FbcSBMLError.h File Reference

Represents SBML errors and other diagnostics. More...

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Enumerations
enum	FbcSBMLErrorCode_t {   FbcUnknown = 2010100,   FbcNSUndeclared = 2010101,   FbcElementNotInNs = 2010102,   FbcDuplicateComponentId = 2010301,   FbcSBMLSIdSyntax = 2010302,   FbcAttributeRequiredMissing = 2020101,   FbcAttributeRequiredMustBeBoolean = 2020102,   FbcRequiredFalse = 2020103,   FbcOnlyOneEachListOf = 2020201,   FbcNoEmptyListOfs = 2020202,   FbcLOFluxBoundsAllowedElements = 2020203,   FbcLOObjectivesAllowedElements = 2020204,   FbcLOFluxBoundsAllowedAttributes = 2020205,   FbcLOObjectivesAllowedAttributes = 2020206,   FbcActiveObjectiveSyntax = 2020207,   FbcActiveObjectiveRefersObjective = 2020208,   FbcModelMustHaveStrict = 2020209,   FbcModelStrictMustBeBoolean = 2020210,   FbcLOGeneProductsAllowedElements = 2020211,   FbcLOGeneProductsAllowedAttributes = 2020212,   FbcSpeciesAllowedL3Attributes = 2020301,   FbcSpeciesChargeMustBeInteger = 2020302,   FbcSpeciesFormulaMustBeString = 2020303,   FbcFluxBoundAllowedL3Attributes = 2020401,   FbcFluxBoundAllowedElements = 2020402,   FbcFluxBoundRequiredAttributes = 2020403,   FbcFluxBoundRectionMustBeSIdRef = 2020404,   FbcFluxBoundNameMustBeString = 2020405,   FbcFluxBoundOperationMustBeEnum = 2020406,   FbcFluxBoundValueMustBeDouble = 2020407,   FbcFluxBoundReactionMustExist = 2020408,   FbcFluxBoundsForReactionConflict = 2020409,   FbcObjectiveAllowedL3Attributes = 2020501,   FbcObjectiveAllowedElements = 2020502,   FbcObjectiveRequiredAttributes = 2020503,   FbcObjectiveNameMustBeString = 2020504,   FbcObjectiveTypeMustBeEnum = 2020505,   FbcObjectiveOneListOfObjectives = 2020506,   FbcObjectiveLOFluxObjMustNotBeEmpty = 2020507,   FbcObjectiveLOFluxObjOnlyFluxObj = 2020508,   FbcObjectiveLOFluxObjAllowedAttribs = 2020509,   FbcFluxObjectAllowedL3Attributes = 2020601,   FbcFluxObjectAllowedElements = 2020602,   FbcFluxObjectRequiredAttributes = 2020603,   FbcFluxObjectNameMustBeString = 2020604,   FbcFluxObjectReactionMustBeSIdRef = 2020605,   FbcFluxObjectReactionMustExist = 2020606,   FbcFluxObjectCoefficientMustBeDouble = 2020607,   FbcFluxObjectCoefficientWhenStrict = 2020608,   FbcReactionOnlyOneGeneProdAss = 2020701,   FbcReactionAllowedAttributes = 2020702,   FbcReactionLwrBoundSIdRef = 2020703,   FbcReactionUpBoundSIdRef = 2020704,   FbcReactionLwrBoundRefExists = 2020705,   FbcReactionUpBoundRefExists = 2020706,   FbcReactionMustHaveBoundsStrict = 2020707,   FbcReactionConstantBoundsStrict = 2020708,   FbcReactionBoundsMustHaveValuesStrict = 2020709,   FbcReactionBoundsNotAssignedStrict = 2020710,   FbcReactionLwrBoundNotInfStrict = 2020711,   FbcReactionUpBoundNotNegInfStrict = 2020712,   FbcReactionLwrLessThanUpStrict = 2020713,   FbcSpeciesReferenceConstantStrict = 2020714,   FbcSpeciesRefsStoichMustBeRealStrict = 2020715,   FbcSpeciesRefNotAssignedStrict = 2020716,   FbcGeneProdAssocAllowedCoreAttribs = 2020801,   FbcGeneProdAssocAllowedCoreElements = 2020802,   FbcGeneProdAssocAllowedAttribs = 2020803,   FbcGeneProdAssocIdSyntax = 2020804,   FbcGeneProdAssocContainsOneElement = 2020805,   FbcGeneProdAssocNameMustBeString = 2020806,   FbcGeneProdRefAllowedCoreAttribs = 2020901,   FbcGeneProdRefAllowedCoreElements = 2020902,   FbcGeneProdRefAllowedAttribs = 2020903,   FbcGeneProdRefGeneProductSIdRef = 2020904,   FbcGeneProdRefGeneProductExists = 2020908,   FbcAndAllowedCoreAttributes = 2021001,   FbcAndAllowedCoreElements = 2021002,   FbcAndTwoChildren = 2021003,   FbcOrAllowedCoreAttributes = 2021101,   FbcOrAllowedCoreElements = 2021102,   FbcOrTwoChildren = 2021103,   FbcGeneProductAllowedCoreAttributes = 2021201,   FbcGeneProductAllowedCoreElements = 2021202,   FbcGeneProductAllowedAttributes = 2021203,   FbcGeneProductLabelMustBeString = 2021204,   FbcGeneProductLabelMustBeUnique = 2021205,   FbcGeneProductNameMustBeString = 2021206,   FbcGeneProductAssocSpeciesMustExist = 2021207 }
	Codes for all SBML-level errors and warnings from the 'fbc' package. More...

