|
libSBML C++ API
5.20.2
|
Represents SBML errors and other diagnostics. More...
Classes | |
| class | SBMLError |
Represents SBML errors and other diagnostics.
| enum SBMLErrorCategory_t |
Category codes for SBMLError diagnostics.
Note that these are distinct from XMLError's category codes. User programs receiving an SBMLError object can use this distinction to check whether the error represents a low-level XML problem or an SBML problem.
| Enumerator | |
|---|---|
| LIBSBML_CAT_SBML | General SBML error not falling into another category below. |
| LIBSBML_CAT_SBML_L1_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model from SBML Level 2 to SBML Level 1. |
| LIBSBML_CAT_SBML_L2V1_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 1. |
| LIBSBML_CAT_SBML_L2V2_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 2. |
| LIBSBML_CAT_GENERAL_CONSISTENCY | Category of errors that can occur while validating general SBML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
| LIBSBML_CAT_IDENTIFIER_CONSISTENCY | Category of errors that can occur while validating symbol identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
| LIBSBML_CAT_UNITS_CONSISTENCY | Category of errors that can occur while validating the units of measurement on quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
| LIBSBML_CAT_MATHML_CONSISTENCY | Category of errors that can occur while validating MathML formulas in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
| LIBSBML_CAT_SBO_CONSISTENCY | Category of errors that can occur while validating SBO identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
| LIBSBML_CAT_OVERDETERMINED_MODEL | Error in the system of equations in the model: the system is overdetermined, therefore violating a tenet of proper SBML. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
| LIBSBML_CAT_SBML_L2V3_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 3. |
| LIBSBML_CAT_MODELING_PRACTICE | Category of warnings about recommended good practices involving SBML and computational modeling. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) |
| LIBSBML_CAT_INTERNAL_CONSISTENCY | Category of errors that can occur while validating libSBML's internal representation of SBML constructs. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) |
| LIBSBML_CAT_SBML_L2V4_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 4. |
| LIBSBML_CAT_SBML_L3V1_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 3 Version 1. |
| LIBSBML_CAT_SBML_L3V2_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 3 Version 1. |
| LIBSBML_CAT_SBML_COMPATIBILITY | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. |
| enum SBMLErrorCode_t |
Codes for all SBML-level errors and warnings from the core specification.
| Enumerator | |
|---|---|
| UnknownError | Encountered unknown internal libSBML error. |
| NotUTF8 | File does not use UTF-8 encoding. |
| UnrecognizedElement | Encountered unrecognized element. |
| NotSchemaConformant | Document does not conform to the SBML XML schema. |
| L3NotSchemaConformant | Document is not well-formed XML. |
| InvalidMathElement | Invalid MathML. |
| DisallowedMathMLSymbol | Disallowed MathML symbol found. |
| DisallowedMathMLEncodingUse | Use of the MathML 'encoding' attribute is not allowed on this element. |
| DisallowedDefinitionURLUse | Use of the MathML 'definitionURL' attribute is not allowed on this element. |
| BadCsymbolDefinitionURLValue | Invalid |
| DisallowedMathTypeAttributeUse | Use of the MathML 'type' attribute is not allowed on this element. |
| DisallowedMathTypeAttributeValue | Disallowed MathML 'type' attribute value. |
| LambdaOnlyAllowedInFunctionDef | Use of |
| BooleanOpsNeedBooleanArgs | Non-Boolean argument given to Boolean operator. |
| NumericOpsNeedNumericArgs | Non-numerical argument given to numerical operator. |
| ArgsToEqNeedSameType | Arguments to |
| PiecewiseNeedsConsistentTypes | Terms in a |
| PieceNeedsBoolean | The second argument of a |
| ApplyCiMustBeUserFunction | A |
| ApplyCiMustBeModelComponent | A |
| KineticLawParametersAreLocalOnly | Cannot use a KineticLaw local parameter outside of its local scope. |
| MathResultMustBeNumeric | A formula's result in this context must be a numerical value. |
| OpsNeedCorrectNumberOfArgs | Incorrect number of arguments given to MathML operator. |
| InvalidNoArgsPassedToFunctionDef | Incorrect number of arguments given to function invocation. |
| DisallowedMathUnitsUse | Attribute 'units' is only permitted on |
| InvalidUnitsValue | Invalid value given for the 'units' attribute. |
| CiCannotReference0DCompartment | A |
| RateOfTargetMustBeCi | A 'rateOf' |
| RateOfTargetCannotBeAssigned | The target of a 'rateOf' |
| RateOfSpeciesTargetCompartmentNot | Compartments of non-substance |
| DuplicateComponentId | Duplicate 'id' attribute value. |
| DuplicateUnitDefinitionId | Duplicate unit definition 'id' attribute value. |
| DuplicateLocalParameterId | Duplicate local parameter 'id' attribute value. |
| MultipleAssignmentOrRateRules | Multiple rules for the same variable are not allowed. |
