- C_DOT - Static variable in class org.sbml.jsbml.math.compiler.HTMLFormula
-
Multiplication symbol “⋅”.
- C_DOT - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula
-
Multiplication symbol “⋅”.
- cache - Static variable in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
Caches the constraints with SoftReferences
- cachedJson - Static variable in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory
-
- CallableSBase - Interface in org.sbml.jsbml
-
The interface
CallableSBase represents an
SBase that can be
called in mathematical expressions, i.e.,
ASTNode, via its
identifier.
- canConvert(Class) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
-
- canConvert(Class) - Method in class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
-
- categories - Variable in class org.sbml.jsbml.validator.offline.ValidationContext
-
- category - Variable in exception org.sbml.jsbml.SBMLError
-
- category - Variable in exception org.sbml.jsbml.SBMLException
-
The category of this exception.
- Category() - Constructor for enum org.sbml.jsbml.SBMLException.Category
-
- category - Variable in class org.sbml.jsbml.util.Detail
-
- ceiling(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- ceiling(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- characters - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
Represents the text of a SBML component to write.
- characters - Variable in class org.sbml.jsbml.xml.XMLToken
-
- charge - Variable in class org.sbml.jsbml.Species
-
Deprecated.
- charge - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- check(ValidationContext, T) - Method in interface org.sbml.jsbml.validator.offline.constraints.AnyConstraint
-
Checks if the object conforms to the specific rule in the given context.
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
- check(ValidationContext, SBase) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedElementValidationFunction
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedMathValidationFunction
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.ElementOrderValidationFunction
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UniqueValidation
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UnknownAttributeValidationFunction
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UnknownElementValidationFunction
-
- check(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.ValidationConstraint
-
- check(ValidationContext, T) - Method in interface org.sbml.jsbml.validator.offline.constraints.ValidationFunction
-
Returns true if the constraint is valid and false
if it's broken.
- CHECK_CATEGORY() - Constructor for enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
-
- checkAbout(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Checks and Sets about String, that correspond to the value of the
rdf:about attribute.
- checkAndSetPackageNamespaceAndVersion(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks whether or not the given
SBase has the same package
version configuration than this element or the SBMLDocument.
- checkAndSetPackageNamespaceAndVersion(SBasePlugin, SBMLDocument) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks whether or not the given
SBasePlugin has the same package
configuration than the SBMLDocument.
- checkAndSetVariable(String) - Method in class org.sbml.jsbml.EventAssignment
-
Sets the variableID of this EventAssignment to 'variable'.
- checkAndSetVariable(String) - Method in class org.sbml.jsbml.InitialAssignment
-
- checkAttribute(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks if the attribute conforms to the SBML specifications of the level
and version of this object.
- checkBrackets(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Creates brackets if needed.
- checkBrackets(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Creates brackets if needed.
- checkBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Creates brackets if needed.
- checkBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Creates brackets if needed.
- checkChildren(Model, SBase) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
- checkChildren(Model, MathContainer) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
- checkChildren(Model, Reaction) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
- checkChildren(Model, ASTNode) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
- checkConsistency() - Method in class org.sbml.jsbml.SBMLDocument
-
Validates the
SBMLDocument using the
SBML.org online validator (http://sbml.org/validator/).
- checkConsistency(String, Map<String, String>) - Static method in class org.sbml.jsbml.validator.SBMLValidator
-
Validates an SBML model using the
SBML.org online validator (http://sbml.org/validator/).
- checkConsistency(String) - Static method in class org.sbml.jsbml.validator.SBMLValidator
-
Parses the XML String returned by the libSBML online validator or web services.
- checkConsistencyOffline() - Method in class org.sbml.jsbml.SBMLDocument
-
Validates the
SBMLDocument using the BETA version of the
offline validator (
do not use for production).
- checkConsistencyParameters - Variable in class org.sbml.jsbml.SBMLDocument
-
Contains all the parameter to validate the SBML document
- checkContainsNumbersReferingToUnits(Node) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
Recursively checks whether the given Node contains any numbers
that refer to unit declarations.
- checkDenominatorBrackets(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Creates brackets if needed.
- checkDenominatorBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Creates brackets if needed.
- checkDerivedUnit - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- checkForDimensionlessOrInvalidUnits(UnitDefinition) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
Throws an IllegalArgumentException if the given units do not
represent a dimensionless or invalid unit.
- checkForDimensionlessOrInvalidUnits(UnitDefinition) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
Throws an IllegalArgumentException if the given units do not
represent a dimensionless or invalid unit.
- checkIdentifier(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks if the sID is a valid identifier.
- checkLevelAndVersionCompatibility(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks whether or not the given
SBase has the same level and
version configuration than this element.
- checkMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- checkPackages(SBMLDocument) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the whole
SBMLDocument, including all siblings, to make sure
that the package version and namespace is set properly.
- checkPackages(SBMLDocument, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the whole
SBMLDocument, including all siblings, to make sure
that the package version and namespace is set properly.
- checkPackages(SBase, List<String>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the given
SBase, including all it's siblings, to make sure
that the package version and namespace is set properly.
- checkPackages(SBase, Map<String, PackageInfo>, Map<String, PackageInfo>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the given
SBase, including all it's siblings, to make sure
that the package version and namespace is set properly.
- checkRelationalArgumentBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Creates brackets if needed.
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- checkTerm(int) - Static method in class org.sbml.jsbml.SBO
-
Checks the format of the given SBO integer portion.
- checkTerm(String) - Static method in class org.sbml.jsbml.SBO
-
Checks the format of the given SBO string.
- chemicalFormulaPattern - Static variable in class org.sbml.jsbml.validator.SyntaxChecker
-
- CHILD_ELEMENT_NAMES - Static variable in class org.sbml.jsbml.JSBML
-
Key used to store the list of the xml child element names of an SBase.
- childElements - Variable in class org.sbml.jsbml.xml.XMLNode
-
- childNode - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- children() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- children() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- children - Variable in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-
- classBlacklist - Static variable in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
Stores class names which didn't have a constraint declaration
- className - Variable in class org.sbml.jsbml.ASTNode
-
- className - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- cleanTreeNode(AbstractTreeNode) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Cleans the given node by removing user object(s) set during reading/parsing.
- clear() - Method in class org.sbml.jsbml.ListOf
-
- clear() - Method in class org.sbml.jsbml.UnitDefinition
-
Removes all
Unit elements from the list of Units in this object.
- clear() - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- clear() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Clears the loaded constraints
- clear() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
Sets all the variable of this object to null.
- clear() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
- clear() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Clears (deletes) all XML namespace declarations in this
XMLNamespaces
object.
- clearAttributes() - Method in class org.sbml.jsbml.xml.XMLToken
-
Clears (deletes) all attributes in this
XMLToken.
- clearErrorLog() - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
Clears the error log.
- clearListOfEventAssignments() - Method in class org.sbml.jsbml.Event
-
Remove all the EventAssignments of the listOfEventAssignments of this
Event.
- clearLog() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Clears the log.
