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libSBML 5.8.0 |
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ASTNode object item to this
list.
CVTerm object item to this
list.
Date object item to this
list.
ModelCreator object item to this
list.
SBase object item to this
list.
SBMLNamespaces object item to this
list.
XMLAttributes object,
optionally with a prefix and URI defining a namespace.
XMLAttributes object,
optionally with a prefix and URI defining a namespace.
XMLAttributes object,
optionally with a prefix and URI defining a namespace.
XMLTriple/value pair to this XMLAttributes set.
XMLToken optionally
with a prefix and URI defining a namespace.
XMLToken optionally
with a prefix and URI defining a namespace.
XMLToken optionally
with a prefix and URI defining a namespace.
XMLTriple/value pair to the attribute set
in this XMLToken.
ASTNode.
node as a child of this XMLNode.
Compartment object to this Model.
CompartmentType object to this Model.
Constraint object to this Model.
ModelCreator object to the list of 'model creator'
values stored in this ModelHistory object.
CVTerm object to this SBML object.
CVTerm object to this SBML object.
Event object to this Model.
EventAssignment to this Event.
SBMLExtension to this SBMLExtensionRegistry.
FunctionDefinition object to this Model.
InitialAssignment object to this Model.
LocalParameter object to the list of local
parameters in this KineticLaw.
Date object to the list of 'modified date' values
stored in this ModelHistory object.
ModifierSpeciesReference object as a product in this
Reaction.
SBMLNamespaces object.
XMLToken.
XMLToken.
SBMLNamespaces object.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
ConversionOption object with the given parameters.
SBMLNamespaces object.
SBMLNamespaces object.
SBMLNamespaces object (Non-package XML namespaces are not added
by this function).
Parameter object to the list of local
parameters in this KineticLaw.
Parameter object to this Model.
SpeciesReference object as a product in this Reaction.
SpeciesReference object as a reactant in this Reaction.
Reaction object to this Model.
CVTerm object.
Rule object to this Model.
XMLNode as a semantic annotation of this ASTNode.
Species object to this Model.
SpeciesType object to this Model.
Unit to this UnitDefinition.
UnitDefinition object to this Model.
AlgebraicRule using the given SBML level and version
values.
AlgebraicRule using the given SBMLNamespaces object
sbmlns.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
ListOf.
ListOf.
annotation to the 'annotation' subelement of this
object.
annotation to the 'annotation' subelement of this
object.
ListOf to this object.
Model, makes copies of everything,
and appends those copies to the appropriate places in this Model.
notes to the 'notes' subelement of this object.
notes to the 'notes' subelement of this object.
SBMLError.
SBMLError.
true if
Unit objects are equivalent.
true if two
UnitDefinition objects are equivalent.
true if two
Unit objects are identical.
true if two
UnitDefinition objects are identical.
SBMLError.
AssignmentRule using the given SBML level and version
values.
AssignmentRule using the given SBMLNamespaces object
sbmlns.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode types.
ASTNode.
ASTNode.
ASTNode.
ASTNode objects.SBMLError.
SBMLError.
SBMLError.
CVTerm.
SBMLError.
SBMLError.
SBMLError.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
CVTerm.
SBMLError.
ASTNode to a canonical form and returns true if
successful, false otherwise.
SBMLError.
Model.
SBMLError.
ListOf object.
ListOf object.
XMLAttributes object.
XMLNamespaces
object.
XMLToken.
XMLNamespaces of
this XMLToken.
Rule.
Rule.
Compartment object.
CompartmentType.
Constraint.
ConversionOption object.
ConversionProperties object.
CVTerm object.
Date.
Delay.
Event.
EventAssignment.
FunctionDefinition.
InitialAssignment.
KineticLaw object.
ListOf.
ListOfCompartments instance.
ListOfCompartmentTypes instance.
ListOfConstraints instance.
ListOfEventAssignments.
ListOfEvents.
ListOfFunctionDefinitions instance.
ListOfInitialAssignments instance.
ListOfLocalParameters object.
ListOfParameters instance.
ListOfReactions instance.
ListOfRules instance.
ListOfSpeciesReferences
instance.
ListOfSpeciesTypes instance.
ListOfUnitDefinitions instance.
ListOfUnits.
LocalParameter.
Model object.
ModelCreator.
ModelHistory object
ModifierSpeciesReference
instance.
Parameter.
Priority.
Rule.
Reaction.
Rule.
SBase object.
SBasePlugin object.
SBMLConverter object.
SBMLDocument.
SBMLDocumentPlugin object.
SBMLFunctionDefinitionConverter
object.
SBMLInitialAssignmentConverter
object.
SBMLConverter object.
SBMLNamespaces.
SBMLLevelVersionConverter
object.
SBMLStripPackageConverter
object.
SBMLConverter object.
Species object.
SpeciesReference instance.
SpeciesType.
StoichiometryMath object.
Trigger.
Unit.
UnitDefinition.
XMLAttributes set.
XMLNamespaces list.
XMLNode.
XMLToken.
XMLTriple set.
ConversionOption value types.
ConversionOption value types.
ConversionOption value types.
ConversionOption value types.
ConversionOption value types.
UnitDefinition objects into a single UnitDefinition.
Compartment using the given SBML level and version
values.
Compartment using the given SBMLNamespaces object
sbmlns.
Compartment.
SBMLError.
SBMLError.
SBMLError.
CompartmentType using the given SBML level and version
values.
CompartmentType using the given SBMLNamespaces object
sbmlns.
CompartmentType.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Constraint using the given SBML level and version
values.
Constraint using the given SBMLNamespaces object
sbmlns.
Constraint.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLErrorLog contains an errorId
true if
the 'math' expression in this Delay instance contains
parameters with undeclared units or literal numbers.
true if the math
expression of this EventAssignment contains literal numbers or
parameters with undeclared units.
true if
the math expression of this InitialAssignment contains
parameters/numbers with undeclared units.
true if
the math expression of this KineticLaw contains
parameters/numbers with undeclared units.
true if
the math expression of this Rule contains
parameters/numbers with undeclared units.
true if the math
expression of this StoichiometryMath object contains literal numbers
or parameters with undeclared units.
SBMLError.
SBMLError.
SBMLError.
ConversionOption.
ConversionOption.
ConversionOption.
ConversionOption.
ConversionOption specialized for string-type options.
ConversionOption specialized for Boolean-type options.
ConversionOption specialized for Boolean-type options.
ConversionOption specialized for double-type options.
ConversionOption specialized for double-type options.
ConversionOption specialized for float-type options.
ConversionOption specialized for float-type options.
ConversionOption specialized for integer-type options.
ConversionOption specialized for integer-type options.
ConversionOption object.
XMLNode which is derived from a string containing XML
content.
XMLNode which is derived from a string containing XML
content.
UnitDefinition object containing the given unit converted
to the appropriate SI unit.
UnitDefinition into a new UnitDefinition object
that uses SI units.
XMLNode.
AlgebraicRule inside this Model and returns it.
XMLNode object.
AssignmentRule inside this Model and returns it.
