subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().
annotation | an XML structure that is to be used as the content of the "annotation" subelement of this object |
Reimplemented from SBase.
|
virtualinherited |
Sets the value of the "annotation" subelement of this SBML object to a copy of annotation
.
Any existing content of the "annotation" subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().
annotation | an XML string that is to be used as the content of the "annotation" subelement of this object |
Reimplemented from SBase.
|
inherited |
Sets the value of the "areaUnits" attribute of this Model.
The string in units
is copied.
units | the new areaUnits for the Model |
|
inherited |
Sets the value of the "conversionFactor" attribute of this Model.
The string in units
is copied.
units | the new conversionFactor for the Model |
|
protectedvirtualinherited |
When overridden allows SBase elements to use the text included in between the elements tags.
The default implementation does nothing.
text | the text string found between the element tags. |
|
inherited |
Sets the value of the "extentUnits" attribute of this Model.
The string in units
is copied.
units | the new extentUnits for the Model |
|
virtualinherited |
Sets the value of the "id" attribute of this Model.
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.
sid | the string to use as the identifier of this Model |
|
inherited |
Sets the value of the "lengthUnits" attribute of this Model.
The string in units
is copied.
units | the new lengthUnits for the Model |
|
inherited |
Sets the value of the "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.
metaid | the identifier string to use as the value of the "metaid" attribute |
|
inherited |
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
|
virtualinherited |
|
inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
|
inherited |
Sets the value of the "notes" subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
notes | an XML structure that is to be used as the content of the "notes" subelement of this object |
|
inherited |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's "notes" subelement is deleted.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
notes | an XML string that is to be used as the content of the "notes" subelement of this object |
addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
virtualinherited |
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.
value | the NNNNNNN integer portion of the SBO identifier |
|
virtualinherited |
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.
sboid | the SBO identifier string of the form "SBO:NNNNNNN" |
|
inherited |
Sets the value of the "substanceUnits" attribute of this Model.
The string in units
is copied.
units | the new substanceUnits for the Model |
|
inherited |
Sets the value of the "timeUnits" attribute of this Model.
The string in units
is copied.
units | the new timeUnits for the Model |
|
inherited |
Sets the user data of this element.
This can be used by the application developer to attach custom information to the node. In case of a deep copy this attribute will passed as it is. The attribute will be never interpreted by this class.
userData | specifies the new user data. |
|
inherited |
Sets the value of the "volumeUnits" attribute of this Model.
The string in units
is copied.
units | the new volumeUnits for the Model |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
Unsets the value of the "annotation" subelement of this SBML object.
Whereas the SBase "notes" subelement is a container for content to be shown directly to humans, the "annotation" element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for "annotation". The element's content type is XML type "any", allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
|
inherited |
|
inherited |
Unsets the value of the "conversionFactor" attribute of this Model.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
inherited |
|
virtualinherited |
|
inherited |
|
inherited |
Unsets the value of the "metaid" attribute of this SBML object.
The optional attribute named "metaid", present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. (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.
|
inherited |
Unsets the ModelHistory object attached to this object.
|
virtualinherited |
|
inherited |
Unsets the value of the "notes" subelement of this SBML object.
The optional SBML element named "notes", present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the "notes" element would be to contain formatted user comments about the model element in which the "notes" element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for "notes", allowing users considerable freedom when adding comments to their models.
The format of "notes" elements must be XHTML 1.0. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how "notes" element content must be structured.
|
inherited |
Unsets the value of the "sboTerm" attribute of this SBML object.
|
inherited |
|
inherited |
|
inherited |