- clearNamespaces() - Method in class org.sbml.jsbml.xml.XMLToken
-
- clearUserObjects() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- clearUserObjects() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- clearUserObjects() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Removes all of the mappings from the map of user objects (optional
operation).
- clone() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- clone() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- clone() - Method in class org.sbml.jsbml.AbstractSBase
-
- clone() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- clone() - Method in class org.sbml.jsbml.AlgebraicRule
-
- clone() - Method in class org.sbml.jsbml.Annotation
-
- clone() - Method in class org.sbml.jsbml.AssignmentRule
-
- clone() - Method in class org.sbml.jsbml.ASTNode
-
- clone() - Method in class org.sbml.jsbml.Compartment
-
- clone() - Method in class org.sbml.jsbml.CompartmentType
-
Deprecated.
- clone() - Method in class org.sbml.jsbml.Constraint
-
- clone() - Method in class org.sbml.jsbml.Creator
-
- clone() - Method in class org.sbml.jsbml.CVTerm
-
- clone() - Method in class org.sbml.jsbml.Delay
-
- clone() - Method in class org.sbml.jsbml.Event
-
- clone() - Method in class org.sbml.jsbml.EventAssignment
-
- clone() - Method in class org.sbml.jsbml.ExplicitRule
-
- clone() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- clone() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- clone() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
- clone() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- clone() - Method in class org.sbml.jsbml.FunctionDefinition
-
- clone() - Method in class org.sbml.jsbml.History
-
- clone() - Method in class org.sbml.jsbml.InitialAssignment
-
- clone() - Method in class org.sbml.jsbml.KineticLaw
-
- clone() - Method in class org.sbml.jsbml.ListOf
-
- clone() - Method in class org.sbml.jsbml.LocalParameter
-
- clone() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- clone() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- clone() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTDivideNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTFunction
-
- clone() - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTMinusNode
-
- clone() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Clone ASTNode2
- clone() - Method in class org.sbml.jsbml.math.ASTNumber
-
- clone() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTPlusNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTQualifierNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTTimesNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- clone() - Method in class org.sbml.jsbml.Model
-
- clone() - Method in class org.sbml.jsbml.ModifierSpeciesReference
-
- clone() - Method in class org.sbml.jsbml.ontology.Term
-
- clone() - Method in class org.sbml.jsbml.ontology.Triple
-
- clone() - Method in class org.sbml.jsbml.Parameter
-
- clone() - Method in class org.sbml.jsbml.Priority
-
- clone() - Method in class org.sbml.jsbml.QuantityWithUnit
-
- clone() - Method in class org.sbml.jsbml.RateRule
-
- clone() - Method in class org.sbml.jsbml.Reaction
-
- clone() - Method in class org.sbml.jsbml.Rule
-
- clone() - Method in interface org.sbml.jsbml.SBase
-
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one.
- clone() - Method in class org.sbml.jsbml.SBMLDocument
-
- clone() - Method in class org.sbml.jsbml.SBMLReader
-
- clone() - Method in class org.sbml.jsbml.SBMLWriter
-
- clone() - Method in class org.sbml.jsbml.Species
-
- clone() - Method in class org.sbml.jsbml.SpeciesReference
-
- clone() - Method in class org.sbml.jsbml.SpeciesType
-
Deprecated.
- clone() - Method in class org.sbml.jsbml.StoichiometryMath
-
Deprecated.
- clone() - Method in class org.sbml.jsbml.Symbol
-
- clone() - Method in class org.sbml.jsbml.Trigger
-
- clone() - Method in class org.sbml.jsbml.Unit
-
- clone() - Method in class org.sbml.jsbml.UnitDefinition
-
- clone() - Method in class org.sbml.jsbml.util.ListOfWithName
-
Deprecated.
- clone() - Method in class org.sbml.jsbml.util.Pair
-
- clone() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- clone() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- clone() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
-
- clone() - Method in class org.sbml.jsbml.util.ValuePair
-
- clone() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
-
Clones this Graph without terminal node
- clone() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
-
- clone() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
- clone() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
- clone() - Method in class org.sbml.jsbml.xml.XMLNode
-
- clone() - Method in class org.sbml.jsbml.xml.XMLToken
-
- clone() - Method in class org.sbml.jsbml.xml.XMLTriple
-
Creates and returns a deep copy of this
XMLTriple set.
- cloneAsAssignmentRule() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
-
- cloneAsRateRule() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
-
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- CobraFormulaParser - Class in org.sbml.jsbml.text.parser
-
Class used to parse infix mathematical formula written by the COBRA toolbox
and returns a representation of it as an Abstract Syntax Tree (AST).
- CobraFormulaParser(InputStream) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor with InputStream.
- CobraFormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor with InputStream and supplied encoding
- CobraFormulaParser(Reader) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor.
- CobraFormulaParser(CobraFormulaParserTokenManager) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor with generated Token Manager.
- CobraFormulaParser.JJCalls - Class in org.sbml.jsbml.text.parser
-
- CobraFormulaParser.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
-
- CobraFormulaParserConstants - Interface in org.sbml.jsbml.text.parser
-
Token literal values and constants.
- CobraFormulaParserTokenManager - Class in org.sbml.jsbml.text.parser
-
Token Manager.
- CobraFormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Constructor.
- CobraFormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Constructor.
- CobraUtil - Class in org.sbml.jsbml.util
-
Contains some useful methods to manipulate 'COBRA SBML'
- CobraUtil() - Constructor for class org.sbml.jsbml.util.CobraUtil
-
- code - Variable in exception org.sbml.jsbml.SBMLError
-
- code - Variable in exception org.sbml.jsbml.SBMLException
-
- Code() - Constructor for enum org.sbml.jsbml.SBMLException.Code
-
- collectMetaIds(Map<String, SBase>, SBase, boolean, boolean) - Method in class org.sbml.jsbml.SBMLDocument
-
Collects all meta identifiers of this
AbstractSBase and all of
its sub-elements if recursively is
true.
- colorbox(String, Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- colorbox(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- column - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- column - Variable in exception org.sbml.jsbml.SBMLError
-
- column - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- column - Variable in class org.sbml.jsbml.xml.XMLToken
-
- command(String, Object) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- command(String, Object, Object) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- command(String, Object) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- command(String, Object, Object) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- COMP_10100 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010100:
- COMP_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010101:
To conform to Version 1 of the Hierarchical Model Composition package
specification for SBML Level 3, an SBML document must declare the use of the
following XML Namespace:
'http://www.sbml.org/sbml/level3/version1/comp/version1' Reference: L3V1 Comp V1
Section 3.1
- COMP_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010102:
Wherever they appear in an SBML document, elements and attributes from the
Hierarchical Model Composition package must be declared either implicitly or
explicitly to be in the XML namespace
'http://www.sbml.org/sbml/level3/version1/comp/version1' Reference: L3V1 Comp V1
Section 3.1
- COMP_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010301:
(Extends validation rule #10301 in the SBML Level 3 Version 1 Core
specification.) Within a <model> or <modelDefinition> object, the values of the
attributes id and comp:id on every instance of the following classes of objects
must be unique across the set of all id and comp:id attribute values of all such
objects in a model: the model itself, plus all contained <functionDefinition>,
<compartment>, <species>, <reaction>, <speciesReference>,
<modifierSpeciesReference>, <event>, and <parameter> objects, plus the
<submodel> and <deletion> objects defined by the Hierarchical Model Composition
package, plus any objects defined by any other package with 'package:id'
attributes defined as falling in the 'SId' namespace.