| MultipleEventAssignmentsForId | Multiple event assignments for the same variable are not allowed. |
| EventAndAssignmentRuleForId | An event assignment and an assignment rule must not have the same value for 'variable'. |
| DuplicateMetaId | Duplicate 'metaid' attribute value. |
| InvalidSBOTermSyntax | Invalid syntax for an 'sboTerm' attribute value. |
| InvalidMetaidSyntax | Invalid syntax for a 'metaid' attribute value. |
| InvalidIdSyntax | Invalid syntax for an 'id' attribute value. |
| InvalidUnitIdSyntax | Invalid syntax for the identifier of a unit. |
| InvalidNameSyntax | Invalid syntax for a 'name' attribute value. |
| DanglingUnitReference | Dangling reference to a unit. |
| MissingAnnotationNamespace | Missing declaration of the XML namespace for the annotation. |
| DuplicateAnnotationNamespaces | Multiple annotations using the same XML namespace. |
| SBMLNamespaceInAnnotation | The SBML XML namespace cannot be used in an Annotation object. |
| MultipleAnnotations | Only one Annotation object is permitted under a given SBML object. |
| InconsistentArgUnits | The units of the function call's arguments are not consistent with its definition. |
| InconsistentKineticLawUnitsL3 | The kinetic law's units are inconsistent with those of other kinetic laws in the model. |
| AssignRuleCompartmentMismatch | Mismatched units in assignment rule for compartment. |
| AssignRuleSpeciesMismatch | Mismatched units in assignment rule for species. |
| AssignRuleParameterMismatch | Mismatched units in assignment rule for parameter. |
| AssignRuleStoichiometryMismatch | Mismatched units in assignment rule for stoichiometry. |
| InitAssignCompartmenMismatch | Mismatched units in initial assignment to compartment. |
| InitAssignSpeciesMismatch | Mismatched units in initial assignment to species. |
| InitAssignParameterMismatch | Mismatched units in initial assignment to parameter. |
| InitAssignStoichiometryMismatch | Mismatched units in initial assignment to stoichiometry. |
| RateRuleCompartmentMismatch | Mismatched units in rate rule for compartment. |
| RateRuleSpeciesMismatch | Mismatched units in rate rule for species. |
| RateRuleParameterMismatch | Mismatched units in rate rule for parameter. |
| RateRuleStoichiometryMismatch | Mismatched units in rate rule for stoichiometry. |
| KineticLawNotSubstancePerTime | The units of the kinetic law are not 'substance'/'time'. |
| SpeciesInvalidExtentUnits | The species' units are not consistent with units of extent. |
| DelayUnitsNotTime | The units of the delay expression are not units of time. |
| EventAssignCompartmentMismatch | Mismatched units in event assignment for compartment. |
| EventAssignSpeciesMismatch | Mismatched units in event assignment for species. |
| EventAssignParameterMismatch | Mismatched units in event assignment for parameter. |
| EventAssignStoichiometryMismatch | Mismatched units in event assignment for stoichiometry. |
| PriorityUnitsNotDimensionless | The units of a priority expression must be 'dimensionless'. |
| UpperUnitBound | Upper boundary of unit validation diagnostic codes. |
| OverdeterminedSystem | The model is overdetermined. |
| InvalidModelSBOTerm | Invalid 'sboTerm' attribute value for a Model object. |
| InvalidFunctionDefSBOTerm | Invalid 'sboTerm' attribute value for a FunctionDefinition object. |
| InvalidParameterSBOTerm | Invalid 'sboTerm' attribute value for a Parameter object. |
| InvalidInitAssignSBOTerm | Invalid 'sboTerm' attribute value for an InitialAssignment object. |
| InvalidRuleSBOTerm | Invalid 'sboTerm' attribute value for a Rule object. |
| InvalidConstraintSBOTerm | Invalid 'sboTerm' attribute value for a Constraint object. |
| InvalidReactionSBOTerm | Invalid 'sboTerm' attribute value for a Reaction object. |
| InvalidSpeciesReferenceSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesReference object. |
| InvalidKineticLawSBOTerm | Invalid 'sboTerm' attribute value for a KineticLaw object. |
| InvalidEventSBOTerm | Invalid 'sboTerm' attribute value for an Event object. |
| InvalidEventAssignmentSBOTerm | Invalid 'sboTerm' attribute value for an EventAssignment object. |
| InvalidCompartmentSBOTerm | Invalid 'sboTerm' attribute value for a Compartment object. |
| InvalidSpeciesSBOTerm | Invalid 'sboTerm' attribute value for a Species object. |
| InvalidCompartmentTypeSBOTerm | Invalid 'sboTerm' attribute value for a CompartmentType object. |
| InvalidSpeciesTypeSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesType object. |
| InvalidTriggerSBOTerm | Invalid 'sboTerm' attribute value for an Event Trigger object. |
| InvalidDelaySBOTerm | Invalid 'sboTerm' attribute value for an Event Delay object. |
| InvalidLocalParameterSBOTerm | Invalid 'sboTerm' attribute value for a LocalParameter object. |
| InvalidSBMLElementSBOTerm | Invalid 'sboTerm' attribute value for the |
| NotesNotInXHTMLNamespace | Notes must be placed in the XHTML XML namespace. |
| NotesContainsXMLDecl | XML declarations are not permitted in Notes objects. |
| NotesContainsDOCTYPE | XML DOCTYPE elements are not permitted in Notes objects. |
