- c -

• CallbackRegistry() : CallbackRegistry
• canonicalize() : ASTNode
• changeErrorSeverity() : XMLErrorLog
• checkCompatibility() : CobraToFbcConverter
• checkConsistency() : SBMLDocument , SBMLInternalValidator
• checkConsistencyWithStrictUnits() : SBMLDocument
• checkInternalConsistency() : SBMLDocument , SBMLInternalValidator
• checkL1Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL2v1Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL2v2Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL2v3Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL2v4Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL2v5Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL3v1Compatibility() : SBMLDocument , SBMLInternalValidator
• checkL3v2Compatibility() : SBMLDocument , SBMLInternalValidator
• checkTerm() : SBO
• clear() : ListOf , XMLAttributes , XMLNamespaces
• clearAdditionalDirs() : SBMLFileResolver
• clearAllElementIdList() : Model
• clearAllElementMetaIdList() : Model
• clearAssociations() : Association
• clearAttributes() : XMLToken
• clearCallbacks() : CallbackRegistry
• clearDashes() : GraphicalPrimitive1D
• clearDefinitions() : DefinitionURLRegistry
• clearFailures() : SBMLValidator , Validator
• clearInstantiation() : Submodel
• clearLog() : XMLErrorLog
• clearNamespaces() : XMLToken
• clearPlugins() : ASTNode
• clearReferencedElement() : SBaseRef
• clearReplacedElements() : CompSBasePlugin
• clearStoredURIDocuments() : CompSBMLDocumentPlugin
• clone() : AdjacentDomains , AdvectionCoefficient , AlgebraicRule , AnalyticGeometry , AnalyticVolume , AssignmentRule , Association , BindingSiteSpeciesType , Boundary , BoundaryCondition , BoundingBox , CobraToFbcConverter , ColorDefinition , Compartment , CompartmentGlyph , CompartmentMapping , CompartmentReference , CompartmentType , CompExtension , CompFlatteningConverter , CompModelPlugin , CompSBasePlugin , CompSBMLDocumentPlugin , Constraint , ConversionOption , ConversionProperties , CoordinateComponent , CSGeometry , CSGHomogeneousTransformation , CSGNode , CSGObject , CSGPrimitive , CSGRotation , CSGScale , CSGSetOperator , CSGTransformation , CSGTranslation , CubicBezier , Curve , CVTerm , Date , DefaultTerm , DefaultValues , Delay , Deletion , DiffusionCoefficient , Dimensions , DistribASTPlugin , DistribBase , DistribExtension , DistribSBasePlugin , DistribSBMLDocumentPlugin , Domain , DomainType , Ellipse , Event , EventAssignment , ExpressionAnalyser , ExternalModelDefinition , FbcAnd , FbcAssociation , FbcExtension , FbcModelPlugin , FbcOr , FbcReactionPlugin , FbcSBasePlugin , FbcSBMLDocumentPlugin , FbcSpeciesPlugin , FbcToCobraConverter , FbcV1ToV2Converter , FbcV2ToV1Converter , FluxBound , FluxObjective , FunctionDefinition , FunctionTerm , GeneAssociation , GeneProduct , GeneProductAssociation , GeneProductRef , GeneralGlyph , Geometry , GeometryDefinition , GlobalRenderInformation , GlobalStyle , GradientBase , GradientStop , GraphicalObject , GraphicalPrimitive1D , GraphicalPrimitive2D , Group , GroupsExtension , GroupsModelPlugin , GroupsSBMLDocumentPlugin , Image , InitialAssignment , Input , InSpeciesTypeBond , InteriorPoint , IntraSpeciesReaction , KeyValuePair , KineticLaw , Layout , LayoutExtension , LayoutModelPlugin , LayoutSBMLDocumentPlugin , LayoutSpeciesReferencePlugin , LinearGradient , LineEnding , LineSegment , ListOf , ListOfAdjacentDomains , ListOfAnalyticVolumes , ListOfColorDefinitions , ListOfCompartmentGlyphs , ListOfCompartmentReferences , ListOfCompartments , ListOfCompartmentTypes , ListOfConstraints , ListOfCoordinateComponents , ListOfCSGNodes , ListOfCSGObjects , ListOfCurveElements , ListOfDeletions , ListOfDomains , ListOfDomainTypes , ListOfDrawables , ListOfEventAssignments , ListOfEvents , ListOfExternalModelDefinitions , ListOfFbcAssociations , ListOfFluxBounds , ListOfFluxObjectives , ListOfFunctionDefinitions , ListOfFunctionTerms , ListOfGeneAssociations , ListOfGeneProducts , ListOfGeometryDefinitions , ListOfGlobalRenderInformation , ListOfGlobalStyles , ListOfGradientDefinitions , ListOfGradientStops , ListOfGraphicalObjects , ListOfGroups , ListOfInitialAssignments , ListOfInputs , ListOfInSpeciesTypeBonds , ListOfInteriorPoints , ListOfKeyValuePairs , ListOfLayouts , ListOfLineEndings , ListOfLineSegments , ListOfLocalParameters , ListOfLocalRenderInformation , ListOfLocalStyles , ListOfMembers , ListOfModelDefinitions , ListOfMultiSpeciesTypes , ListOfObjectives , ListOfOrdinalMappings , ListOfOutputs , ListOfOutwardBindingSites , ListOfParameters , ListOfParametricObjects , ListOfPorts , ListOfPossibleSpeciesFeatureValues , ListOfQualitativeSpecies , ListOfReactionGlyphs , ListOfReactions , ListOfReferenceGlyphs , ListOfReplacedElements , ListOfRules , ListOfSampledFields , ListOfSampledVolumes , ListOfSpecies , ListOfSpeciesFeatures , ListOfSpeciesFeatureTypes , ListOfSpeciesFeatureValues , ListOfSpeciesGlyphs , ListOfSpeciesReferenceGlyphs , ListOfSpeciesReferences , ListOfSpeciesTypeComponentIndexes , ListOfSpeciesTypeComponentMapInProducts , ListOfSpeciesTypeInstances , ListOfSpeciesTypes , ListOfSubmodels , ListOfTextGlyphs , ListOfTransitions , ListOfUncertainties , ListOfUncertParameters , ListOfUnitDefinitions , ListOfUnits , ListOfUserDefinedConstraintComponents , ListOfUserDefinedConstraints , LocalParameter , LocalRenderInformation , LocalStyle , Member , MixedGeometry , Model , ModelCreator , ModelDefinition , ModelHistory , ModifierSpeciesReference , MultiASTPlugin , MultiCompartmentPlugin , MultiExtension , MultiListOfReactionsPlugin , MultiModelPlugin , MultiSBMLDocumentPlugin , MultiSimpleSpeciesReferencePlugin , MultiSpeciesPlugin , MultiSpeciesReferencePlugin , MultiSpeciesType , Objective , OrdinalMapping , Output , OutwardBindingSite , Parameter , ParametricGeometry , ParametricObject , Point , Polygon , Port , PossibleSpeciesFeatureValue , Priority , QualExtension , QualitativeSpecies , QualModelPlugin , QualSBMLDocumentPlugin , RadialGradient , RateRule , Reaction , ReactionGlyph , Rectangle , ReferenceGlyph , RelAbsVector , RenderCubicBezier , RenderCurve , RenderExtension , RenderGraphicalObjectPlugin , RenderGroup , RenderInformationBase , RenderLayoutConverter , RenderLayoutPlugin , RenderListOfLayoutsPlugin , RenderPoint , RenderSBMLDocumentPlugin , ReplacedBy , ReplacedElement , Rule , SampledField , SampledFieldGeometry , SampledVolume , SBase , SBaseExtensionPoint , SBasePlugin , SBasePluginCreator< SBasePluginType, SBMLExtensionType > , SBasePluginCreatorBase , SBaseRef , SBMLConverter , SBMLDocument , SBMLDocumentPlugin , SBMLExtension , SBMLExtensionNamespaces< SBMLExtensionType > , SBMLFileResolver , SBMLFunctionDefinitionConverter , SBMLIdConverter , SBMLInferUnitsConverter , SBMLInitialAssignmentConverter , SBMLInternalValidator , SBMLLevel1Version1Converter , SBMLLevelVersionConverter , SBMLLocalParameterConverter , SBMLNamespaces , SBMLRateOfConverter , SBMLRateRuleConverter , SBMLReactionConverter , SBMLResolver , SBMLRuleConverter , SBMLStripPackageConverter , SBMLUnitsConverter , SBMLUri , SBMLValidator , SpatialCompartmentPlugin , SpatialExtension , SpatialModelPlugin , SpatialParameterPlugin , SpatialPoints , SpatialReactionPlugin , SpatialSBMLDocumentPlugin , SpatialSpeciesPlugin , SpatialSymbolReference , Species , SpeciesFeature , SpeciesFeatureType , SpeciesFeatureValue , SpeciesGlyph , SpeciesReference , SpeciesReferenceGlyph , SpeciesType , SpeciesTypeComponentIndex , SpeciesTypeComponentMapInProduct , SpeciesTypeInstance , StoichiometryMath , Style , SubListOfSpeciesFeatures , Submodel , Text , TextGlyph , Transformation2D , Transformation , TransformationComponent , Transition , Trigger , Uncertainty , UncertParameter , UncertSpan , Unit , UnitDefinition , UserDefinedConstraint , UserDefinedConstraintComponent , XMLAttributes , XMLNamespaces , XMLNode , XMLToken , XMLTriple