- COMP_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010302:
The values of the attributes 'id' and 'comp:id' on every instance of all
<model>, <modelDefinition>, and <externalModelDefinition> objects must be unique
across the set of all 'id' and 'comp:id' attribute values of such objects in the
SBML document to which they belong.
- COMP_10303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010303:
Within <model> and <modelDefinition> objects inside an SBML document, the value
of the attribute 'comp:id' on every instance of a <port> object must be unique
across the set of all 'comp:id' attribute values of all such objects in the
model.
- COMP_10304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010304:
The value of a comp:id attribute must always conform to the syntax of the SBML
data type SId.
- COMP_10308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010308:
The value of a 'comp:submodelRef' attribute on <replacedElement> and
<replacedBy> objects must always conform to the syntax of the SBML data type
SId.
- COMP_10309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010309:
The value of a 'comp:deletion' attribute on <replacedElement> objects must
always conform to the syntax of the SBML data type SId.
- COMP_10310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010310:
The value of a 'comp:conversionFactor' attribute on <replacedElement> objects
must always conform to the syntax of the SBML data type SId.
- COMP_10311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010311:
The value of a 'comp:name' attribute must always conform to the syntax of type
string.
- COMP_10501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010501:
If one element replaces another, whether it is the target of a <replacedBy>
element, or whether it has a child <replacedElement>, the units of the replaced
element, multiplied by the units of any applicable conversion factor, should
equal the units of the replacement element.
- COMP_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020101:
Any object derived from the extended SBase class (defined in the Hierarchical
Model Composition package) may contain at most one instance of a
<listOfReplacedElements> subobject.
- COMP_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020102:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfReplacedElements> container object may only contain
<replacedElement> objects.
- COMP_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020103:
A <listOfReplacedElements> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- COMP_20104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020104:
The <listOfReplacedElements> in an SBase object is optional, but if present,
must not be empty.
- COMP_20105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020105:
Any object derived from the extended SBase class (defined in the Hierarchical
Model Composition package) may contain at most one instance of a <replacedBy>
subobject.
- COMP_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020201:
In all SBML documents using the HierarchicalModel Composition package, the SBML
object must include a value for the attribute 'comp:required' attribute.
- COMP_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020202:
The value of attribute 'comp:required' on the SBML object must be of the data
type Boolean.
- COMP_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020203:
The value of attribute 'comp:required' on the SBML object must be set to 'true'
if the Model object within the SBML object contains any Submodel with Species,
Parameter, Compartment, Reaction, or Event objects that have not been either
directly or indirectly replaced.
- COMP_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020204:
The value of attribute 'comp:required' on the SBML object must be set to 'false'
if the Model object within the SBML object contains no Submodel objects, or if
all Submodel objects that are present contain no Species, Parameter,
Compartment, Reaction, or Event objects that have not been either directly or
indirectly replaced.
- COMP_20205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020205:
There may be at most one instance of the <listOfModelDefinitions> within an SBML
object that uses the SBML Level 3 Hierarchical Model Composition package.
- COMP_20206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020206:
The various 'ListOf' subobjects within an SBML object are optional, but if
present, these container objects must not be empty.
- COMP_20207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020207:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfModelDefinitions> container may only contain <modelDefinition>
objects.
- COMP_20208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020208:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfExternalModelDefinitions> container may only contain
<externalModelDefinition> objects.
- COMP_20209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020209:
A <listOfModelDefinitions> object may have the optional attributes 'metaid' and
'sboTerm'.
- COMP_20210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020210:
A <listOfExternalModelDefinitions> object may have the optional attributes
'metaid' and 'sboTerm'.
- COMP_20211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020211:
There may be at most one instance of the <listOfExternalModelDefinitions> within
an SBML object that uses the SBML Level 3 Hierarchical Model Composition
package.
- COMP_20212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020212:
The value of attribute 'comp:required' on the SBML object must be set to 'true'.
- COMP_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020301:
An <externalModelDefinition> object may have the optional SBML Level 3 Core
attributes 'metaid' and 'sboTerm'.
- COMP_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020302:
An <externalModelDefinition> object may have the optional SBML Level 3 Core
subobjects for notes and annotation.
- COMP_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020303:
An <externalModelDefinition> object must have the attributes 'comp:id' and
'comp:source', and may have the optional attributes 'comp:name',
'comp:modelRef', and 'comp:md5'.
- COMP_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020304:
The value of the 'comp:source' attribute on an <externalModelDefinition> object
must reference an SBML Level 3 Version 1 document.
- COMP_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020305:
The value of the 'comp:modelRef' attribute on an <externalModelDefinition>
object must be the value of an id attribute on a <model>, <modelDefinition>, or
<externalModelDefinition> object in the SBML document referenced by the
'comp:source' attribute.
- COMP_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020306:
The value of the 'comp:md5' attribute, if present on an
<externalModelDefinition> object, should match the calculated MD5 checksum of
the SBML document referenced by the 'comp:source' attribute.
- COMP_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020307:
The value of a 'comp:source' attribute on an <externalModelDefinition> object
must always conform to the syntax of the XML Schema 1.0 data type 'anyURI'.
- COMP_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020308:
The value of a comp:modelRef attribute on an <externalModelDefinition> object
must always conform to the syntax of the SBML data type SId.
- COMP_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020309:
The value of a comp:md5 attribute on an <externalModelDefinition> object must
always conform to the syntax of type string.
- COMP_20310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020310:
An <externalModelDefinition> object must not reference an
<externalModelDefinition> in a different SBML document that, in turn, refers
back to the original <externalModelDefinition object, whether directly or
indirectly through a chain of <externalModelDefinition> objects.
- COMP_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020501:
There may be at most one instance of each of the following kinds of objects
within a <model> or <modelDefinition> object using Hierarchical Model
Composition: <listOfSubmodels> and <listOfPorts>.
- COMP_20502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020502:
The various ListOf subobjects with a <model> object are optional, but if
present, these container object must not be empty.
- COMP_20503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020503:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfSubmodels> container object may only contain <submodel>
objects.
- COMP_20504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020504:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfPorts> container object may only contain <port> objects.
- COMP_20505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020505:
A <listOfSubmodels> object may have the optional attributes 'metaid' and
'sboTerm'.
- COMP_20506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020506:
A <listOfPorts> object may have the optional attributes 'metaid' and 'sboTerm'.
- COMP_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020601:
A <submodel> object may have the optional SBML Level 3 Core attributes 'metaid'
and 'sboTerm'.