| InvalidNotesContent | Invalid notes content found. |
| OnlyOneNotesElementAllowed | Only one Notes subobject is permitted on a given SBML object. |
| InvalidNamespaceOnSBML | Invalid XML namespace for the SBML container element. |
| MissingOrInconsistentLevel | Missing or inconsistent value for the 'level' attribute. |
| MissingOrInconsistentVersion | Missing or inconsistent value for the 'version' attribute. |
| PackageNSMustMatch | Inconsistent or invalid SBML Level/Version for the package namespace declaration. |
| LevelPositiveInteger | The 'level' attribute must have a positive integer value. |
| VersionPositiveInteger | The 'version' attribute must have a positive integer value. |
| AllowedAttributesOnSBML | Invalid attribute found on the SBML container element. |
| L3PackageOnLowerSBML | An L3 package ns found on the SBML container element. |
| MissingModel | No model definition found. |
| IncorrectOrderInModel | Incorrect ordering of components within the Model object. |
| EmptyListElement | Empty ListOf___ object found. |
| NeedCompartmentIfHaveSpecies | The presence of a species requires a compartment. |
| OneOfEachListOf | Only one of each kind of ListOf___ object is allowed inside a Model object. |
| OnlyFuncDefsInListOfFuncDefs | Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions. |
| OnlyUnitDefsInListOfUnitDefs | Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects. |
| OnlyCompartmentsInListOfCompartments | Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects. |
| OnlySpeciesInListOfSpecies | Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects. |
| OnlyParametersInListOfParameters | Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects. |
| OnlyInitAssignsInListOfInitAssigns | Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects. |
| OnlyRulesInListOfRules | Only Rule, Notes and Annotation objects are allowed in ListOfRules objects. |
| OnlyConstraintsInListOfConstraints | Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects. |
| OnlyReactionsInListOfReactions | Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects. |
| OnlyEventsInListOfEvents | Only Event, Notes and Annotation objects are allowed in ListOfEvents objects. |
| L3ConversionFactorOnModel | A 'conversionFactor' attribute value must reference a Parameter object. |
| L3TimeUnitsOnModel | Invalid 'timeUnits' attribute value. |
| L3VolumeUnitsOnModel | Invalid 'volumeUnits' attribute value. |
| L3AreaUnitsOnModel | Invalid 'areaUnits' attribute value. |
| L3LengthUnitsOnModel | Invalid 'lengthUnits' attribute value. |
| L3ExtentUnitsOnModel | Invalid 'extentUnits' attribute value. |
| AllowedAttributesOnModel | Invalid attribute found on the Model object. |
| AllowedAttributesOnListOfFuncs | Invalid attribute found on the ListOfFunctionDefinitions object. |
| AllowedAttributesOnListOfUnitDefs | Invalid attribute found on the ListOfUnitDefinitions object. |
| AllowedAttributesOnListOfComps | Invalid attribute found on the ListOfCompartments object. |
| AllowedAttributesOnListOfSpecies | Invalid attribute found on the ListOfSpecies object. |
| AllowedAttributesOnListOfParams | Invalid attribute found on the ListOfParameters object. |
| AllowedAttributesOnListOfInitAssign | Invalid attribute found on the ListOfInitialAssignments object. |
| AllowedAttributesOnListOfRules | Invalid attribute found on the ListOfRules object. |
| AllowedAttributesOnListOfConstraints | Invalid attribute found on the ListOfConstraints object. |
| AllowedAttributesOnListOfReactions | Invalid attribute found on the ListOfReactions object. |
| AllowedAttributesOnListOfEvents | Invalid attribute found on the ListOfEvents object. |
| L3V2SubstanceUnitsOnModel | Invalid 'substanceUnits' attribute value. |
| FunctionDefMathNotLambda | Invalid expression found in the function definition. |
| InvalidApplyCiInLambda | Invalid forward reference in the MathML |
| RecursiveFunctionDefinition | Recursive function definitions are not permitted. |
| InvalidCiInLambda | Invalid |
| InvalidFunctionDefReturnType | A function's return type must be either a number or a Boolean. |
| OneMathElementPerFunc | A FunctionDefinition object may contain one |
| AllowedAttributesOnFunc | Invalid attribute found on the FunctionDefinition object. |
| OnlyCiInsideBVar | |
| InvalidUnitDefId | Invalid 'id' attribute value for a UnitDefinition object. |
| InvalidSubstanceRedefinition | Invalid redefinition of built-in type 'substance'. |
| InvalidLengthRedefinition | Invalid redefinition of built-in type 'length'. |
| InvalidAreaRedefinition | Invalid redefinition of built-in type name 'area'. |
| InvalidTimeRedefinition | Invalid redefinition of built-in type name 'time'. |
| InvalidVolumeRedefinition | Invalid redefinition of built-in type name 'volume'. |
| VolumeLitreDefExponentNotOne | Must use 'exponent'=1 when defining 'volume' in terms of litres. |
| VolumeMetreDefExponentNot3 | Must use 'exponent'=3 when defining 'volume' in terms of metres. |
| EmptyListOfUnits | An empty list of Unit objects is not permitted in a UnitDefinition object. |