Detailed Description

Represents SBML errors and other diagnostics.

Author

Michael Hucka

Sarah Keating

Enumeration Type Documentation

enum FbcSBMLErrorCode_t

Codes for all SBML-level errors and warnings from the 'fbc' package.

These are distinguished from other SBML error codes by having a number between 2000000 and 2099999.

Calling programs may wish to check which enumeration a given SBMLError object's error identifier is actually from:

• 0000000 to 0009999: XMLErrorCode_t (a low-level XML problem)

• 0010000 to 0099999: SBMLErrorCode_t (a problem with the SBML core specification)
• 1000000 to 1099999: CompSBMLErrorCode_t (a problem with the SBML Level 3 Hierarchical Model Composition package specification).

• 2000000 to 2099999: FbcSBMLErrorCode_t (a problem with the SBML Level 3 Flux Balance Constraints package specification).

• 3000000 to 3099999: QualSBMLErrorCode_t (a problem with the SBML Level 3 Qualitative Models package specification).

• 6000000 to 6099999: LayoutSBMLErrorCode_t (a problem with the SBML Level 3 Layout package specification).

Other error code ranges are reserved for other packages.

Enumerator
FbcUnknown	Unknown error from fbc
FbcNSUndeclared	The fbc ns is not correctly declared
FbcElementNotInNs	Element not in fbc namespace
FbcDuplicateComponentId	Duplicate 'id' attribute value
FbcSBMLSIdSyntax	Invalid 'id' attribute
FbcAttributeRequiredMissing	Required fbc:required attribute on <sbml>
FbcAttributeRequiredMustBeBoolean	The fbc:required attribute must be Boolean
FbcRequiredFalse	The fbc:required attribute must be 'false'
FbcOnlyOneEachListOf	One of each list of allowed
FbcNoEmptyListOfs	ListOf elements cannot be empty
FbcLOFluxBoundsAllowedElements	Allowed elements on ListOfFluxBounds
FbcLOObjectivesAllowedElements	Allowed elements on ListOfObjectives
FbcLOFluxBoundsAllowedAttributes	Allowed attributes on ListOfFluxBounds
FbcLOObjectivesAllowedAttributes	Allowed attributes on ListOfObjectives
FbcActiveObjectiveSyntax	Type of activeObjective attribute
FbcActiveObjectiveRefersObjective	ActiveObjective must reference Objective
FbcModelMustHaveStrict	'Strict' attribute required on <model>
FbcModelStrictMustBeBoolean	'Strict' attribute must be boolean
FbcLOGeneProductsAllowedElements	Allowed elements on ListOfGeneProducts
FbcLOGeneProductsAllowedAttributes	Allowed attributes on ListOfGeneProducts
FbcSpeciesAllowedL3Attributes	Species allowed attributes
FbcSpeciesChargeMustBeInteger	Charge must be integer
FbcSpeciesFormulaMustBeString	Chemical formula must be string
FbcFluxBoundAllowedL3Attributes	<fluxBound> may only have 'metaId' and 'sboTerm' from L3 namespace
FbcFluxBoundAllowedElements	<fluxBound> may only have <notes> and <annotations> from L3 Core
FbcFluxBoundRequiredAttributes	Invalid attribute found on <fluxBound> object
FbcFluxBoundRectionMustBeSIdRef	Datatype for 'fbc:reaction' must be SIdRef
FbcFluxBoundNameMustBeString	The attribute 'fbc:name' must be of the data type string
FbcFluxBoundOperationMustBeEnum	The attribute 'fbc:operation' must be of data type FbcOperation
FbcFluxBoundValueMustBeDouble	The attribute 'fbc:value' must be of the data type double
FbcFluxBoundReactionMustExist	'fbc:reaction' must refer to valid reaction
FbcFluxBoundsForReactionConflict	Conflicting set of FluxBounds for a reaction
FbcObjectiveAllowedL3Attributes	<objective> may only have 'metaId' and 'sboTerm' from L3 namespace
FbcObjectiveAllowedElements	<objective> may only have <notes> and <annotations> from L3 Core
FbcObjectiveRequiredAttributes	Invalid attribute found on <objective> object
FbcObjectiveNameMustBeString	The attribute 'fbc:name' must be of the data type string
FbcObjectiveTypeMustBeEnum	The attribute 'fbc:type' must be of data type FbcType.
FbcObjectiveOneListOfObjectives	An <objective> must have one <listOfFluxObjectives>.