- COMP_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020602:
A <submodel> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- COMP_20603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020603:
There may be at most one <listOfDeletions> container object within a <submodel>
object.
- COMP_20604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020604:
A <listOfDeletions> container object within a <submodel> object is optional, but
if present, must not be empty.
- COMP_20605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020605:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfDeletions> container object may only contain <deletion>
objects.
- COMP_20606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020606:
A <listOfDeletions> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- COMP_20607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020607:
A <submodel> object must have the attributes 'comp:id' and 'comp:modelRef'
because they are required, and may also have the optional attributes
'comp:name', 'comp:timeConversionFactor, and/or 'comp:extentConversionFactor'.
- COMP_20608 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020608:
The value of a 'comp:modelRef' attribute on a <submodel> object must always
conform to the syntax of the SBML data type SId.
- COMP_20613 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020613:
The value of a 'comp:timeConversionFactor' attribute on a <submodel> object must
always conform to the syntax of the SBML data type SId.
- COMP_20614 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020614:
The value of a 'comp:extentConversionFactor' attribute on a <submodel> object
must always conform to the syntax of the SBML data type SId.
- COMP_20615 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020615:
The value of a 'comp:modelRef' attribute on a <submodel> must be the identifier
of a <model>, <modelDefinition>, or <externalModelDefinition> object in the same
SBML object as the <submodel>.
- COMP_20616 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020616:
A <model> or <modelDefinition> object must not contain a <submodel> which
references that model object itself.
- COMP_20617 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020617:
A <model> object must not contain a <submodel> which references that <model>
indirectly.
- COMP_20622 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020622:
The value of a 'comp:timeConversionFactor' attribute on a given <submodel>
object must be the identifier of a <parameter> object defined in the same Model
containing the <submodel>.
- COMP_20623 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020623:
The value of a 'comp:extentConversionFactor' attribute on a given <submodel>
object must be the identifier of a <parameter> object defined in the same Model
containing the <submodel>.
- COMP_20701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020701:
The value of a 'comp:portRef' attribute on an <sBaseRef> object must be the
identifier of a <port> object in the <model> referenced by that <sBaseRef>.
- COMP_20702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020702:
The value of a 'comp:idRef' attribute on an <sBaseRef> object must be the
identifier of an object contained in (that is, within the SId namespace of) the
<model> referenced by that <sBaseRef>.
- COMP_20703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020703:
The value of a 'comp:unitRef' attribute on an <sBaseRef> object must be the
identifier of a <unitDefinition< object contained in the <model> referenced by
that <sBaseRef>.
- COMP_20704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020704:
The value of a 'comp:metaIdRef' attribute on an <sBaseRef> object must be the
value of a 'comp:metaid' attribute on an element contained in the <model>
referenced by that <sBaseRef>.
- COMP_20705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020705:
If an <sBaseRef> object contains an <sBaseRef> child, the parent <sBaseRef> must
point to a <submodel> object, or a <port> that itself points to a <submodel>
object.
- COMP_20706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020706:
The value of a 'comp:portRef' attribute on an SBaseRef object must always
conform to the syntax of the SBML data type SId.
- COMP_20707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020707:
The value of a 'comp:idRef' attribute on an SBaseRef object must always conform
to the syntax of the SBML data type SId.
- COMP_20708 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020708:
The value of a 'comp:unitRef' attribute on an SBaseRef object must always
conform to the syntax of the SBML data type SId.
- COMP_20709 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020709:
The value of a 'comp:metaIdRef' attribute on an SBaseRef object must always
conform to the syntax of the XML data type ID.
- COMP_20710 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020710:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, an SBaseRef object may only contain a single <sBaseRef> child.
- COMP_20711 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020711:
The 'sbaseRef' spelling of an SBaseRef child of an SBaseRef object is considered
deprecated, and 'sBaseRef' should be used instead.
- COMP_20712 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020712:
An <sBaseRef> object must point to another object; that is, a <sBaseRef> object
must always have a value for one of the attributes 'comp:portRef', 'comp:idRef',
'comp:unitRef', or 'comp:metaIdRef'.
- COMP_20713 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020713:
An <sBaseRef> object can only point to one other object; that is, a given
<sBaseRef> object can only have a value for one of the attributes
'comp:portRef', 'comp:idRef', 'comp:unitRef', or 'comp:metaIdRef'.
- COMP_20714 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020714:
Any one SBML object may only be referenced in one of the following ways:
referenced by a single <port> object; referenced by a single <deletion> object;
referenced by a single <replacedElement>; be the parent of a single <replacedBy>
child; be referenced by one or more <replacedBy> objects; or be referenced by
one or more <replacedElement> objects all using the 'deletion' attribute.
- COMP_20801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020801:
A <port> object must point to another object; that is, a <port> object must
always have a value for one of the attributes 'comp:idRef', 'comp:unitRef', or
'comp:metaIdRef'.
- COMP_20802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020802:
A <port> object can only point to one other object; that is, a given <port>
object can only have a value for one of the attributes 'comp:idRef',
'comp:unitRef', or 'comp:metaIdRef'.
- COMP_20803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020803:
A <port> object must have a value for the required attribute 'comp:id', and one,
and only one, of the attributes 'comp:idRef', 'comp:unitRef', or
'comp:metaIdRef'.
- COMP_20804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020804:
Port definitions must be unique; that is, no two <port> objects in a given Model
may reference the same object in that Model.
- COMP_20901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020901:
A <deletion> object must point to another object; that is, a <deletion> object
must always have a value for one of the attributes 'comp:portRef', 'comp:idRef',
'comp:unitRef', or 'comp:metaIdRef' Reference: L3V1 Comp V1 Section 3.5.3
- COMP_20902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020902:
A <deletion> object can only point to one other object; that is, a given
<deletion> object can only have a value for one of the attributes
'comp:portRef', 'comp:idRef', 'comp:unitRef', or 'comp:metaIdRef' Reference:
L3V1 Comp V1 Section 3.5.3
- COMP_20903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020903:
A <deletion> object must have a value for one, and only one, of the attributes
'comp:portRef', 'comp:idRef', 'comp:unitRef', and 'comp:metaIdRef'.
- COMP_21001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021001:
A <replacedElement> object must point to another object; that is, a
<replacedElement> object must always have a value for one of the attributes
'comp:portRef', 'comp:idRef', 'comp:unitRef', 'comp:metaIdRef' or
'comp:deletion'.
- COMP_21002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021002:
A <replacedElement> object can only point to one other object; that is, a given
<replacedElement> object can only have a value for one of the attributes
'comp:portRef', 'comp:idRef', 'comp:unitRef', 'comp:metaIdRef' or
'comp:deletion'.
- COMP_21003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021003:
A <replacedElement> object must have a value for the required attribute
'comp:submodelRef', and a value for one, and only one, of the following
attributes: 'comp:portRef', 'comp:idRef', 'comp:unitRef', 'comp:metaIdRef', or
'comp:deletion'.
- COMP_21004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021004:
The value of a 'comp:submodelRef' attribute on a <replacedElement> object must
be the identifier of a <submodel> present in the <replacedElement> object's
parent Model.