| InvalidUnitKind | Invalid value for the 'kind' attribute of a UnitDefinition object. |
| OffsetNoLongerValid | Unit attribute 'offset' is not supported in this Level+Version of SBML. |
| CelsiusNoLongerValid | Unit name 'Celsius' is not defined in this Level+Version of SBML. |
| EmptyUnitListElement | A ListOfUnits object must not be empty. |
| OneListOfUnitsPerUnitDef | At most one ListOfUnits object is allowed inside a UnitDefinition object. |
| OnlyUnitsInListOfUnits | Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects. |
| AllowedAttributesOnUnitDefinition | Invalid attribute found on the UnitDefinition object. |
| AllowedAttributesOnListOfUnits | Invalid attribute found on the ListOfUnits object. |
| AllowedAttributesOnUnit | Invalid attribute found on the Unit object. |
| ZeroDimensionalCompartmentSize | Invalid use of the 'size' attribute for a zero-dimensional compartment. |
| ZeroDimensionalCompartmentUnits | Invalid use of the 'units' attribute for a zero-dimensional compartment. |
| ZeroDimensionalCompartmentConst | Zero-dimensional compartments must be defined to be constant. |
| UndefinedOutsideCompartment | Invalid value for the 'outside' attribute of a Compartment object. |
| RecursiveCompartmentContainment | Recursive nesting of compartments via the 'outside' attribute is not permitted. |
| ZeroDCompartmentContainment | Invalid nesting of zero-dimensional compartments. |
| Invalid1DCompartmentUnits | Invalid value for the 'units' attribute of a one-dimensional compartment. |
| Invalid2DCompartmentUnits | Invalid value for the 'units' attribute of a two-dimensional compartment. |
| Invalid3DCompartmentUnits | Invalid value for the 'units' attribute of a three-dimensional compartment. |
| InvalidCompartmentTypeRef | Invalid value for the 'compartmentType' attribute of a compartment. |
| OneDimensionalCompartmentUnits | No units defined for 1-D compartment. |
| TwoDimensionalCompartmentUnits | No units defined for 2-D compartment. |
| ThreeDimensionalCompartmentUnits | No units defined for 3-D Compartment object. |
| AllowedAttributesOnCompartment | Invalid attribute found on Compartment object. |
| NoUnitsOnCompartment | No units defined for Compartment object. |
| InvalidSpeciesCompartmentRef | Invalid value found for Species 'compartment' attribute. |
| HasOnlySubsNoSpatialUnits | Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true'. |
| NoSpatialUnitsInZeroD | Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional. |
| NoConcentrationInZeroD | Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional. |
| SpatialUnitsInOneD | Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment. |
| SpatialUnitsInTwoD | Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment. |
| SpatialUnitsInThreeD | Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment. |
| InvalidSpeciesSusbstanceUnits | Invalid value for a Species 'units' attribute. |
| BothAmountAndConcentrationSet | Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously. |
| NonBoundarySpeciesAssignedAndUsed | Cannot use a non-boundary species in both reactions and rules simultaneously. |
| NonConstantSpeciesUsed | Cannot use a constant, non-boundary species as a reactant or product. |
| InvalidSpeciesTypeRef | Invalid value for the 'speciesType' attribute of a species. |
| MultSpeciesSameTypeInCompartment | Cannot have multiple species of the same species type in the same compartment. |
| MissingSpeciesCompartment | Missing value for the 'compartment' attribute. |
| SpatialSizeUnitsRemoved | Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML. |
| SubstanceUnitsOnSpecies | No substance units defined for the species. |
| ConversionFactorOnSpecies | Invalid value for the 'conversionFactor' attribute. |
| AllowedAttributesOnSpecies | Invalid attribute found on Species object. |
| InvalidParameterUnits | Invalid value for the 'units' attribute of a Parameter object. |
| ParameterUnits | No units defined for the parameter. |
| ConversionFactorMustConstant | A conversion factor must reference a Parameter object declared to be a constant. |
| AllowedAttributesOnParameter | Invalid attribute found on Parameter object. |
| InvalidInitAssignSymbol | Invalid value for the 'symbol' attribute of an InitialAssignment object. |
| MultipleInitAssignments | Multiple initial assignments for the same 'symbol' value are not allowed. |
| InitAssignmentAndRuleForSameId | Cannot set a value using both an initial assignment and an assignment rule simultaneously. |
| OneMathElementPerInitialAssign | An InitialAssignment object may contain one |
| AllowedAttributesOnInitialAssign | Invalid attribute found on an InitialAssignment object. |
| InitAssignmentCannotRef0DComp | InitialAssignment cannot reference 0D compartment. |
| InvalidAssignRuleVariable | Invalid value for the 'variable' attribute of an AssignmentRule object. |
| InvalidRateRuleVariable | Invalid value for the 'variable' attribute of a RateRule object. |
| AssignmentToConstantEntity | An assignment rule cannot assign an entity declared to be constant. |
| RateRuleForConstantEntity | A rate rule cannot assign an entity declared to be constant. |