• CobraToFbcConverter() : CobraToFbcConverter
• collectDeletions() : SBaseRef
• collectDeletionsAndDeleteSome() : CompModelPlugin
• collectRenameAndConvertReplacements() : CompModelPlugin
• ColorDefinition() : ColorDefinition
• combine() : UnitDefinition
• combineNumbers() : ASTNode
• Compartment() : Compartment
• CompartmentGlyph() : CompartmentGlyph
• CompartmentMapping() : CompartmentMapping
• CompartmentReference() : CompartmentReference
• CompartmentType() : CompartmentType
• CompBase() : CompBase
• CompExtension() : CompExtension
• CompFlatteningConverter() : CompFlatteningConverter
• CompModelPlugin() : CompModelPlugin
• compress() : ParametricObject , SampledField , SpatialPoints
• CompSBasePlugin() : CompSBasePlugin
• CompSBMLDocumentPlugin() : CompSBMLDocumentPlugin
• CompValidator() : CompValidator
• Constraint() : Constraint
• contains() : SBMLErrorLog , XMLErrorLog
• containsChild() : XMLInputStream
• containsUndeclaredUnits() : Delay , EventAssignment , InitialAssignment , KineticLaw , Rule , StoichiometryMath
• containsUri() : XMLNamespaces
• ConversionOption() : ConversionOption
• ConversionProperties() : ConversionProperties
• convert() : CobraToFbcConverter , CompFlatteningConverter , FbcToCobraConverter , FbcV1ToV2Converter , FbcV2ToV1Converter , RenderLayoutConverter , SBMLConverter , SBMLDocument , SBMLFunctionDefinitionConverter , SBMLIdConverter , SBMLInferUnitsConverter , SBMLInitialAssignmentConverter , SBMLLevel1Version1Converter , SBMLLevelVersionConverter , SBMLLocalParameterConverter , SBMLRateOfConverter , SBMLRateRuleConverter , SBMLReactionConverter , SBMLRuleConverter , SBMLStripPackageConverter , SBMLUnitsConverter
• convertCSymbols() : Submodel
• convertRootToPower() : ASTNode
• convertStringToXMLNode() : XMLNode
• convertTimeAndExtent() : Submodel
• convertTimeAndExtentWith() : Submodel
• convertToSI() : Unit , UnitDefinition
• convertXMLNodeToString() : XMLNode
• CoordinateComponent() : CoordinateComponent
• copyInformationToNestedLists() : GroupsModelPlugin
• countIf() : List
• createAdditionalGraphicalObject() : Layout
• createAdjacentDomains() : Geometry , ListOfAdjacentDomains
• createAdvectionCoefficient() : SpatialParameterPlugin
• createAlgebraicRule() : Model
• createAnalyticGeometry() : Geometry , ListOfGeometryDefinitions , MixedGeometry
• createAnalyticVolume() : AnalyticGeometry , ListOfAnalyticVolumes
• createAnd() : Association , FbcAnd , FbcOr , GeneProductAssociation , ListOfFbcAssociations
• createAnnotation() : RDFAnnotationParser
• createAssignmentRule() : Model
• createAssociation() : GeneAssociation
• createBindingSiteSpeciesType() : MultiModelPlugin
• createBoundaryCondition() : SpatialParameterPlugin
• createBoundaryMax() : CoordinateComponent
• createBoundaryMin() : CoordinateComponent
• createBoundingBox() : LineEnding
• createColorDefinition() : ListOfColorDefinitions , RenderInformationBase
• createCompartment() : Model
• createCompartmentGlyph() : Layout
• createCompartmentMapping() : SpatialCompartmentPlugin
• createCompartmentReference() : MultiCompartmentPlugin
• createCompartmentType() : Model
• createConstraint() : Model
• createCoordinateComponent() : Geometry , ListOfCoordinateComponents
• createCSGeometry() : Geometry , ListOfGeometryDefinitions , MixedGeometry