- COMP_21005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021005:
The value of a 'comp:deletion' attribute on a <replacedElement> object must be
the identifier of a <deletion> present in the <replacedElement> object's parent
Model.
- COMP_21006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021006:
The value of a 'comp:conversionFactor' attribute on a <replacedElement> object
must be the identifier of a <parameter> present in the <replacedElement>
object's parent Model Reference: L3V1 Comp V1 Section 3.6.2
- COMP_21010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021010:
No two <replacedElement> objects in the same Model may reference the same object
unless that object is a <deletion> Reference: L3V1 Comp V1 Section 3.6.2
- COMP_21011 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021011:
If a <replacedElement> uses the 'comp:deletion' attribute, then it should not
also use the 'comp:conversionFactor' attribute.
- COMP_21101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021101:
A <replacedBy> object must point to another object; that is, a <replacedBy>
object must always have a value for one of the attributes 'comp:portRef',
'comp:idRef', 'comp:unitRef' or 'comp:metaIdRef'.
- COMP_21102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021102:
A <replacedBy> object can only point to one other object; that is, a given
<replacedBy> object can only have a value for one of the attributes
'comp:portRef', 'comp:idRef', 'comp:unitRef', or 'comp:metaIdRef'.
- COMP_21103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021103:
A <replacedBy> object must have a value for the required attribute
'comp:submodelRef', and a value for one, and only one, of the following
attributes: 'comp:portRef', 'comp:idRef', 'comp:unitRef' or 'comp:metaIdRef'.
- COMP_21104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021104:
The value of a 'comp:submodelRef' attribute on a <replacedBy> object must be the
identifier of a <submodel> present in the <replacedBy> object's parent Model.
- COMP_21201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021201:
If one element replaces another, whether it is the target of a <replacedBy>
element, or whether it has a child <replacedElement>, the SBML class of the
replacement element must match the SBML class of the replaced element, with two
exceptions: an element of a derived class may replace an object of its base
class (for base classes other than SBase), and any SBML class with mathematical
meaning may replace a <parameter>.
- COMP_21202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021202:
If one element replaces another, whether it is the target of a <replacedBy>
element, or whether it has a child <replacedElement>, if the replaced element
has the 'id' attribute set, the replacement !element must also have the 'id'
attribute set.
- COMP_21203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021203:
If one element replaces another, whether it is the target of a <replacedBy>
element, or whether it has a child <replacedElement>, if the replaced element
has the 'metaid' attribute set, the replacement element must also have the
'metaid' attribute set.
- COMP_21204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021204:
If one element replaces another, whether it is the target of a <replacedBy>
element, or whether it has a child <replacedElement>, if the replaced element
has an identifier attribute from some other SBML package set, the replacement
element must also have that same identifier attribute set.
- COMP_90101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090101:
The external model referenced in this model could not be resolved.
- COMP_90102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090102:
The external document referenced in this model did not contain any models.
- COMP_90103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090103:
An external model definition referenced by an external model definition in this
model was itself unresolvable.
- COMP_90104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090104:
Errors arose during the attempt to flatten the model.
- COMP_90105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090105:
The interpretation the Hierarchical Model Composition constructs to produce a
kind of 'flattened' version of the model devoid of the comp package constructs
must produce a valid SBML Level 3 model.
- COMP_90106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090106:
Due to the need to instantiate models, modelDefinitions, submodels etc.
- COMP_90107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090107:
The CompFlatteningConverter has encountered a required package for which libSBML
does not recognize the information.
- COMP_90108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090108:
The CompFlatteningConverter has encountered an unrequired package for which
libSBML does not recognize the information.
- COMP_90109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090109:
The CompFlatteningConverter has encountered an unrequired package for which the
necessary routines to allow flattening have not yet been implemented.
- COMP_90110 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090110:
The CompFlatteningConverter has encountered a required package for which the
necessary routines to allow flattening have not yet been implemented.
- COMP_90111 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090111:
The CompFlatteningConverter has encountered an unknown reference which may be
due to the presence of an unknown package.
- COMP_90112 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090112:
The software used to process this hierarchical model used the deprecated
function performDeletions to do so.
- COMP_90113 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090113:
The software used to process this hierarchical model used the deprecated
function performReplacementsAndConversions to do so.
- COMP_90114 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090114:
The model contained a deletion whose subelement was replaced.
- COMP_90115 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090115:
The value of a 'comp:idRef' attribute on an <sBaseRef> object must be the
identifier of an object contained in (that is, within the SId namespace of) the
<model> referenced by that <sBaseRef>.
- COMP_90116 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1090116:
The value of a 'comp:metaIdRef' attribute on an <sBaseRef> object must be the
value of a 'comp:metaid' attribute on an element contained in the <model>
referenced by that <sBaseRef>.
- compareString(String, String) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- compareTo(Term) - Method in class org.sbml.jsbml.ontology.Term
-
- compareTo(Triple) - Method in class org.sbml.jsbml.ontology.Triple
-
- compareTo(L, V) - Method in class org.sbml.jsbml.util.ValuePair
-
Convenient method to compare two values to this
ValuePair.
- compareTo(ValuePair<L, V>) - Method in class org.sbml.jsbml.util.ValuePair
-
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- Compartment - Class in org.sbml.jsbml
-
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
- Compartment() - Constructor for class org.sbml.jsbml.Compartment
-
Creates a Compartment instance.
- Compartment(Compartment) - Constructor for class org.sbml.jsbml.Compartment
-
Creates a Compartment instance from a given compartment.
- Compartment(int, int) - Constructor for class org.sbml.jsbml.Compartment
-
Creates a Compartment instance from a level and version.
- Compartment(String) - Constructor for class org.sbml.jsbml.Compartment
-
Creates a Compartment instance with the given id.
- Compartment(String, int, int) - Constructor for class org.sbml.jsbml.Compartment
-
Creates a Compartment instance from an id, level and version.
- Compartment(String, String, int, int) - Constructor for class org.sbml.jsbml.Compartment
-
Creates a Compartment instance from an id, name, level and version.
- compartment - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- CompartmentalizedSBase - Interface in org.sbml.jsbml
-
- CompartmentConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
ConstraintDeclaration for Compartment class
- CompartmentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints
-
- compartmentID - Variable in class org.sbml.jsbml.Reaction
-
Represents the 'compartment' XML attribute of a reaction element.
- compartmentID - Variable in class org.sbml.jsbml.Species
-
Represents the 'compartment' attribute of a Species element.
- CompartmentType - Class in org.sbml.jsbml
-
- CompartmentType() - Constructor for class org.sbml.jsbml.CompartmentType
-
Deprecated.
- CompartmentType(CompartmentType) - Constructor for class org.sbml.jsbml.CompartmentType
-
Deprecated.
- CompartmentType(int, int) - Constructor for class org.sbml.jsbml.CompartmentType
-
Deprecated.
- CompartmentType(String) - Constructor for class org.sbml.jsbml.CompartmentType
-
Deprecated.