| RepeatedRule10304 | |
| CircularRuleDependency | Circular dependencies involving rules and reactions are not permitted. |
| OneMathElementPerRule | A rule object may contain one |
| AllowedAttributesOnAssignRule | Invalid attribute found on an AssignmentRule object. |
| AllowedAttributesOnRateRule | Invalid attribute found on a RateRule object. |
| AllowedAttributesOnAlgRule | Invalid attribute found on an AlgebraicRule object. |
| RuleCannotRef0DComp | Rule cannot reference 0D compartment. |
| CircularDependencyRateOf | Circular dependencies are not permitted in RateRule and KineticLaw objects. |
| ConstraintMathNotBoolean | A Constraint object's |
| IncorrectOrderInConstraint | Subobjects inside the Constraint object are not in the prescribed order. |
| ConstraintNotInXHTMLNamespace | A Constraint's Message subobject must be in the XHTML XML namespace. |
| ConstraintContainsXMLDecl | XML declarations are not permitted within Constraint's Message objects. |
| ConstraintContainsDOCTYPE | XML DOCTYPE elements are not permitted within Constraint's Message objects. |
| InvalidConstraintContent | Invalid content for a Constraint object's Message object. |
| OneMathElementPerConstraint | A Constraint object may contain one |
| OneMessageElementPerConstraint | A Constraint object can only have one Message subobject. |
| AllowedAttributesOnConstraint | Invalid attribute found on Constraint object. |
| NoReactantsOrProducts | Cannot have a reaction with neither reactants nor products. |
| IncorrectOrderInReaction | Subobjects inside the Reaction object are not in the prescribed order. |
| EmptyListInReaction | Reaction components, if present, cannot be empty. |
| InvalidReactantsProductsList | Invalid object found in the list of reactants or products. |
| InvalidModifiersList | Invalid object found in the list of modifiers. |
| OneSubElementPerReaction | A Reaction object can only contain one of each allowed type of object. |
| CompartmentOnReaction | Invalid value for the Reaction 'compartment' attribute. |
| AllowedAttributesOnReaction | Invalid attribute for a Reaction object. |
| InvalidSpeciesReference | Invalid 'species' attribute value in SpeciesReference object. |
| RepeatedRule20611 | |
| BothStoichiometryAndMath | The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive. |
| AllowedAttributesOnSpeciesReference | Invalid attribute found on the SpeciesReference object. |
| AllowedAttributesOnModifier | Invalid attribute found on the ModifierSpeciesReference object. |
| UndeclaredSpeciesRef | Unknown species referenced in the kinetic law |
| IncorrectOrderInKineticLaw | Incorrect ordering of components in the KineticLaw object. |
| EmptyListInKineticLaw | The list of parameters, if present, cannot be empty. |
| NonConstantLocalParameter | Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true'. |
| SubsUnitsNoLongerValid | Attribute 'substanceUnits' is not supported in this Level+Version of SBML. |
| TimeUnitsNoLongerValid | Attribute 'timeUnits' is not supported in this Level+Version of SBML. |
| OneListOfPerKineticLaw | Only one ListOfLocalParameters object is permitted within a KineticLaw object. |
| OnlyLocalParamsInListOfLocalParams | Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects. |
| AllowedAttributesOnListOfLocalParam | Invalid attribute found on the ListOfLocalParameters object. |
| OneMathPerKineticLaw | Only one |
| UndeclaredSpeciesInStoichMath | Unknown species referenced in the StoichiometryMath object's |
| AllowedAttributesOnKineticLaw | Invalid attribute found on the KineticLaw object. |
| AllowedAttributesOnListOfSpeciesRef | Invalid attribute found on the ListOfSpeciesReferences object. |
| AllowedAttributesOnListOfMods | Invalid attribute found on the ListOfModifiers object. |
| L3V2FastDeprecated | Fast attribute deprecated. |
| AllowedAttributesOnLocalParameter | Invalid attribute found on the LocalParameter object. |
| LocalParameterShadowsSpecies | Invalid attribute found on the LocalParameter object. |
| MissingTriggerInEvent | |
| TriggerMathNotBoolean | A Trigger object's |
| MissingEventAssignment | The Event object is missing an EventAssignment subobject. |
| TimeUnitsEvent | Units referenced by 'timeUnits' attribute are not compatible with units of time. |
| IncorrectOrderInEvent | Incorrect ordering of components in Event object. |
| ValuesFromTriggerTimeNeedDelay | Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay. |
| DelayNeedsValuesFromTriggerTime | The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime'. |
| OneMathPerTrigger | A Trigger object may have one |
| OneMathPerDelay | A Delay object may have one |
| InvalidEventAssignmentVariable | Invalid 'variable' attribute value in Event object. |
| EventAssignmentForConstantEntity | An EventAssignment object cannot assign to a component having attribute 'constant'='true'. |
| OneMathPerEventAssignment | An EventAssignment object may have one |
| AllowedAttributesOnEventAssignment | Invalid attribute found on the EventAssignment object. |
| OnlyOneDelayPerEvent | |
