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libSBML Perl API
libSBML 5.12.0 Perl API
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libSBML Perl API
libSBML 5.12.0 Perl API
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Represents SBML errors and other diagnostics. More...
Classes | |
| class | SBMLError |
| {core} More... | |
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 Version 1 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 Version 1 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 Version 1 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 Version 1 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 Version 1 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 Version 1 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. |
| 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 | |
| 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 aLocal Parameter object. |
| 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 must contain one |
| AllowedAttributesOnFunc |
Invalid attribute found on the FunctionDefinition object. |
| 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 must contain one |
| AllowedAttributesOnInitialAssign |
Invalid attribute found on an InitialAssignment object. |
| InitAssignmentCannotRef0DComp | |
| 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 must 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 | |
| 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 must contain one |
| OneMessageElementPerConstraint |
A Constraint object must contain 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 deprecated. |
| AllowedAttributesOnLocalParameter |
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 must have one |
| OneMathPerDelay |
A Delay object must 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 must 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 must 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 units 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 a predefined unit kind or a 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. |
| InvalidSBMLLevelVersion |
Unknown 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. |
| 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. |
| 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. |
| 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