Compartment inside this Model and returns it.
CompartmentType inside this Model and returns it.
Constraint inside this Model and returns it.
CVTerm objects and creates a the RDF 'Description'
element.
Delay, adds it to this Event and
returns the Delay.
Delay inside the last Event object created in
this Model, and returns a pointer to it.
Event inside this Model and returns it.
EventAssignment, adds it to this Event's list of
event assignments and returns the EventAssignment.
EventAssignment inside the last Event object created in
this Model, and returns a pointer to it.
FunctionDefinition inside this Model and returns it.
InitialAssignment inside this Model and returns it.
KineticLaw inside the last Reaction object created in
this Model, and returns a pointer to it.
KineticLaw object, installs it as this Reaction's
'kineticLaw' subelement, and returns it.
LocalParameter inside the KineticLaw object of the last
Reaction created inside this Model, and returns a pointer to it.
Parameter inside the KineticLaw object of the last
Reaction created inside this Model, and returns a pointer to it.
LocalParameter object, adds it to this KineticLaw's list
of local parameters, and returns the LocalParameter object created.
Model inside this SBMLDocument, and returns a pointer to
it.
Model inside this SBMLDocument, and returns a pointer to
it.
ModifierSpeciesReference object for a modifier species
inside the last Reaction object in this Model, and returns a pointer
to it.
ModifierSpeciesReference, adds it to this Reaction's
list of modifiers and returns it.
Parameter object, adds it to this KineticLaw's list of
local parameters, and returns the Parameter object created.
Parameter inside this Model and returns it.
Priority, adds it to this
Event and returns the Priority.
SpeciesReference object for a product inside the last
Reaction object in this Model, and returns a pointer to it.
SpeciesReference, adds it to this Reaction's list of
products, and returns it.
RateRule inside this Model and returns it.
SpeciesReference object for a reactant inside the last
Reaction object in this Model, and returns a pointer to it.
SpeciesReference, adds it to this Reaction's list of
reactants, and returns it.
Reaction inside this Model and returns it.
Species inside this Model and returns it.
SpeciesType inside this Model and returns it.
StoichiometryMath object, adds it to this
SpeciesReference, and returns it.
Trigger, adds it to this Event and
returns the Trigger.
Trigger inside the last Event object created in
this Model, and returns a pointer to it.
Unit object within the last UnitDefinition object
created in this model and returns a pointer to it.
Unit, adds it to this UnitDefinition's list of
units, and returns it.
UnitDefinition inside this Model and returns it.
CVTerm, optionally with the given qualifier type.
CVTerm, optionally with the given qualifier type.
CVTerm from the given XMLNode.
CVTerm object.
CVTerm objects.ModelHistory.Date object from a string expressing a date and time value.
Date.
Date objects.Delay using the given SBML level and version
values.
Delay using the given SBMLNamespaces object
sbmlns.
Delay.
SBMLError.
SBMLError.
XMLNode
tree and returns
any remaining annotation content.
CVTerm' annotation found in the given
XMLNode tree and returns
any remaining annotation content.
XMLNode tree and returns
any remaining annotation content.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Event using the given SBML level and version
values.
Event using the given SBMLNamespaces object
sbmlns.
Event.
SBMLError.
SBMLError.
EventAssignment using the given SBML level and version
values.
EventAssignment using the given SBMLNamespaces object
sbmlns.
EventAssignment.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
FunctionDefinition constructs from the document and expands
any instances of their use within <math> elements.
InitialAssignment constructs from the document and
replaces them with appropriate values.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
ASTNode and sets it to null.
SBMLError.
FunctionDefinition using the given SBML level and version
values.
FunctionDefinition using the given SBMLNamespaces object
sbmlns.
FunctionDefinition.
SBMLError.
SBMLError.
Compartment from the ListOfCompartments.
Compartment from the ListOfCompartments
based on its identifier.
CompartmentType from the ListOfCompartmentTypes.
CompartmentType from the ListOfCompartmentTypes
based on its identifier.
Constraint from the ListOfConstraints.
EventAssignment from the ListOfEventAssignments.
EventAssignment from the ListOfEventAssignments
based on its identifier.
Event from the ListOfEvents.
Event from the ListOfEvents
based on its identifier.
FunctionDefinition from the ListOfFunctionDefinitions.
FunctionDefinition from the ListOfFunctionDefinitions
based on its identifier.
InitialAssignment from the ListOfInitialAssignments.
InitialAssignment from the ListOfInitialAssignments
based on its identifier.
LocalParameter object located at position n within this
ListOfLocalParameters instance.
LocalParameter object matching the given identifier.
Parameter object located at position n within this
ListOfParameters instance.
Parameter object matching the given identifier.
Reaction from the ListOfReactions.
Reaction from the ListOfReactions
based on its identifier.
Rule from the ListOfRules.
Rule from the ListOfRules
based on its identifier.
Species from the ListOfSpecies.
Species from the ListOfSpecies
based on its identifier.
SpeciesReference from the ListOfSpeciesReferences.
SpeciesReference from the ListOfSpeciesReferences
based on its identifier.
SpeciesType from the ListOfSpeciesTypes.
SpeciesType from the ListOfSpeciesTypes
based on its identifier.
UnitDefinition from the ListOfUnitDefinitions.
UnitDefinition from the ListOfUnitDefinitions
based on its identifier.
Unit from the ListOfUnits.
XMLNode objects.
Model.
nth argument to this function.
name to this FunctionDefinition.
XMLTriple.
XMLToken (by position).
XMLToken (by position).
XMLToken (by position).
XMLToken (by position).
XMLToken
(by position).
XMLTriple.
CVTerm object.
FunctionDefinition object.
nth child of this XMLNode.
XMLNode with the corresponding name.
ASTNode.
XMLToken occurred in the input
document or data stream.
Compartment object in this Model.
Compartment object based on its identifier.
Reaction.
Compartment
object.
CompartmentType object in this Model.
CompartmentType object based on its identifier.
Compartment.
Parameter instance.
Constraint object in this Model.
Model.
ModelHistory object.
ModelCreator object stored in this ModelHistory object.
CVTerm in the list of CVTerms of this SBML
object.
CVTerm objects in the annotations of this SBML
object.
Date value in text-string form.
Date.
libsbml.parseL3Formula(String formula).
SBMLDocument objects.
SBMLDocument objects.
definitionURL attribute value.
Event, if there is one.
UnitDefinition that corresponds to the units
of this Compartment's designated size.
UnitDefinition that expresses the units
of measurement assumed for the 'math' expression of this Delay.
UnitDefinition that expresses the units
of measurement assumed for the 'math' expression of this
EventAssignment.
UnitDefinition that expresses the units
of measurement assumed for the 'math' expression of this
InitialAssignment.
UnitDefinition that expresses the units
of measurement assumed for the 'math' expression of this
KineticLaw.
UnitDefinition that corresponds to the units
of this LocalParameter's value.
UnitDefinition that corresponds to the units
of this Parameter's value.
UnitDefinition that expresses the units of
measurement assumed for the 'math' expression of this Rule.