FbcObjectiveLOFluxObjMustNotBeEmpty	<listOfFluxObjectives> subobject must not be empty
FbcObjectiveLOFluxObjOnlyFluxObj	Invalid element found in <listOfFluxObjectives>
FbcObjectiveLOFluxObjAllowedAttribs	<listOfFluxObjectives> may only have 'metaId' and 'sboTerm' from L3 core
FbcFluxObjectAllowedL3Attributes	<fluxObjective> may only have 'metaId' and 'sboTerm' from L3 namespace
FbcFluxObjectAllowedElements	<fluxObjective> may only have <notes> and <annotations> from L3 Core
FbcFluxObjectRequiredAttributes	Invalid attribute found on <fluxObjective> object
FbcFluxObjectNameMustBeString	The attribute 'fbc:name' must be of the data type string
FbcFluxObjectReactionMustBeSIdRef	Datatype for 'fbc:reaction' must be SIdRef
FbcFluxObjectReactionMustExist	'fbc:reaction' must refer to valid reaction
FbcFluxObjectCoefficientMustBeDouble	The attribute 'fbc:coefficient' must be of the data type double
FbcFluxObjectCoefficientWhenStrict	The 'fbc:coefficient' must be declared when strict
FbcReactionOnlyOneGeneProdAss	One GeneProductAssociation in a Reaction
FbcReactionAllowedAttributes	Fbc attributes on a Reaction
FbcReactionLwrBoundSIdRef	LowerBound must be SIdRef
FbcReactionUpBoundSIdRef	UpperBound must be SIdRef
FbcReactionLwrBoundRefExists	LowerBound must point to Parameter
FbcReactionUpBoundRefExists	UpperBound must point to Parameter
FbcReactionMustHaveBoundsStrict	Reaction must have bounds when strict
FbcReactionConstantBoundsStrict	Reaction bounds constant when strict
FbcReactionBoundsMustHaveValuesStrict	Reaction bounds must have values when strict
FbcReactionBoundsNotAssignedStrict	Reaction bounds not assigned when strict
FbcReactionLwrBoundNotInfStrict	LowerBound cannot be INF when strict
FbcReactionUpBoundNotNegInfStrict	UpperBound cannot be -INF when strict
FbcReactionLwrLessThanUpStrict	LowerBound less than upperBound when strict
FbcSpeciesReferenceConstantStrict	SpeciesReferences must be constant when strict
FbcSpeciesRefsStoichMustBeRealStrict	Stoichiometry of SpeciesReferences must be real valued when strict
FbcSpeciesRefNotAssignedStrict	SpeciesReference not target of InitialAssignment when strict"
FbcGeneProdAssocAllowedCoreAttribs	Allowed core attributes on <GeneProductAssociation>
FbcGeneProdAssocAllowedCoreElements	Allowed core elements on <GeneProductAssociation>
FbcGeneProdAssocAllowedAttribs	Allowed fbc attributes on <GeneProductAssociation>
FbcGeneProdAssocIdSyntax	'fbc:id' must have SId syntax
FbcGeneProdAssocContainsOneElement	<GeneProductAssociation> must contain one concrete object
FbcGeneProdAssocNameMustBeString	'fbc:name' must be string
FbcGeneProdRefAllowedCoreAttribs	Allowed core attributes on <GeneProductRef>
FbcGeneProdRefAllowedCoreElements	Allowed core elements on <GeneProductRef>
FbcGeneProdRefAllowedAttribs	Allowed fbc attributes on <GeneProductRef>
FbcGeneProdRefGeneProductSIdRef	'fbc:geneProduct' must be SIdRef
FbcGeneProdRefGeneProductExists	'fbc:geneProduct' must point to existing <GeneProduct>
FbcAndAllowedCoreAttributes	Allowed core attributes on <And>
FbcAndAllowedCoreElements	Allowed core elements on <And>
FbcAndTwoChildren	<And> must have at least two child elements
FbcOrAllowedCoreAttributes	Allowed core attributes on <Or>
FbcOrAllowedCoreElements	Allowed core elements on <Or>
FbcOrTwoChildren	<Or> must have at least two child elements
FbcGeneProductAllowedCoreAttributes	Allowed core attributes on <GeneProduct>
FbcGeneProductAllowedCoreElements	Allowed core elements on <GeneProduct>
FbcGeneProductAllowedAttributes	Allowed fbc attributes on <GeneProduct>
FbcGeneProductLabelMustBeString	'fbc:label' must be string
FbcGeneProductLabelMustBeUnique	'fbc:label' must be unique
FbcGeneProductNameMustBeString	'fbc:name' must be string
FbcGeneProductAssocSpeciesMustExist	'fbc:associatedSpecies' must point to existing <species>