- CompartmentType(String, int, int) - Constructor for class org.sbml.jsbml.CompartmentType
-
Deprecated.
- CompartmentType(String, String, int, int) - Constructor for class org.sbml.jsbml.CompartmentType
-
Deprecated.
- compartmentType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- CompartmentTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- CompartmentTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints
-
- compartmentTypeID - Variable in class org.sbml.jsbml.Compartment
-
Deprecated.
- compile(ASTNodeCompiler) - Method in class org.sbml.jsbml.ASTNode
-
Compiles this
ASTNode and returns the result.
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTDivideNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTFunction
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTMinusNode
-
- compile(ASTNode2Compiler) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Compiles this
ASTNode2 and returns the result.
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPlusNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTQualifierNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTRootNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTTimesNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- compile(Compartment) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(double, int, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Creates an
ASTNode2Value that represents a real number in
scientific notation, i.e., mantissa * 10^exponent, and the given units.
- compile(double, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(int, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(CallableSBase) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
A compiler will also have to deal with a name.
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
This method returns the correct LaTeX expression for a function which
returns the size of a compartment.
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
Compiles this
ASTNode2 and produce an XMLStreamWriter representing this node in mathML.
- compile(boolean) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
Compile boolean values
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(Compartment) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- compile(double, int, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Creates an
ASTNodeValue that represents a real number in
scientific notation, i.e., mantissa * 10^exponent, and the given units.
- compile(double, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- compile(int, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- compile(CallableSBase) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- compile(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
A compiler will also have to deal with a name.
- compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- compile(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- compile(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
This method returns the correct LaTeX expression for a function which
returns the size of a compartment.
- compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- compile(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(double, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
Compiles this
ASTNode and produce an XMLStreamWriter representing this node in mathML.
- compile(boolean) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
Compile boolean values
- compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- compile(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- compileBvar(ASTQualifierNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileBvar(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileCi(ASTCSymbolBaseNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileCi(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileConstantElement(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileConstantElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileCSymbol(ASTCSymbolNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileCSymbol(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileElement(ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileElement(String, ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileElement(String, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileExponentiale(ASTConstantNumber) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileExponentiale(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileFunctionElement(ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileFunctionElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileInteger(ASTCnIntegerNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileInteger(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileLambda(ASTLambdaFunctionNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileLambda(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileLog(ASTLogarithmNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileLog(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileLogicalOperator(ASTLogicalOperatorNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileLogicalOperator(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileNegativeInfinity(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileNegativeInfinity(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileNotANumber(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileNotANumber(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compilePi(ASTConstantNumber) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compilePi(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compilePiecewise(ASTPiecewiseFunctionNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compilePiecewise(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compilePositiveInfinity(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compilePositiveInfinity(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compiler - Variable in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- compiler - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- compileRational(ASTCnRationalNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileRational(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileReal(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileReal(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileReal_e(ASTCnExponentialNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileReal_e(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileRelationalOperator(ASTRelationalOperatorNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileRelationalOperator(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileRootElement(ASTRootNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileRootElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileSemanticAnnotations(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileUserFunction(ASTCiFunctionNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileUserFunction(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileVector(ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileVector(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- concat(Object...) - Static method in class org.sbml.jsbml.util.StringTools
-
This method concatenates two or more Object Strings
(obtained by calling Object.toString() if the current
Object is not null) into a new StringBuffer.
- concatStringBuilder(Object...) - Static method in class org.sbml.jsbml.util.StringTools
-
This method concatenates two or more Object Strings
(obtained by calling Object.toString() if the current
Object is not null) into a new StringBuilder.
- connection - Variable in class org.sbml.jsbml.validator.MultipartPost
-
- constant - Variable in class org.sbml.jsbml.SpeciesReference
-
Represents the 'constant' XML attribute of this SpeciesReference.
- constant - Variable in class org.sbml.jsbml.Symbol
-
The constant attribute of this variable.
- constant - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- CONSTANT_E - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- CONSTANT_E - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- CONSTANT_FALSE - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- CONSTANT_FALSE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- CONSTANT_PI - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
The constant pi
- CONSTANT_PI - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
The constant pi
- CONSTANT_TRUE - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- CONSTANT_TRUE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- Constraint - Class in org.sbml.jsbml
-
Represents the constraint XML element of a SBML file.
- Constraint() - Constructor for class org.sbml.jsbml.Constraint
-
- Constraint(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Constraint
-
- Constraint(Constraint) - Constructor for class org.sbml.jsbml.Constraint
-
- Constraint(int, int) - Constructor for class org.sbml.jsbml.Constraint
-
Creates a
Constraint instance from a level and a version.
- CONSTRAINT_ELEMENTS_ORDER - Static variable in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints
-
- ConstraintConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- ConstraintConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints
-
- ConstraintDeclaration - Interface in org.sbml.jsbml.validator.offline.constraints
-
Basic interface for constraint declarations.
- ConstraintFactory - Class in org.sbml.jsbml.validator.offline.factory
-
- ConstraintFactory() - Constructor for class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
- ConstraintGroup<T> - Class in org.sbml.jsbml.validator.offline.constraints
-
- ConstraintGroup() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
- constraints - Variable in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
- constraintType - Variable in class org.sbml.jsbml.validator.offline.ValidationContext
-
- contains(Object) - Method in class org.sbml.jsbml.ListOf
-
- contains(ListOf<? extends SimpleSpeciesReference>, Species) - Static method in class org.sbml.jsbml.util.SubModel
-
- contains(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
Checks if the errorCode is in the group.
- contains(AnyConstraint<T>) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
Checks if the constraint is in the group.
- containsAll(Collection<?>) - Method in class org.sbml.jsbml.ListOf
-
- containsArith(Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Tests whether the String representation of the given object contains any
arithmetic symbols and if the given object is already sorrounded by
brackets.
- containsArith(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Tests whether the String representation of the given object contains any
arithmetic symbols and if the given object is already surrounded by
brackets.
- containsCompartment(String) - Method in class org.sbml.jsbml.Model
-
Returns
true if this model contains a reference to a
Compartment
with the given identifier.
- containsFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
Returns
true if this model contains a reference to a
FunctionDefinition with the given identifier.
- containsMathOnlyPredefinedFunctions(ASTNode) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- containsMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument
-
A check to see whether elements have been registered to this
SBMLDocument with the given meta identifier.
- containsParameter(String) - Method in class org.sbml.jsbml.Model
-
Returns
true if this model contains a reference to a
Parameter with
the given identifier.
- containsQuantity(Quantity) - Method in class org.sbml.jsbml.Model
-
Returns
true if this
Model contains a reference to the
given
Quantity.
- containsReaction(String) - Method in class org.sbml.jsbml.Model
-
Returns
true if this
Model contains a reference to the
given
Reaction.