UnitDefinition that corresponds to the units
of this Species' amount or concentration.
UnitDefinition object that expresses the
units returned by the math expression in this StoichiometryMath
object.
double.
double.
metaid, or null if no such object is found.
metaid, or null if no such object is found.
metaid, or null if no such object is found.
metaid, or
null if no such object is found.
metaid, or null if no such object is found.
null if no such object is found.
metaid, or null if no such object is found.
metaid, or itself if it has the given metaid, or null if no such object is found.
metaid, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the
model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the
model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
id in the model-wide SId namespace, or null if no such object is found.
Compartment, is
always 'compartment'.
CompartmentType, is always 'compartmentType'.
Constraint, is
always 'constraint'.
Delay, is
always 'delay'.
Event, is
always 'event'.
EventAssignment, is always 'eventAssignment'.
FunctionDefinition, is always 'functionDefinition'.
InitialAssignment, is always 'initialAssignment'.
Species, is
always 'kineticLaw'.
ListOf, is
always 'listOf'.
LocalParameter,
is always 'localParameter'.
Model, is
always 'model'.
Species, is
always 'modifierSpeciesReference'.
Parameter, is
always 'parameter'.
Priority, is
always 'priority'.
Reaction, is
always 'reaction'.
SBMLDocument,
is always 'sbml'.
Species, is
always 'species'.
SpeciesReference, is always 'speciesReference'.
SpeciesType, is always 'compartmentType'.
StoichiometryMath, is
always 'stoichiometryMath'.
Trigger, is
always 'trigger'.
Unit, is
always 'unit'.
UnitDefinition,
is always 'unitDefinition'.
ModelCreator object.
SBMLError object in this log.
XMLError object in this log.
XMLError code.
Event object in this Model.
Event object based on its identifier.
EventAssignment object of this Event.
variable.
ASTNode.
SBMLExtension object with the given package URI or package name (string).
Model.
ModelCreator object.
Reaction.
float.
float.
KineticLaw object and return
it as as a text string.
Rule in text-string form.
Model.
FunctionDefinition object based on its identifier.
ModelCreator object.
Date.
Date.
ASTNode.
Compartment object.
CompartmentType.
Event.
FunctionDefinition.
true if
all the required elements for this InitialAssignment object
have been set.
Model.
Parameter.
Reaction.
SimpleSpeciesReference.
Species object.
SpeciesType.
UnitDefinition.
XMLTriple.
XMLNode with the given name.
InitialAssignment object in this Model.
InitialAssignment object based on the symbol to which it
assigns a value.
Trigger.
SBMLExtensionRegistry class.
integer.
ListOf.
ListOf
(i.e., Compartment objects, if the list is non-empty).
ListOf
(i.e., CompartmentType objects, if the list is non-empty).
ListOf
(i.e., Constraint objects, if the list is non-empty).
ListOf
(i.e., EventAssignment objects, if the list is non-empty).
ListOf
(i.e., Event objects, if the list is non-empty).
ListOf
(i.e., FunctionDefinition objects, if the list is non-empty).
ListOf
(i.e., InitialAssignment objects, if the list is non-empty).
ListOf
(i.e., LocalParameter objects, if the list is non-empty).
ListOf
(i.e., Parameter objects, if the list is non-empty).
ListOf
(i.e., Reaction objects, if the list is non-empty).
ListOf
(i.e., Rule objects, if the list is non-empty).
ListOf
(i.e., Species objects, if the list is non-empty).
ListOf
(i.e., SpeciesReference objects, if the list is non-empty).
ListOf
(i.e., SpeciesType objects, if the list is non-empty).
ListOf
(i.e., UnitDefinition objects, if the list is non-empty).
ListOf
(i.e., Unit objects, if the list is non-empty).
Unit this is.
KineticLaw object contained in this Reaction.
Rule object.
XMLNamespaces instance.
Model.
SBMLDocument object containing this
object.
SBMLNamespaces object.
XMLToken occurred in the input document
or data stream.
ModelCreator objects stored in this ModelHistory
object.
Date objects) stored in
this ModelHistory object.
SBaseList of all child SBase objects,
including those nested to an arbitrary depth.
SBaseList of all child SBase objects,
including those nested to an arbitrary depth.
SBaseList of all child SBase objects
contained in SBML package plugins.
ListOfCompartments object in this Model.
ListOfCompartmentTypes object in this Model.
ListOfConstraints object in this Model.
Event.
ListOfEvents object in this Model.
ListOfFunctionDefinitions object in this Model.
ListOfInitialAssignments object in this Model.
KineticLaw object.
Reaction object.
ASTNode
object, and returns an ASTNodeList of all nodes.
KineticLaw object.
ListOfParameters object in this Model.
Reaction object.
Reaction object.
ListOfReactions object in this Model.
ListOfRules object in this Model.
ListOfSpecies object in this Model.
ListOfSpeciesTypes object in this Model.
ListOfUnitDefinitions object in this Model.
UnitDefinition instance.
LocalParameter object in the list of local parameters in
this KineticLaw instance.
SBMLDocument.
Constraint
EventAssignment's 'math'
subelement.
FunctionDefinition.
InitialAssignment.
KineticLaw object and return
it as as an AST.
Rule as an ASTNode tree.
StoichiometryMath and
return it as an AST.
Constraint
Constraint
Date.
Date.
Model object referenced by this L3ParserSettings object.
Model object in which the current object is located.
Model object stored in this SBMLDocument.
Model object stored in the SBMLDocument.
ModelHistory object, if any, attached to this object.
CVTerm object.
ModelHistory object.
Date object in the list of 'modified date' values stored
in this ModelHistory object.
ModifierSpeciesReference object)
in the list of modifiers of this Reaction.
ModifierSpeciesReference object)
having a specific identifier in this Reaction.
Date.
Unit.
Compartment object.
CompartmentType.
Event.
FunctionDefinition.
Model.
Parameter.
Reaction.
SimpleSpeciesReference.
Species object.
SpeciesType.
UnitDefinition.
XMLAttributes set (by position).
XMLTriple.
SBMLNamespaces object.
XMLNamespaces
of this XMLToken.
XMLNode objects.
FunctionDefinition.
XMLNode.
Compartment objects in this Model.
CompartmentType objects in this Model.
Constraint objects in this Model.
ModelCreator objects stored in this ModelHistory
object.
CVTerm objects in the annotations of this SBML
object.
EventAssignment objects attached to this
Event.
Event objects in this Model.
SBMLExtension with the given extension point.
FunctionDefinition objects in this Model.
InitialAssignment objects in this Model.
KineticLaw instance.
Date objects in this ModelHistory object's list of
'modified dates'.
Reaction.
XMLNamespaces instance.
KineticLaw instance.
Parameter objects in this Model.
Reaction.
Reaction.
Reaction objects in this Model.
CVTerm object.
Rule objects in this Model.
Model.
SpeciesType objects in this Model.
Species in this Model having their
'boundaryCondition' attribute value set to true.
UnitDefinition objects in this Model.