| OneListOfEventAssignmentsPerEvent | An Event object can only have one ListOfEventAssignments subobject. |
| OnlyEventAssignInListOfEventAssign | Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments. |
| AllowedAttributesOnListOfEventAssign | Invalid attribute found on the ListOfEventAssignments object. |
| AllowedAttributesOnEvent | Invalid attribute found on the Event object. |
| AllowedAttributesOnTrigger | Invalid attribute found on the Trigger object. |
| AllowedAttributesOnDelay | Invalid attribute found on the Delay object. |
| PersistentNotBoolean | The Trigger attribute 'persistent' must evaluate to a Boolean value. |
| InitialValueNotBoolean | The Trigger attribute 'initialValue' must evaluate to a Boolean value. |
| OnlyOnePriorityPerEvent | |
| OneMathPerPriority | A Priority object may have one |
| AllowedAttributesOnPriority | Invalid attribute found on the Priority object. |
| GeneralWarningNotSpecified | Unknown error. |
| CompartmentShouldHaveSize | It's best to define a size for every compartment in a model. |
| SpeciesShouldHaveValue | It's best to define an initial amount or initial concentration for every species in a model. |
| ParameterShouldHaveUnits | It's best to declare units for every parameter in a model. |
| ParameterShouldHaveValue | It's best to declare values for every parameter in a model. |
| LocalParameterShadowsId | Local parameters defined within a kinetic law shadow global object symbols. |
| LibSBMLAdditionalCodesLowerBound | Lower boundary of libSBML-specific diagnostic codes. |
| CannotConvertToL1V1 | Cannot convert to SBML Level 1 Version 1. |
| NoEventsInL1 | SBML Level 1 does not support events. |
| NoFunctionDefinitionsInL1 | SBML Level 1 does not support function definitions. |
| NoConstraintsInL1 | SBML Level 1 does not support constraints. |
| NoInitialAssignmentsInL1 | SBML Level 1 does not support initial assignments. |
| NoSpeciesTypesInL1 | SBML Level 1 does not support species types. |
| NoCompartmentTypeInL1 | SBML Level 1 does not support compartment types. |
| NoNon3DCompartmentsInL1 | SBML Level 1 only supports three-dimensional compartments. |
| NoFancyStoichiometryMathInL1 | SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas. |
| NoNonIntegerStoichiometryInL1 | SBML Level 1 does not support non-integer 'stoichiometry' attribute values. |
| NoUnitMultipliersOrOffsetsInL1 | SBML Level 1 does not support multipliers or offsets in unit definitions. |
| SpeciesCompartmentRequiredInL1 | In SBML Level 1, a value for 'compartment' is mandatory in species definitions. |
| NoSpeciesSpatialSizeUnitsInL1 | SBML Level 1 does not support species 'spatialSizeUnits' settings. |
| NoSBOTermsInL1 | SBML Level 1 does not support the 'sboTerm' attribute. |
| StrictUnitsRequiredInL1 | SBML Level 1 requires strict unit consistency. |
| ConversionFactorNotInL1 | SBML Level 1 does not support the 'conversionFactor' attribute. |
| CompartmentNotOnL1Reaction | SBML Level 1 does not support the 'compartment' attribute on Reaction objects. |
| ExtentUnitsNotSubstance | Units of extent must be compatible with units of substance. |
| GlobalUnitsNotDeclared | Global units must be refer to unit kind or unitDefinition. |
| HasOnlySubstanceUnitsNotinL1 | The concept of hasOnlySubstanceUnits was not available in SBML Level 1. |
| AvogadroNotSupported | Avogadro not supported in Levels 2 and 1. |
| NoConstraintsInL2v1 | SBML Level 2 Version 1 does not support Constraint objects. |
| NoInitialAssignmentsInL2v1 | SBML Level 2 Version 1 does not support InitialAssignment objects. |
| NoSpeciesTypeInL2v1 | SBML Level 2 Version 1 does not support SpeciesType objects. |
| NoCompartmentTypeInL2v1 | SBML Level 2 Version 1 does not support CompartmentType objects. |
| NoSBOTermsInL2v1 | SBML Level 2 Version 1 does not support the 'sboTerm' attribute. |
| NoIdOnSpeciesReferenceInL2v1 | SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects. |
| NoDelayedEventAssignmentInL2v1 | SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute. |
| StrictUnitsRequiredInL2v1 | SBML Level 2 Version 1 requires strict unit consistency. |
| IntegerSpatialDimensions | SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3. |
| StoichiometryMathNotYetSupported | Conversion to StoichiometryMath objects not yet supported. |
| PriorityLostFromL3 | SBML Level 2 Version 1 does not support priorities on Event objects. |
| NonPersistentNotSupported | SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects. |
| InitialValueFalseEventNotSupported | SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects. |
| SBOTermNotUniversalInL2v2 | The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2. |
| NoUnitOffsetInL2v2 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
| NoKineticLawTimeUnitsInL2v2 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
| NoKineticLawSubstanceUnitsInL2v2 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
| NoDelayedEventAssignmentInL2v2 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute. |
| ModelSBOBranchChangedBeyondL2v2 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