- containsSpecies(String) - Method in class org.sbml.jsbml.Model
-
Returns
true if this
Model contains a reference to the
given
Species.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true or
false depending on whether this
ASTNode refers to elements such as parameters or numbers with
undeclared units.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.Compartment
-
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Returns
true or
false depending on whether this
ASTCiNumberNode refers to elements such as parameters or
numbers with undeclared units.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Flag to indicate whether or not units have been fully declared for this
value.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.Reaction
-
- containsUndeclaredUnits() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit
-
Returns
true or
false depending on whether this
SBaseWithDerivedUnit refers to elements such as parameters or
numbers with undeclared units.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.Species
-
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.SpeciesReference
-
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
Flag to indicate whether or not units have been fully declared for this
value.
- containsUniqueNamedSBase(String) - Method in class org.sbml.jsbml.Model
-
- containsUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- containsUserObjectKey(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- containsUserObjectKey(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- containsUserObjectKey(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- conversionFactor - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- conversionFactorID - Variable in class org.sbml.jsbml.Model
-
Represents the 'conversionFactor' XML attribute of a model element.
- conversionFactorID - Variable in class org.sbml.jsbml.Species
-
Represents the 'conversionFactor' attribute of a Species element.
- convertAlias2SBO(String) - Static method in class org.sbml.jsbml.SBO
-
Returns an SBO id corresponding to the given alias.
- convertModel(T) - Method in interface org.sbml.jsbml.SBMLInputConverter
-
Takes a model in an arbitrary (but type-secure) format and delivers a
corresponding JSBML-compliant model.
- convertSBMLDocument(File) - Method in interface org.sbml.jsbml.SBMLInputConverter
-
- convertSBMLDocument(String) - Method in interface org.sbml.jsbml.SBMLInputConverter
-
- convertSBO2Alias(int) - Static method in class org.sbml.jsbml.SBO
-
Returns an alias corresponding to the given SBO id.
- convertStringToXMLNode(String) - Static method in class org.sbml.jsbml.xml.XMLNode
-
Returns an
XMLNode which is derived from a
String
containing XML content.
- convertStringToXMLNode(String, XMLNamespaces) - Static method in class org.sbml.jsbml.xml.XMLNode
-
Returns an
XMLNode which is derived from a string containing XML
content.
- convertToArray(Set<Integer>) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- convertToGMT(Date) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
-
Convert timezone of datetime string to GMT.
- convertToGMT(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
-
Convert timezone of datetime string to GMT.
- convertToGMT(Timestamp) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
-
Convert timezone of datetime string to GMT.
- convertToSI(Unit) - Static method in class org.sbml.jsbml.Unit
-
Returns a UnitDefinition object which contains the argument Unit
converted to the appropriate SI unit.
- convertToSIUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
This method converts this unit definition to a
- convertXMLNodeToString(XMLNode) - Static method in class org.sbml.jsbml.xml.XMLNode
-
Returns a string representation of a given
XMLNode.
- copy(InputStream, OutputStream) - Method in class org.sbml.jsbml.validator.MultipartPost
-
- CORE_00000 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 0:
Unrecognized error encountered internally.
- CORE_00001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1:
Out of memory.
- CORE_00002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 2:
File unreadable.
- CORE_00003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 3:
File unwritable.
- CORE_00004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4:
Error encountered while attempting file operation.
- CORE_00005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 5:
Network access error.
- CORE_00101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 101:
Internal XML parser state error.
- CORE_00102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 102:
XML parser returned an unrecognized error code.
- CORE_00103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 103:
Character transcoder error.
- CORE_01001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1001:
Missing XML declaration at beginning of XML input.
- CORE_01002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1002:
Missing encoding attribute in XML declaration.
- CORE_01003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1003:
Invalid or unrecognized XML declaration or XML encoding.
- CORE_01004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1004:
Invalid, malformed or unrecognized XML DOCTYPE declaration.
- CORE_01005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1005:
Invalid character in XML content.
- CORE_01006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1006:
XML content is not well-formed.
- CORE_01007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1007:
Unclosed XML token.
- CORE_01008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1008:
XML construct is invalid or not permitted.
- CORE_01009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1009:
Element tag mismatch or missing tag.
- CORE_01010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1010:
Duplicate XML attribute.
- CORE_01011 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1011:
Undefined XML entity.
- CORE_01012 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1012:
Invalid, malformed or unrecognized XML processing instruction.
- CORE_01013 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1013:
Invalid or undefined XML namespace prefix.
- CORE_01014 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1014:
Invalid XML namespace prefix value.
- CORE_01015 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1015:
Missing a required XML attribute.
- CORE_01016 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1016:
Data type mismatch for the value of an attribute.
- CORE_01017 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1017:
Invalid UTF8 content.
- CORE_01018 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1018:
Missing or improperly formed attribute value.
- CORE_01019 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1019:
Invalid or unrecognizable attribute value.
- CORE_01020 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1020:
Invalid, unrecognized or malformed attribute.
- CORE_01021 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1021:
Element either not recognized or not permitted.
- CORE_01022 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1022:
Badly formed XML comment.
- CORE_01023 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1023:
XML declaration not permitted in this location.
- CORE_01024 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1024:
Reached end of input unexpectedly.
- CORE_01025 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1025:
Value is invalid for XML ID, or has already been used.
- CORE_01026 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1026:
XML ID value was never declared.
- CORE_01027 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1027:
Unable to interpret content.
- CORE_01028 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1028:
Bad XML document structure.
- CORE_01029 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1029:
Encountered invalid content after expected content.
- CORE_01030 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1030:
Expected to find a quoted string.
- CORE_01031 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1031:
An empty value is not permitted in this context.
- CORE_01032 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1032:
Invalid or unrecognized number.
- CORE_01033 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1033:
Colon characters are invalid in this context.
- CORE_01034 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1034:
One or more expected elements are missing.
- CORE_01035 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1035:
Main XML content is empty.
- CORE_09999 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 9999:
- CORE_10000 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10000:
Unrecognized error encountered by libSBML
- CORE_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10101:
An SBML XML file must use UTF-8 as the character encoding.
- CORE_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10102:
An SBML XML document must not contain undefined elements or attributes in the
SBML namespace.
- CORE_10103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10103:
An SBML XML document must conform to the XML Schema for the corresponding SBML
Level, Version and Release.
- CORE_10104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10104:
An SBML document must conform to the rules of XML well-formedness defined in the
XML 1.0 specification.
- CORE_10201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10201:
All MathML content in SBML must appear within a <math> element, and the <math>
element must be either explicitly or implicitly in the XML namespace
"http://www.w3.org/1998/Math/MathML".
- CORE_10202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10202:
The only permitted MathML 2.0 elements in SBML Level 2 are the following: <cn>,
<ci>, <csymbol>, <sep>, <apply>, <piecewise>, <piece>, <otherwise>, <eq>, <neq>,
<gt>, <lt>, <geq>, <leq>, <plus>, <minus>, <times>, <divide>, <power>, <root>,
<abs>, <exp>, <ln>, <log>, <floor>, <ceiling>, <factorial>, <and>, <or>, <xor>,
<not>, <degree>, <bvar>, <logbase>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>,
<sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>,
<arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>,
<arccsch>, <arccoth>, <true>, <false>, <notanumber>, <pi>, <infinity>,
<exponentiale>, <semantics>, <annotation>, and <annotation-xml>.