Unit objects contained within this
UnitDefinition.
Unit.
ConversionOption object for a given key.
ModelCreator object.
ModelCreator object.
XMLError code.
required attribute of the given package
extension.
Parameter object in the list of local parameters in
this KineticLaw instance.
Parameter object in this Model.
Parameter object based on its identifier.
SBase object to which this plugin
object connected.
true if the current settings are oriented towards handling
avogadro for SBML Level 3.
log with one argument.
if the current settings allow units in text-string
mathematical formulas.
Trigger.
XMLAttributes set (by position).
XMLTriple.
XMLAttributes set (by position).
XMLTriple.
Event.
SpeciesReference object) in
the list of products in this Reaction.
SpeciesReference object) having
a specific identifier in this Reaction.
CVTerm object.
SpeciesReference object) in
the list of reactants in this Reaction.
SpeciesReference object) having
a specific identifier in this Reaction.
Reaction object in this Model.
Reaction object based on its identifier.
SBMLDocument element.
CVTerm object.
CVTerm object.
Reaction as a
boolean value.
Rule object in this Model.
Rule object based on the variable to which it assigns a value.
SBMLDocument object containing this object instance.
SBMLDocument of this plugin object.
level and version of SBML.
Date.
Date.
Compartment.
Compartment object.
Compartment object
as a double.
Species object in this Model.
Species object based on its identifier.
SpeciesReference object based on its identifier.
SpeciesType object in this Model.
SpeciesType object based on its identifier.
Species object object.
XMLError code.
ASTNode
tree.
ASTNode.
KineticLaw object.
Model.
SBMLNamespaces in this version of
libsbml.
InitialAssignment.
Event, if it has one.
KineticLaw object.
Model.
Event.
ASTNode.
SBML_LIST_OF.
Unit instance belonging to this UnitDefinition.
UnitDefinition object in this Model.
UnitDefinition based on its identifier.
ASTNode.
Parameter.
Rule.
XMLAttributes set (by position).
XMLTriple.
Event.
Parameter.
XMLAttributes set (by position).
XMLTriple.
EventAssignment's 'variable' attribute.
Rule object.
SBMLDocument object
containing this object.
SBMLNamespaces object.
Compartment.
Model.
Date.
true or false depending on whether
an attribute with the given index exists in the attribute set in this
XMLToken.
true or false depending on whether
an attribute with the given local name and namespace URI exists
in the attribute set in this XMLToken.
true or false depending on whether
an attribute with the given local name and namespace URI exists
in the attribute set in this XMLToken.
true or false depending on whether
an attribute with the given XML triple exists in the attribute set in
this XMLToken
true or false depending on whether
an attribute with the given index exists in this XMLAttributes.
true or false depending on whether
an attribute with the given local name and namespace URI exists in this
XMLAttributes.
true or false depending on whether
an attribute with the given local name and namespace URI exists in this
XMLAttributes.
true or false depending on whether
an attribute with the given XML triple exists in this XMLAttributes.
true if this copy of libSBML supports
bzip2 format compression.
true if this copy of libSBML has been linked
with the bzip2 library.
XMLNode has a child with the
given name.
true or false depending on whether this
ASTNode has the correct number of children for it's type.
true or false depending on whether the given XMLNode
object contains valid XHTML content.
true or false depending on whether the given XMLNode
object contains valid XHTML content.
true or false depending on whether
an XML Namespace with the given uri/prefix pair is contained in the
XMLNamespaces ofthis XMLToken.
true or false depending on whether
an XML Namespace with the given prefix is contained in the XMLNamespaces of
this XMLToken.
true or false depending on whether
an XML Namespace with the given URI is contained in the XMLNamespaces of
this XMLToken.
true or false depending on whether an XML
Namespace with the given URI and prefix pair is contained in this
XMLNamespaces list.
SBMLError.
SBMLError.
true if this properties object contains an option with
the given key.
true or false depending on whether an XML
Namespace with the given prefix is contained in this XMLNamespaces
list.
true if
all the required attributes for this AlgebraicRule object
have been set.
true if
all the required attributes for this AssignmentRule object
have been set.
true if
all the required attributes for this Compartment object
have been set.
true if
all the required attributes for this CompartmentType object
have been set.
true if all the required elements for this
CVTerm object have been set.
true if all the required attributes for this
Event object have been set.
true if
all the required attributes for this EventAssignment object
have been set.
true if
all the required attributes for this FunctionDefinition object
have been set.
true if
all the required attributes for this InitialAssignment object
have been set.
true if
all the required attributes for this KineticLaw object
have been set.
true if
all the required attributes for this LocalParameter object
have been set.
true if all the required elements for this
ModelCreator object have been set.
true if all the required elements for this
ModelHistory object have been set.
true if
all the required attributes for this ModifierSpeciesReference object
have been set.
true if
all the required attributes for this Parameter object
have been set.
true if
all the required attributes for this RateRule object
have been set.
true if all the required attributes for this
Reaction object have been set.
true if all the
required attributes for this Rule object have been set.
true if
all the required attributes for this Species object
have been set.
true if
all the required attributes for this SpeciesReference object
have been set.
true if
all the required attributes for this SpeciesType object
have been set.
true if
all the required attributes for this Trigger object
have been set.
true if
all the required attributes for this Unit object
have been set.
true if
all the required attributes for this UnitDefinition object
have been set.
true if
all the required elements for this Constraint object
have been set.
true if
all the required elements for this Delay object
have been set.
true if
all the required elements for this Event object
have been set.
true if
all the required elements for this EventAssignment object
have been set.
true if
all the required elements for this FunctionDefinition object
have been set.
true if
all the required elements for this InitialAssignment object
have been set.
true if
all the required elements for this KineticLaw object
have been set.
true if
all the required elements for this Model object
have been set.
true if
all the required elements for this Priority object
have been set.
true if all the
required elements for this Rule object have been set.
true if
all the required elements for this StoichiometryMath object
have been set.
true if
all the required elements for this Trigger object
have been set.
true if
all the required elements for this UnitDefinition object
have been set.
true if the target SBML namespace has been set.
true (non-zero) if this node or any of its
children nodes have the attribute sbml:units.
true or false depending on whether an XML
Namespace with the given URI is contained in this XMLNamespaces list.
true if this
object's level/version and namespace values correspond to a valid
SBML specification.
true if this copy of libSBML supports
gzip and zip format compression.
true if this copy of libSBML has been linked
with the zlib library.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Compartment object to 'typical' default
values.
Parameter object to 'typical' defaults
values.
Reaction object to 'typical' default
values.
Species object to 'typical' defaults
values.
SpeciesReference object to 'typical'
default values.
Unit object to 'typical' default
values.
InitialAssignment using the given SBML level and version
values.
InitialAssignment using the given SBMLNamespaces object
sbmlns.
InitialAssignment.
SBMLError.
SBMLError.
SBMLError.
ListOf
ListOf
ASTNode at point n in the list of children
of this ASTNode.
nth child of this
XMLNode.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
true if this stream object is currently
associated with a file.
true if this
Rule is an AlgebraicRule.