• createCSGHomogeneousTransformation() : CSGObject , CSGSetOperator , CSGTransformation , ListOfCSGNodes
• createCSGObject() : CSGeometry , ListOfCSGObjects
• createCSGPrimitive() : CSGObject , CSGSetOperator , CSGTransformation , ListOfCSGNodes
• createCSGRotation() : CSGObject , CSGSetOperator , CSGTransformation , ListOfCSGNodes
• createCSGScale() : CSGObject , CSGSetOperator , CSGTransformation , ListOfCSGNodes
• createCSGSetOperator() : CSGObject , CSGSetOperator , CSGTransformation , ListOfCSGNodes
• createCSGTranslation() : CSGObject , CSGSetOperator , CSGTransformation , ListOfCSGNodes
• createCubicBezier() : Curve , GeneralGlyph , Layout , ListOfCurveElements , Polygon , ReactionGlyph , ReferenceGlyph , RenderCurve , SpeciesReferenceGlyph
• createCurve() : ListOfDrawables , RenderGroup
• createCVTerms() : RDFAnnotationParser
• createDefaultTerm() : ListOfFunctionTerms , Transition
• createDefaultValues() : ListOfGlobalRenderInformation , ListOfLocalRenderInformation
• createDelay() : Event , Model
• createDeletion() : Submodel
• createDiffusionCoefficient() : SpatialParameterPlugin
• createDomain() : Geometry , ListOfDomains
• createDomainType() : Geometry , ListOfDomainTypes
• createEllipse() : ListOfDrawables , RenderGroup
• createEvent() : Model
• createEventAssignment() : Event , Model
• createExternalModelDefinition() : CompSBMLDocumentPlugin
• createFluxBound() : FbcModelPlugin
• createFluxObjective() : ListOfFluxObjectives , Objective
• createForwardTransformation() : CSGHomogeneousTransformation
• createFunctionDefinition() : Model
• createFunctionTerm() : Transition
• createGene() : Association
• createGeneAssociation() : FbcModelPlugin
• createGeneProduct() : FbcModelPlugin , ListOfGeneProducts
• createGeneProductAssociation() : FbcReactionPlugin
• createGeneProductRef() : FbcAnd , FbcOr , GeneProductAssociation , ListOfFbcAssociations
• createGeneralGlyph() : Layout
• createGeometry() : SpatialModelPlugin
• createGlobalRenderInformation() : ListOfGlobalRenderInformation , RenderListOfLayoutsPlugin
• createGlobalStyle() : GlobalRenderInformation , ListOfGlobalStyles
• createGradientStop() : GradientBase , ListOfGradientStops
• createGroup() : GroupsModelPlugin , LineEnding , ListOfDrawables , ListOfGroups , RenderGroup , Style
• createIdString() : LocalStyle
• createImage() : ListOfDrawables , RenderGroup
• createInitialAssignment() : Model
• createInput() : Transition
• createInSpeciesTypeBond() : MultiSpeciesType
• createInteriorPoint() : Domain , ListOfInteriorPoints
• createIntraSpeciesReaction() : MultiModelPlugin
• createKeyValuePair() : FbcSBasePlugin , ListOfKeyValuePairs
• createKineticLaw() : Model , Reaction
• createKineticLawLocalParameter() : Model
• createKineticLawParameter() : Model
• createLayout() : LayoutModelPlugin
• createLinearGradient() : ListOfGradientDefinitions
• createLinearGradientDefinition() : RenderInformationBase
• createLineEnding() : ListOfDrawables , ListOfLineEndings , RenderGroup , RenderInformationBase
• createLineSegment() : Curve , GeneralGlyph , Layout , ReactionGlyph , ReferenceGlyph , SpeciesReferenceGlyph
• createListOfReplacedElements() : CompSBasePlugin
• createLocalParameter() : KineticLaw
• createLocalRenderInformation() : ListOfLocalRenderInformation , RenderLayoutPlugin
• createLocalStyle() : ListOfLocalStyles , LocalRenderInformation
• createMember() : Group , ListOfMembers
• createMixedGeometry() : Geometry , ListOfGeometryDefinitions , MixedGeometry
• createModel() : SBMLDocument
• createModelDefinition() : CompSBMLDocumentPlugin
• createModifier() : Model , Reaction
• createMultiSpeciesType() : MultiModelPlugin
• createNewConversionFactor() : Submodel