| StrictUnitsRequiredInL2v2 | SBML Level 2 Version 2 requires strict unit consistency. |
| StrictSBORequiredInL2v2 | SBML Level 2 Version 2 requires strict SBO term consistency. |
| DuplicateAnnotationInvalidInL2v2 | Duplicate top-level annotations are invalid in SBML Level 2 Version 2. |
| NoUnitOffsetInL2v3 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
| NoKineticLawTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
| NoKineticLawSubstanceUnitsInL2v3 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
| NoSpeciesSpatialSizeUnitsInL2v3 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects. |
| NoEventTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
| NoDelayedEventAssignmentInL2v3 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute. |
| ModelSBOBranchChangedBeyondL2v3 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
| StrictUnitsRequiredInL2v3 | SBML Level 2 Version 3 requires strict unit consistency. |
| StrictSBORequiredInL2v3 | SBML Level 2 Version 3 requires strict SBO term consistency. |
| DuplicateAnnotationInvalidInL2v3 | Duplicate top-level annotations are invalid in SBML Level 2 Version 3. |
| NoUnitOffsetInL2v4 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
| NoKineticLawTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
| NoKineticLawSubstanceUnitsInL2v4 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
| NoSpeciesSpatialSizeUnitsInL2v4 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects. |
| NoEventTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
| ModelSBOBranchChangedInL2v4 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
| DuplicateAnnotationInvalidInL2v4 | Duplicate top-level annotations are invalid in SBML Level 2 Version 4. |
| NoSpeciesTypeInL3v1 | SBML Level 3 Version 1 does not support SpeciesType objects. |
| NoCompartmentTypeInL3v1 | SBML Level 3 Version 1 does not support CompartmentType objects. |
| NoUnitOffsetInL3v1 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
| NoKineticLawTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
| NoKineticLawSubstanceUnitsInL3v1 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
| NoSpeciesSpatialSizeUnitsInL3v1 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects. |
| NoEventTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
| ModelSBOBranchChangedInL3v1 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
| DuplicateAnnotationInvalidInL3v1 | Duplicate top-level annotations are invalid in SBML Level 3 Version 1. |
| NoCompartmentOutsideInL3v1 | This Level+Version of SBML does not support the 'outside' attribute on Compartment objects. |
| NoStoichiometryMathInL3v1 | This Level+Version of SBML does not support the StoichiometryMath object. |
| DoubleExponentNotSupported | Exponent of type double not supported in Levels 2 and 1. |
| MathMLElementNotSupported | This MathML element is only permitted in L3V2. |
| EmptyListOfElementNotSupported | Empty 'ListOf' element is only permitted in L3V2. |
| MissingMathElementNotSupported | Missing |
| MissingTriggerElementNotSupported | missing |
| BooleanNumericDiscrepancy | Interchange of Boolean and numeric values only permitted in L3V2. |
| IdNameSBaseInL3V2 | Conversion will lose attributes only available in L3V2 and higher. |
| MissingParticipantsNotSupported | Omission of both |
| ConvertibleMathInitialAssignment | Some L3V2-specific MathML elements are not permitted in InitialAssignment objects. |
| FastReactionsNotSupported | Conversion of reactions employing the 'fast' attribute is not supported. |
| SpeciesRefIdInMathMLNotSupported | This MathML element is only permitted in L3V2. |
| InvalidSBMLLevelVersion | Unknown Level+Version combination of SBML. |
| InvalidPackageLevelVersion | Invalid package Level+Version combination of SBML. |
| AnnotationNotesNotAllowedLevel1 | Annotation objects on the SBML container element are not permitted in SBML Level 1. |
| InvalidRuleOrdering | Invalid ordering of rules. |
| RequiredPackagePresent | The SBML document requires an SBML Level 3 package unavailable in this software. |
| UnrequiredPackagePresent | The SBML document uses an SBML Level 3 package unavailable in this software. |
| PackageRequiredShouldBeFalse | This package expects required to be false. |
| SubsUnitsAllowedInKL | Disallowed value for attribute 'substanceUnits' on KineticLaw object. |
| TimeUnitsAllowedInKL | Disallowed value for attribute 'timeUnits' on KineticLaw object. |
| FormulaInLevel1KL | Only predefined functions are allowed in SBML Level 1 formulas. |
| L3SubstanceUnitsOnModel | Invalid 'substanceUnits' attribute value. |
| StoichiometryMathMissingMath | The |
| TimeUnitsRemoved | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
| BadMathML | Invalid MathML expression. |
| FailedMathMLReadOfDouble | Missing or invalid floating-point number in MathML expression. |
| FailedMathMLReadOfInteger | Missing or invalid integer in MathML expression. |
| FailedMathMLReadOfExponential | Missing or invalid exponential expression in MathML. |
| FailedMathMLReadOfRational | Missing or invalid rational expression in MathML. |