Unit is of the kind ampere.
true if this
Rule is an AssignmentRule.
true or false depending on whether
the attribute set in this XMLToken set is empty.
true (non-zero) if this node is the special
symbol avogadro. The predicate returns false (zero) otherwise.
Unit is of the kind avogadro.
Unit is of the kind becquerel
true (non-zero) if this node has a boolean type
(a logical operator, a relational operator, or the constants true
or false).
Unit is of the kind candela
Unit is of the kind Celsius
true if this Rule is an CompartmentVolumeRule
or equivalent.
true if the given term identifier comes from the stated branch of SBO.
true (non-zero) if this node represents a MathML
constant (e.g., true, Pi).
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind coulomb
Unit is of the kind
dimensionless.
true if the given term identifier comes from the stated branch of SBO.
true or false depending on whether
this XMLToken is an XML element.
true or false depending on whether
this XMLAttributes set is empty.
true or false depending on whether this
XMLNamespaces list is empty.
true or false depending on whether
this XMLTriple is empty.
true if a default namespace is added to each top-level
element defined in the given package extension, otherwise returns
false.
true or false depending on whether
this XMLToken is an XML end element.
true or false depending on whether
this XMLToken is an XML end element for the given start element.
true if the given term identifier comes from the stated branch of SBO.
true or false depending on whether
this XMLToken is an end of file marker.
true or false depending on whether this
error is a significant error.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind farad
true or false depending on whether this
error is a fatal run-time error.
true (non-zero) if this node represents a
MathML function (e.g., abs()), or an SBML Level 1
function, or a user-defined function.
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind gram
Unit is of the kind gray
Unit is of the kind henry
Unit is of the kind hertz
true if the given package extension is one of an ignored
packages, otherwise returns false.
true (non-zero) if this node represents
the special IEEE 754 value infinity, false (zero) otherwise.
true or false depending on whether this
error object is for information purposes only.
true (non-zero) if this node contains an
integer value, false (zero) otherwise.
true if the given term identifier comes from the stated branch of SBO.
true or false depending on whether this
error resulted from an internal program error.
Unit is of the kind item
Unit is of the kind joule
Unit is of the kind katal
Unit is of the kind kelvin
Unit is of the kind kilogram
true if the given term identifier comes from the stated branch of SBO.
true (non-zero) if this node is a MathML
<lambda>, false (zero) otherwise.
Unit is of the kind litre
true (non-zero) if this node represents a
log10 function, false (zero) otherwise.
true (non-zero) if this node is a MathML
logical operator (i.e., and, or, not, xor).
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind lumen
Unit is of the kind lux
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind metre
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
true if this
is a ModifierSpeciesReference.
Unit is of the kind mole
true (non-zero) if this node is a user-defined
variable name in SBML L1, L2 (MathML), or the special symbols delay
or time. The predicate returns false (zero) otherwise.
true or false depending on whether
the XMLNamespaces of this XMLToken is empty.
true (non-zero) if this node represents the
special IEEE 754 value 'not a number' (NaN), false (zero)
otherwise.
true (non-zero) if this node represents the
special IEEE 754 value 'negative infinity', false (zero) otherwise.
Unit is of the kind newton
true (non-zero) if this node contains a number,
false (zero) otherwise.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind ohm
true (non-zero) if this node is a mathematical
operator, meaning, +, -, *,
/ or ^ (power).
true if the given SBML Level 3 package is
enabled with this object.
true if an SBML Level 3 package with the
given URI is enabled with this object.
true if this Rule is an ParameterRule or
equivalent.
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind pascal
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
true (non-zero) if this node is the MathML
<piecewise> construct, false (zero) otherwise.
true if
the list of FormulaUnitsData is populated.
true if the given term identifier comes from the stated branch of SBO.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind radian
true if this Rule
is a RateRule (SBML Levels 2–3) or has a 'type' attribute
value of 'rate' (SBML Level 1).
true if the given term identifier comes from the stated branch of SBO.
true (non-zero) if this node represents a rational
number, false (zero) otherwise.
true if the given term identifier comes from the stated branch of SBO.
true (non-zero) if this node can represent a
real number, false (zero) otherwise.
true (non-zero) if this node is a MathML
relational operator, meaning ==, >=,
>, <, and !=.
true if the given
URL is one of SBML XML namespaces.
true if this Rule
is an AssignmentRule (SBML Levels 2–3) or has a 'type'
attribute value of 'scalar' (SBML Level 1).
Unit is of the kind second
true if this
object's 'annotation' subelement exists and has content.
true if this
Model's 'areaUnits' attribute is set.
true if the body of this
FunctionDefinition has set.
true if this
Species object's 'boundaryCondition' attribute is set.
true if this
Species object's 'charge' attribute is set.
true (non-zero) if this node has the mathml attribute
class.
true if this
Reaction's 'compartment' attribute is set.
true if this
Species object's 'compartment' attribute is set.
true if this
Compartment's 'compartmentType' attribute is set.
true if this
Compartment's 'constant' attribute is set.
true if the
'constant' attribute of this Parameter is set.
true if this
Species object's 'constant' attribute is set.
true if this
SpeciesReference's 'constant' attribute is set
true if this
Model's 'conversionFactor' attribute is set.
true if this
Species object's 'conversionFactor' attribute is set.
true or false depending on whether this
ModelHistory's 'creation date' is set.
Event is set.
true or false depending on whether this
ModelCreator's 'email' part is set.
Unit
is set.
true if this
Model's 'extentUnits' attribute is set.
true or false depending on whether this
ModelCreator's 'family name' part is set.
true if the value of
the 'fast' attribute on this Reaction.
true if this
KineticLaw's 'formula' attribute is set.
true if this
Rule's mathematical expression is set.
true or false depending on whether this
ModelCreator's 'given name' part is set.
true if this
Species object's 'hasOnlySubstanceUnits' attribute is set.
true (non-zero) if this node has the mathml attribute
id.
true if this
Compartment's 'id' attribute is set.
true if this
CompartmentType's 'id' attribute is set.
true if this
Event's 'id' attribute is set.
true if this
FunctionDefinition's 'id' attribute is set.
true if this
Model's 'id' attribute is set.
true if this
Parameter's 'id' attribute is set.
true if this
Reaction's 'id' attribute is set.
true if this
SimpleSpeciesReference's 'id' attribute is set.
true if this
Species object's 'id' attribute is set.
true if this
SpeciesType's 'id' attribute is set.
true if this
UnitDefinition's 'id' attribute is set.
true if this
Species object's 'initialAmount' attribute is set.
true if this
Species object's 'initialConcentration' attribute is set.
Unit is set.
true if this
Reaction contains a kinetic law object.
true if this
Model's 'lengthUnits' attribute is set.
true if a
mathematical formula is defined for this Constraint.
EventAssignment is set.
true if this
FunctionDefinition's 'math' subelement contains a value.
true if this
InitialAssignment's 'math' subelement contains a value.
true if this
Kinetic's 'math' subelement is set.
true if this
Rule's mathematical expression is set.