• createNonBinaryTree() : ASTNode
• createObject() : Transition
• createObjective() : FbcModelPlugin , ListOfObjectives
• createOr() : Association , FbcAnd , FbcOr , GeneProductAssociation , ListOfFbcAssociations
• createOrdinalMapping() : ListOfOrdinalMappings , MixedGeometry
• createOutput() : Transition
• createOutwardBindingSite() : MultiSpeciesPlugin
• createParameter() : KineticLaw , Model
• createParametricGeometry() : Geometry , ListOfGeometryDefinitions , MixedGeometry
• createParametricObject() : ListOfParametricObjects , ParametricGeometry
• createPlugin() : SBasePluginCreator< SBasePluginType, SBMLExtensionType > , SBasePluginCreatorBase
• createPoint() : Polygon , RenderCurve
• createPolygon() : ListOfDrawables , RenderGroup
• createPort() : CompModelPlugin
• createPossibleSpeciesFeatureValue() : SpeciesFeatureType
• createPriority() : Event
• createProduct() : Model , Reaction
• createQualitativeSpecies() : QualModelPlugin
• createRadialGradient() : ListOfGradientDefinitions
• createRadialGradientDefinition() : RenderInformationBase
• createRateRule() : Model , SBMLReactionConverter
• createRateRuleMathForSpecies() : SBMLReactionConverter
• createRDFAnnotation() : RDFAnnotationParser
• createRDFDescription() : RDFAnnotationParser
• createReactant() : Model , Reaction
• createReaction() : Model
• createReactionGlyph() : Layout
• createRectangle() : ListOfDrawables , RenderGroup
• createReferenceGlyph() : GeneralGlyph
• createReplacedBy() : CompSBasePlugin
• createReplacedElement() : CompSBasePlugin
• createRoleString() : Style
• createSampledField() : Geometry , ListOfSampledFields
• createSampledFieldGeometry() : Geometry , ListOfGeometryDefinitions , MixedGeometry
• createSampledVolume() : ListOfSampledVolumes , SampledFieldGeometry
• createSBaseRef() : SBaseRef
• createSpatialPoints() : ParametricGeometry
• createSpatialSymbolReference() : SpatialParameterPlugin
• createSpecies() : Model
• createSpeciesFeature() : MultiSpeciesPlugin , SubListOfSpeciesFeatures
• createSpeciesFeatureType() : MultiSpeciesType
• createSpeciesFeatureValue() : SpeciesFeature
• createSpeciesGlyph() : Layout
• createSpeciesReferenceGlyph() : Layout , ReactionGlyph
• createSpeciesType() : Model
• createSpeciesTypeComponentIndex() : MultiSpeciesType
• createSpeciesTypeComponentMapInProduct() : MultiSpeciesReferencePlugin
• createSpeciesTypeInstance() : MultiSpeciesType
• createStoichiometryMath() : SpeciesReference
• createStyle() : GlobalRenderInformation
• createSubListOfSpeciesFeatures() : MultiSpeciesPlugin
• createSubmodel() : CompModelPlugin
• createText() : ListOfDrawables , RenderGroup
• createTextGlyph() : Layout
• createTransition() : QualModelPlugin
• createTrigger() : Event , Model
• createTypeString() : Style
• createUncertainty() : DistribSBasePlugin , ListOfUncertainties
• createUncertParameter() : ListOfUncertParameters , Uncertainty , UncertParameter
• createUncertSpan() : ListOfUncertParameters , Uncertainty , UncertParameter
• createUnit() : Model , UnitDefinition
• createUnitDefinition() : Model
• createUserDefinedConstraint() : FbcModelPlugin , ListOfUserDefinedConstraints
• createUserDefinedConstraintComponent() : ListOfUserDefinedConstraintComponents , UserDefinedConstraint
• createValueString() : ColorDefinition
• createVectorOfChildTypes() : ASTNode
• CSGeometry() : CSGeometry
• CSGHomogeneousTransformation() : CSGHomogeneousTransformation
• CSGNode() : CSGNode
• CSGObject() : CSGObject
• CSGPrimitive() : CSGPrimitive
• CSGRotation() : CSGRotation
• CSGScale() : CSGScale
• CSGSetOperator() : CSGSetOperator
• CSGTransformation() : CSGTransformation
• CSGTranslation() : CSGTranslation
• CubicBezier() : CubicBezier
• Curve() : Curve
• CVTerm() : CVTerm