| BadMathMLNodeType | Invalid MathML element. |
| InvalidMathMLAttribute | Invalid MathML attribute. |
| NoTimeSymbolInFunctionDef | Use of |
| NoBodyInFunctionDef | There must be a |
| DanglingUnitSIdRef | Units must refer to valid unit or unitDefinition. |
| RDFMissingAboutTag | RDF missing the |
| RDFEmptyAboutTag | RDF empty |
| RDFAboutTagNotMetaid | RDF |
| RDFNotCompleteModelHistory | RDF does not contain valid ModelHistory. |
| RDFNotModelHistory | RDF does not result in a ModelHistory. |
| AnnotationNotElement | Annotation must contain element. |
| NestedAnnotationNotAllowed | Nested annotations not allowed. |
| InconsistentArgUnitsWarnings | This is an internal error that reverts to 10501. |
| InconsistentPowerUnitsWarnings | This is an internal error that reverts to 10501. |
| InconsistentExponUnitsWarnings | This is an internal error that reverts to 10501. |
| UndeclaredUnits | Missing unit declarations on parameters or literal numbers in expression. |
| UndeclaredTimeUnitsL3 | Unable to verify consistency of units: the unit of time has not been declared. |
| UndeclaredExtentUnitsL3 | Unable to verify consistency of units: the units of reaction extent have not been declared. |
| UndeclaredObjectUnitsL3 | Unable to verify consistency of units: encountered a model entity with no declared units. |
| CannotVerifyUnitsObjectNoMath | Unable to verify consistency of units: encountered an object with no |
| UnrecognisedSBOTerm | Unrecognized 'sboTerm' attribute value. |
| ObseleteSBOTerm | Obsolete 'sboTerm' attribute value. |
| IncorrectCompartmentSpatialDimensions | In SBML Level 1, only three-dimensional compartments are allowed. |
| CompartmentTypeNotValidAttribute | CompartmentType objects are not available in this Level+Version of SBML. |
| ConstantNotValidAttribute | This Level+Version of SBML does not support the 'constant' attribute on this component. |
| MetaIdNotValidAttribute | Attribute 'metaid' is not available in SBML Level 1. |
| SBOTermNotValidAttributeBeforeL2V3 | The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3. |
| InvalidL1CompartmentUnits | Invalid units for a compartment in SBML Level 1. |
| L1V1CompartmentVolumeReqd | In SBML Level 1, a compartment's volume must be specified. |
| CompartmentTypeNotValidComponent | CompartmentType objects are not available in this Level+Version of SBML. |
| ConstraintNotValidComponent | Constraint objects are not available in this Level+Version of SBML. |
| EventNotValidComponent | Event objects are not available in this Level+Version of SBML. |
| SBOTermNotValidAttributeBeforeL2V2 | The 'sboTerm' attribute is invalid for this component before Level 2 Version 2. |
| FuncDefNotValidComponent | FunctionDefinition objects are not available in this Level+Version of SBML. |
| InitialAssignNotValidComponent | InitialAssignment objects are not available in this Level+Version of SBML. |
| VariableNotValidAttribute | Attribute 'variable' is not available on this component in this Level+Version of SBML. |
| UnitsNotValidAttribute | Attribute 'units' is not available on this component in this Level+Version of SBML. |
| ConstantSpeciesNotValidAttribute | Attribute 'constant' is not available on Species objects in SBML Level 1. |
| SpatialSizeUnitsNotValidAttribute | Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1. |
| SpeciesTypeNotValidAttribute | Attribute 'speciesType' is not available on Species objects in SBML Level 1. |
| HasOnlySubsUnitsNotValidAttribute | Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1. |
| IdNotValidAttribute | Attribute 'id' is not available on SpeciesReference objects in SBML Level 1. |
| NameNotValidAttribute | Attribute 'name' is not available on SpeciesReference objects in SBML Level 1. |
| SpeciesTypeNotValidComponent | The SpeciesType object is not supported in SBML Level 1. |
| StoichiometryMathNotValidComponent | The StoichiometryMath object is not supported in SBML Level 1. |
| MultiplierNotValidAttribute | Attribute 'multiplier' on Unit objects is not supported in SBML Level 1. |
| OffsetNotValidAttribute | Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1. |
| L3SpatialDimensionsUnset | No value given for 'spatialDimensions' attribute; assuming a value of 3. |
| OperationInterrupted | Operation was interrupted by the user. |
| UnknownCoreAttribute | Encountered an unknown attribute in the SBML Core namespace. |
| UnknownPackageAttribute | Encountered an unknown attribute in an SBML Level 3 package namespace. |
| PackageConversionNotSupported | Conversion of SBML Level 3 package constructs is not yet supported. |
| InvalidTargetLevelVersion | The requested SBML Level/Version combination is not known to exist. |
| L3NotSupported | SBML Level 3 is not yet supported. |
| SBMLCodesUpperBound | Upper boundary of libSBML-specific diagnostic codes. |
| enum SBMLErrorSeverity_t |
Severity codes for SBMLError diagnostics.
The only publicly-reported values of this type are the four from XMLErrorSeverity_t. All other values are used internally only, with translation of those codes done in SBMLError.cpp