StoichiometryMath object
is set.
true if a
message is defined for this Constraint.
true if this object's 'metaid' attribute is set.
true if this
object has a ModelHistory object attached to it.
true or false depending on whether this
ModelHistory's 'modified date' is set.
Unit
is set.
true if this
Compartment's 'name' attribute is set.
true if this
CompartmentType's 'name' attribute is set.
true if this
Event's 'name' attribute is set.
true if this
FunctionDefinition's 'name' attribute is set.
true if this
Model's 'name' attribute is set.
true if this
Parameter's 'name' attribute is set.
true if this
Reaction's 'name' attribute is set.
true if this
SimpleSpeciesReference's 'name' attribute is set.
true if this
Species object's 'name' attribute is set.
true if this
SpeciesType's 'name' attribute is set.
true if this
UnitDefinition's 'name' attribute is set.
true if this
object's 'notes' subelement exists and has content.
true or false depending
on whether this ModelCreator's 'organization' part is set.
true or false depending on whether this
ModelCreator's 'organization' part is set.
true if this
Compartment's 'outside' attribute is set.
true if the required attribute of the given package extension
is defined, otherwise returns false.
Event is set.
true or false depending on whether this
SBMLDocumentPlugin's 'required' attribute has been set.
true if this
Reaction's 'reversible' attribute is set.
true if this
object's 'sboTerm' attribute is set.
Unit
is set.
true if this
Compartment's 'size' attribute is set.
true if this
Compartment's 'spatialDimensions' attribute is set.
true if this
Species object's 'spatialSizeUnits' attribute is set.
true if this
SimpleSpeciesReference's 'species' attribute is set.
true if this Species object's
'speciesType' attribute is set.
true if this
SpeciesReference's 'stoichiometry' attribute is set.
true if this
SpeciesReference's 'stoichiometryMath' subelement is set
true (non-zero) if this node has the mathml attribute
style.
true if
this SpeciesReference's 'substanceUnits' attribute is set.
true if this
Model's 'substanceUnits' attribute is set.
true if this
Species object's 'substanceUnits' attribute is set.
true if this
InitialAssignment's 'symbol' attribute is set.
Event
is set.
true if
this SpeciesReference's 'timeUnits' attribute is set.
true if this
Model's 'timeUnits' attribute is set.
Event is set.
true (non-zero) if this node has the attribute
sbml:units.
true if this
Compartment's 'units' attribute is set.
true if the
'units' attribute of this Parameter is set.
true
if this Rule's 'units' attribute is set.
true if
this Species object's 'units' attribute is set.
Event
is set.
true if the
'value' attribute of this Parameter is set.
EventAssignment is set.
true if this
Rule's 'variable' attribute is set.
true if this Compartment's
'volume' attribute is set.
true if this
Model's 'volumeUnits' attribute is set.
Unit is of the kind siemens
Unit is of the kind sievert
true if this Rule is a
SpeciesConcentrationRule or equivalent.
true (non-zero) if this node represents a
square root function, false (zero) otherwise.
true or false depending on whether
this XMLToken is an XML start element.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind steradian
true or false depending on whether this
error was generated by the operating system.
true if the given term identifier comes from the stated branch of SBO.
Unit is of the kind tesla
true or false depending on whether
this XMLToken is an XML text element.
true (non-zero) if this node is a unary minus
operator, false (zero) otherwise.
'gram' or 'mole').
true (non-zero) if this node has an unknown type.
true (non-zero) if this node is a unary plus
operator, false (zero) otherwise.
true or false depending on whether this
error resulted from a problem or whether it was logged as an unknown
error.
true if the given
set of namespaces represent a valid set
true or false depending on whether the argument
string conforms to the syntax of SBML identifiers.
true or false depending on whether the argument string
conforms to the syntax of SBML unit identifiers.
true or false depending on whether the argument string
conforms to the XML data type ID.
'area'.
'dimensionless'.
'length'.
'mass'.
'substance'.
'substance' divided by the predefined
unit 'time'.
'time'.
'volume'.
Unit is of the kind volt
true or false depending on whether
this error object is a warning.
Unit is of the kind watt
Unit is of the kind weber
true or false depending on whether this
ASTNode is well-formed.
true or false depending on whether this
error resulted from a problem in the XML input (e.g., an XML syntax
error).
KineticLaw using the given SBML level and version
values.
KineticLaw using the given SBMLNamespaces object
sbmlns.
KineticLaw.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
log(x) at all, and set an error message
telling the user to use log10(x), ln(x),
or log(base, x) instead.
log(x) as the natural logarithm of x.
log(x) as the base-10 logarithm of x.
L3ParserSettings object with default values.
L3ParserSettings object with specific values for all
possible settings.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError diagnostics.
SBMLError.
ListOf object.
ListOf object.
ListOf object.
ListOf with SBMLNamespaces object.
ListOf.
ListOfCompartments object.
ListOfCompartments object.
ListOfCompartmentTypes object.
ListOfCompartmentTypes object.
ListOfConstraints object.
ListOfConstraints object.
ListOfEventAssignments object.
ListOfEventAssignments object.
ListOfEvents object.
ListOfEvents object.
ListOfFunctionDefinitions object.
ListOfFunctionDefinitions object.
ListOfInitialAssignments object.
ListOfInitialAssignments object.
ListOfLocalParameters object.
ListOfLocalParameters object.
ListOfParameters object.
ListOfParameters object.
ListOfReactions object.
ListOfReactions object.
ListOfRules object.
ListOfRules object.
ListOfSpecies object.
ListOfSpecies object.
ListOfSpeciesReferences object.
ListOfSpeciesReferences object.
ListOfSpeciesTypes object.
ListOfSpeciesTypes object.
ListOfUnitDefinitions object.
ListOfUnitDefinitions object.
ListOfUnits object.
ListOfUnits object.
LocalParameter object with the given SBML level and
version values.
LocalParameter object with the given SBMLNamespaces
object sbmlns.
LocalParameter object.
LocalParameter object by copying
the attributes of a given Parameter object.
SBMLError.
true if this converter's properties matches a
given set of configuration properties.
true if this converter object's properties match the given
properties.
true if this converter object's properties match the given
properties.
true if this converter's properties matches a
given set of configuration properties.
true if this converter object's properties match the given
properties.
true if this converter object's properties match the given
properties.
true if this converter's properties matches a
given set of configuration properties.
true if this object's set of XML namespaces are a subset
of the given object's XML namespaces.
true if this object's set of XML namespaces are the same
as the given object's XML namespaces.
SBMLError.
Unit objects with the same 'kind' attribute value into a
single Unit.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Model using the given SBML level and version
values.
Model using the given SBMLNamespaces object
sbmlns.
Model object.
CVTerm.
ModelHistory.ModelCreator object.
ModelCreator from an XMLNode.
ModelCreator.
ModelCreator objects.ModelHistory object.
ModelHistory object.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
ModifierSpeciesReference using the given SBML level and version
values.
ModifierSpeciesReference using the given SBMLNamespaces object
sbmlns.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
ofstream.OFStream object for a file.
OFStream object for a file.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
cout,
cerr, and clog.OStream object with one of standard output stream objects.
OStream object with one of standard output stream objects.
ostringstream.OStringStream object
SBMLError.
SBMLError.
Parameter using the given SBML level and version
values.
Parameter using the given SBMLNamespaces object
sbmlns.
Parameter.
SBMLError.
SBMLError.
CVTerm objects and creates a complete SBML annotation
around it.
Model to
resolve symbols, and returns an Abstract Syntax Tree (AST)
representation of the result.
obj and creates the
XML structure for an SBML annotation representing that metadata if
there is a model history stored in obj.
obj and creates the
XML structure for an SBML annotation representing that history.
XMLNode tree) into a list of
CVTerm objects.
XMLNode tree) into a list of
CVTerm objects.
ModelHistory class instance.
ModelHistory class instance.
ModelHistory class instance.
XMLNode tree) into a
list of CVTerm objects.
SBMLError.
SBMLError.
SBMLError.
ASTNode object item to the beginning
of this list.
CVTerm object item to the beginning
of this list.
Date object item to the beginning
of this list.
ModelCreator object item to the beginning
of this list.
SBase object item to the beginning
of this list.
SBMLNamespaces object item to the beginning
of this list.
ASTNode.
SBMLError.
Event.Priority object using the given SBML level and
version values.
Priority object using the given SBMLNamespaces object
sbmlns.
Priority.
SBMLError.
RateRule using the given SBML level and version
values.
RateRule using the given SBMLNamespaces object
sbmlns.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Reaction using the given SBML level and version
values.
Reaction using the given SBMLNamespaces object
sbmlns.
Reaction.
filename.
filename.
SBMLError.
SBMLError.
ASTNode to a binary tree.
ASTNode object from this list and
returns it.
CVTerm object from this list and
returns it.
Date object from this list and
returns it.
ListOf items and returns a
pointer to it.
ListOfCompartments items and returns a pointer to
it.
ListOfCompartments items with the given identifier.
ListOfCompartmentTypes items and returns a pointer to
it.
ListOfCompartmentTypes items with the given identifier.
ListOfConstraints items and returns a
pointer to it.
ListOfEventAssignments items and returns a pointer to
it.
ListOfEventAssignments items with the given identifier.
ListOfEvents items and returns a pointer to
it.
ListOfEvents items with the given identifier.
ListOfFunctionDefinitions items and returns a pointer to
it.
ListOfFunctionDefinitions items with the given identifier.
ListOfInitialAssignments items and returns a pointer to
it.
ListOfInitialAssignments items with the given identifier.
ListOfLocalParameters, and returns a
pointer to it.
LocalParameter object in this ListOfLocalParameters
matching the given identifier, and returns a pointer to it.
ListOfParameters, and returns a pointer
to it.
Parameter object in this ListOfParameters
matching the given identifier, and returns a pointer to it.
ListOfReactions items and returns a pointer to
it.
ListOfReactions items with the given identifier.
ListOfRules items and returns a pointer to
it.
ListOfRules items with the given identifier.
ListOfSpeciesReferences items and returns a pointer to
it.
ListOfSpeciesReferences items with the given identifier.
ListOfSpeciesTypes items and returns a pointer to
it.
ListOfSpeciesTypes items with the given identifier.
ListOfUnitDefinitions items and returns a pointer to
it.
ListOfUnitDefinitions items with the given identifier.
ListOfUnits items and returns a pointer to
it.
ModelCreator object from this list and
returns it.
SBase object from this list and
returns it.
SBMLError list.
SBMLNamespaces object from this list and
returns it.
XMLAttributes set.
XMLAttributes set.
XMLAttributes set.
XMLTriple from this XMLAttributes set.
XMLToken.
XMLToken.
XMLToken.
XMLTriple from the attribute set
in this XMLToken.
ASTNode object.
nth child of this XMLNode and returns the
removed node.
Compartment object from this Model object and
returns a pointer to it.
Compartment object with the given identifier from this Model
object and returns a pointer to it.
CompartmentType object from this Model object and
returns a pointer to it.
CompartmentType object with the given identifier from this Model
object and returns a pointer to it.
Constraint object from this Model object and
returns a pointer to it.
Event object from this Model object and
returns a pointer to it.
Event object with the given identifier from this Model
object and returns a pointer to it.
EventAssignment object from this Event object and
returns a pointer to it.
EventAssignment object with the given 'variable' attribute
from this Event object and returns a pointer to it.
Delay's Event parent and calls unsetDelay() on it, indirectly deleting itself.
KineticLaw's Reaction parent and calls unsetKineticLaw() on it, indirectly deleting itself.
ListOf objects typically live as object children of their parent object and not as pointer children, this function clears itself, but does not attempt to do anything else.
Model's parent SBMLDocument and calls setModel(null) on it,
indirectly deleting itself.
Priority's Event parent and calls unsetPriority() on it, indirectly deleting itself.
StoichiometryMath's SpeciesReference parent and calls unsetStoichiometryMath() on it, indirectly deleting itself.
Trigger's Event parent and calls unsetTrigger() on it, indirectly deleting itself.
FunctionDefinition object from this Model object and
returns a pointer to it.
FunctionDefinition object with the given identifier from this Model
object and returns a pointer to it.
InitialAssignment object from this Model object and
returns a pointer to it.
InitialAssignment object with the given 'symbol' attribute
from this Model object and returns a pointer to it.
LocalParameter object in the list of local parameters
in this KineticLaw instance and returns a pointer to it.
LocalParameter object with the given identifier in the list of
local parameters in this KineticLaw instance and returns a pointer to it.
Reaction and returns a pointer to it.
Reaction and returns a pointer to it.
SBMLNamespaces object.
XMLNamespaces
of this XMLToken.
SBMLNamespaces object.
Parameter object in the list of local parameters
in this KineticLaw instance and returns a pointer to it.
Parameter object with the given identifier in the list of
local parameters in this KineticLaw instance and returns a pointer to it.
Parameter object from this Model object and
returns a pointer to it.
Parameter object with the given identifier from this Model
object and returns a pointer to it.
Reaction and returns a pointer to it.
Reaction and returns a pointer to it.
Reaction and returns a pointer to it.
Reaction and returns a pointer to it.
Reaction object from this Model object and
returns a pointer to it.
Reaction object with the given identifier from this Model
object and returns a pointer to it.
CVTerm
object.
XMLAttributes set.
Rule object from this Model object and
returns a pointer to it.
Rule object with the given 'variable' attribute from this Model
object and returns a pointer to it.
Unit to express the unit with the
value of the scale attribute reduced to zero.
Species object from this Model object and
returns a pointer to it.
Species object with the given identifier from this Model
object and returns a pointer to it.
SpeciesType object from this Model object and
returns a pointer to it.
SpeciesType object with the given identifier from this Model
object and returns a pointer to it.
Unit object from this UnitDefinition object and
returns a pointer to it.
UnitDefinition object from this Model object and
returns a pointer to it.
UnitDefinition object with the given identifier from this Model
object and returns a pointer to it.
MetaIdRef attributes on this element.
SIdRef attributes on this element, including any
found in MathML content (if such exists).
UnitSIdRef attributes on this element.
Unit objects within the ListOfUnits of a
UnitDefinition.
SBMLError.
SBMLError.
ASTNode with the
name/value/formula represented by arg.
ASTNode with the given ASTNode.
SBMLError.
true (non-zero) if this node returns a boolean type
or false (zero) otherwise.
true (non-zero) if this node returns a boolean type
or false (zero) otherwise.
Rule.
Rule object types.
Rule object types.
Rule object types.
SBase objects.SBMLError.
SBMLConverter object.
SBMLConverter object.
SBMLDocument, optionally with given values for the SBML
Level and Version.
SBMLDocument, optionally with given values for the SBML
Level and Version.
SBMLDocument, optionally with given values for the SBML
Level and Version.
SBMLDocument using the given SBMLNamespaces object
sbmlns.
SBMLDocument.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError to report that something occurred during SBML
processing.
SBMLError.
SBMLFunctionDefinitionConverter object.
SBMLFunctionDefinitionConverter
object.
SBMLInitialAssignmentConverter object.
SBMLInitialAssignmentConverter
object.
SBMLLevelVersionConverter object.
SBMLLevelVersionConverter
object.
SBMLError.
SBMLNamespaces object corresponding to the given SBML
level and version.
SBMLNamespaces object corresponding to the given SBML
level and version.
SBMLNamespaces object corresponding to the given SBML
level and version.
SBMLNamespaces.
SBMLNamespaces objects.SBMLReader and returns it.
SBMLLevelVersionConverter object.
SBMLLevelVersionConverter
object.
SBMLStripPackageConverter object.
SBMLStripPackageConverter
object.
SBMLWriter.
SBMLError.
SBMLError.
SBMLError.
annotation.
annotation.
annotation.
annotation.
Model.
XMLAttributes to this XMLToken.
CVTerm object.
CVTerm object.
Species object.
ASTNode to the given character.
Species object.
ASTNode to className.
Reaction.
Species object.
Compartment.
SBMLDocument.checkConsistency() is called.
SBMLDocument.setLevelAndVersion(long lev, long ver, boolean strict) is called.
Compartment.
Parameter to the given boolean
flag.
Species object.
SpeciesReference to the given boolean
flag.
Model.
Species object.
ModelHistory object.
Date object using a date and time value
expressed as a text string.
Date object.
Event to a copy of the given Delay
object instance.
SBMLDocument object.
SBMLDocument object.
double value.
double.
ModelCreator object.
XMLToken is an end-of-file (input) marker.
Unit.
Unit.
Model.
ModelCreator object.
Reaction.
float value.
float.
KineticLaw instance to the
given formula.
Rule to an expression in
text-string form.
ModelCreator object.
Species object.
Date object.
Date object's time zone hour offset.
ASTNode to id.
Compartment.
CompartmentType.
Event.
FunctionDefinition.
Model.
Parameter.
Reaction.
SimpleSpeciesReference.
Species object.
SpeciesType.
UnitDefinition.
Species and marks the field
as set.
Species and marks
the field as set.
Trigger instance.
int value.
Unit.
Reaction to a copy of the
given KineticLaw object.
Rule.
Model.
SBMLDocument instance,
attempting to convert the model as needed.
SBMLDocument instance,
attempting to convert the model as needed.
SBMLDocument.
Constraint to a copy of the
AST given as math.
Delay instance to a copy of the given
ASTNode.
EventAssignment to a copy of the
given ASTNode.
FunctionDefinition to the Abstract
Syntax Tree given in math.
InitialAssignment.
KineticLaw instance to a copy
of the given ASTNode.
Priority instance to a copy of the given
ASTNode.
Rule to a copy of the given
ASTNode.
StoichiometryMath instance to a
copy of the given ASTNode.
Trigger instance to a copy of the given
ASTNode.
Constraint.
Date object.
Date object's time zone minutes offset.
L3ParserSettings object.
Model for this SBMLDocument to a copy of the given Model.
ModelHistory of this object.
CVTerm object.
CVTerm object.
ModelHistory object.
Date object.
Unit.
ASTNode to the given name.
Compartment.
CompartmentType.
Event.
FunctionDefinition.
Model.
Parameter.
Reaction.
SimpleSpeciesReference.
Species object.
SpeciesType.
UnitDefinition.
notes.
notes.
Unit.
ModelCreator object.
ModelCreator object.
Compartment.
required attribute value of the given package
extension.
avogadro in
mathematical formulas.
log in mathematical formulas.
Trigger instance.
Event
to a copy of the given Priority object instance.
SBMLDocument.
SBMLDocument.
CVTerm object.
SBMLDocument element.
Reaction.
Unit.
Date object.
Date object.
Compartment.
Compartment.
Compartment as a double.
Species object.
SimpleSpeciesReference.
Species object.
SpeciesReference.
SpeciesReference.
ASTNode to style.
KineticLaw object to a copy of the identifier given
in sid.
Model.
Species object.
InitialAssignment.
Event to a copy of sid.
KineticLaw object to a copy of the identifier in sid.
Model.
Event to a copy of the given
Trigger object instance.
ASTNode to the given type code.
ASTNode to units.
Compartment.
Parameter to a copy of the given
units identifier units.
Rule.
Species object.
Event to a value.
ASTNode to the given (long) integer and sets
the node type to AST_INTEGER.
ASTNode to the given rational in two parts: the
numerator and denominator.
ASTNode to the given real (double) and sets
the node type to AST_REAL.
ASTNode to the given real (double) in two
parts: the mantissa and the exponent.
Parameter to the given double
value and marks the attribute as set.
EventAssignment to a copy of
the given identifier string.
Rule object.
Compartment.
Model.
Date object.
UnitDefinition such that any given kind of Unit object
occurs only once in the ListOfUnits.
ListOf.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Species using the given SBML level and version
values.
Species using the given SBMLNamespaces object
sbmlns.
Species object.
SBMLError.
SBMLError.
SpeciesReference using the given SBML level and version
values.
SpeciesReference using the given SBMLNamespaces object
sbmlns.
SpeciesReference.
SpeciesType using the given SBML level and version
values.
SpeciesType using the given SBMLNamespaces object
sbmlns.
SpeciesType.
SBMLError.
SBMLError.
StoichiometryMath object using the given SBML level
values.
StoichiometryMath object using the given SBMLNamespaces object
sbmlns.
StoichiometryMath.
SBMLError.
SBMLError.
ostringstream buffer.
s to the string object currently assosiated with
this stream buffer.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
ASTNode object with the children of the
given ASTNode object.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
XMLNode.
Trigger using the given SBML level and version
values.
Trigger using the given SBMLNamespaces object
sbmlns.
Trigger.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
SBMLError.
Unit using the given SBML level and version
values.
Unit using the given SBMLNamespaces object
sbmlns.
Unit.