- CORE_10203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10203:
In the SBML subset of MathML 2.0, the MathML attribute 'encoding' is only
permitted on <csymbol>.
- CORE_10204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10204:
In the SBML subset of MathML 2.0, the MathML attribute 'definitionURL' is only
permitted on <csymbol>, <semantics> or <ci> (Level 2 Version 5 and Level 3
only).
- CORE_10205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10205:
In SBML Level 2, the only values permitted for 'definitionURL' on a <csymbol>
element are "http://www.sbml.org/sbml/symbols/time" and
"http://www.sbml.org/sbml/symbols/delay".
- CORE_10206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10206:
In the SBML subset of MathML 2.0, the MathML attribute 'type' is only permitted
on the <cn> construct.
- CORE_10207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10207:
The only permitted values for the 'type' attribute on MathML <cn> elements are
'e-notation', 'real', 'integer', and 'rational'.
- CORE_10208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10208:
MathML <lambda> elements are only permitted as the first element inside the
'math' element of a <functionDefinition> or as the first element of a semantics
element immediately inside inside the math element of a <functionDefinition>;
they may not be used elsewhere in an SBML model.
- CORE_10209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10209:
The arguments of the MathML logical operators <and>, <or>, <xor>, and <not> must
have Boolean values.
- CORE_10210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10210:
The arguments to the following MathML constructs must have a numeric type:
<plus>, <minus>, <times>, <divide>, <power>, <root>, <abs>, <exp>, <ln>, <log>,
<floor>, <ceiling>, <factorial>, <sin>, <cos>, <tan>, <sec>, <csc>, <cot>,
<sinh>, <cosh>, <tanh>, <sech>, <csch>, <coth>, <arcsin>, <arccos>, <arctan>,
<arcsec>, <arccsc>, <arccot>, <arcsinh>, <arccosh>, <arctanh>, <arcsech>,
<arccsch>, <arccoth>.
- CORE_10211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10211:
The values of all arguments to <eq> and <neq> operators must have the same type
(either all Boolean or all numeric).
- CORE_10212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10212:
The types of values within <piecewise> operators must all be consistent: the set
of expressions that make up the first arguments of the <piece> and <otherwise>
operators within the same <piecewise> operator should all return values of the
same type.
- CORE_10213 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10213:
The second argument of a MathML <piece> operator must have a Boolean value.
- CORE_10214 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10214:
Outside of a <functionDefinition>, if a <ci> element is the first element within
a MathML <apply>, then the <ci>'s value can only be chosen from the set of
identifiers of <functionDefinition>s defined in the SBML model.
- CORE_10215 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10215:
Outside of a <functionDefinition>, if a <ci> element is not the first element
within a MathML <apply>, then the <ci>'s value can only be chosen from the set
of identifiers of <species>, <compartment>, <parameter>, <reaction>, or (in
Level 3) <speciesReference> objects defined in the SBML model.
- CORE_10216 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10216:
The 'id' value of a <parameter> defined within a <kineticLaw> can only be used
in <ci> elements within the MathML content of that same <kineticLaw>; the
identifier is not visible to other parts of the model.
- CORE_10217 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10217:
The MathML formulas in the following elements must yield numeric expressions:
<math> in <kineticLaw>, <stoichiometryMath> in <speciesReference>, <math> in
<initialAssignment>, <math> in <assignmentRule>, <math> in <rateRule>, <math> in
<algebraicRule>, and <delay> in <event>, and <math> in <eventAssignment>.
- CORE_10218 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10218:
A MathML operator must be supplied the number of arguments appropriate for that
operator.
- CORE_10219 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10219:
The number of arguments used in a call to a function defined by a
<functionDefinition> must equal the number of arguments accepted by that
function, or in other words, the number of <bvar> elements inside the <lambda>
element of the function definition.
- CORE_10220 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10220:
The SBML attribute 'units' may only be added to MathML <cn> elements; no other
MathML elements are permitted to have the 'units' attribute.
- CORE_10221 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10221:
The value of the SBML attribute 'units' on a MathML <cn> element must be chosen
from either the set of identifiers of UnitDefinition objects in the model, or
the set of base units defined by SBML.
- CORE_10222 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10222:
The value of a <ci> element may not be the identifier of a <compartment> with a
'spatialDimensions' value of 0.
- CORE_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10301:
The value of the 'id' field on every instance of the following type of object in
a model must be unique: <model>, <functionDefinition>, <compartmentType>,
<compartment>, <speciesType>, <species>, <reaction>, <speciesReference>,
<modifierSpeciesReference>, <event>, and model-wide <parameter>s.
- CORE_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10302:
The value of the 'id' field of every <unitDefinition> must be unique across the
set of all <unitDefinition>s in the entire model.
- CORE_10303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10303:
The value of the 'id' field of each parameter defined locally within a
<kineticLaw> must be unique across the set of all such parameter definitions in
that <kineticLaw>.
- CORE_10304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10304:
The value of the 'variable' field in all <assignmentRule> and <rateRule>
definitions must be unique across the set of all such rule definitions in a
model.
- CORE_10305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10305:
In each <event>, the value of the 'variable' field within every
<eventAssignment> definition must be unique across the set of all
<eventAssignment>s within that <event>.
- CORE_10306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10306:
An identifier used as the value of 'variable' in an <eventAssignment> cannot
also appear as the value of 'variable' in an <assignmentRule>.
- CORE_10307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10307:
Every 'metaid' attribute value must be unique across the set of all 'metaid'
values in a model.
- CORE_10308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10308:
The value of an 'sboTerm' attribute must have the data type 'SBOTerm', which is
a string consisting of the characters 'S', 'B', 'O', ':' followed by exactly
seven digits.
- CORE_10309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10309:
The syntax of 'metaid' attribute values must conform to the syntax of the XML
type 'ID'.
- CORE_10310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10310:
The syntax of 'id' attribute values must conform to the syntax of the SBML type
'SId'.
- CORE_10311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10311:
The syntax of unit identifiers (i.e., the values of the 'id' attribute on
UnitDefinition, the 'units' attribute on Compartment, the 'units' attribute on
Parameter, and the 'substanceUnits' attribute on Species) must conform to the
syntax of the SBML type UnitSId.
- CORE_10312 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10312:
Message Reference: L3V1 Section 3.1.1
- CORE_10313 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10313:
Unit identifier references (i.e the 'units' attribute on <Compartment>, the
'units' attribute on <Parameter>, and the 'substanceUnits' attribute on
<Species>) must be the identifier of a <UnitDefinition> in the <Model>, or the
identifier of a predefined unit in SBML.
- CORE_10401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10401:
Every top-level element within an annotation element must have a namespace
declared.
- CORE_10402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10402:
There cannot be more than one top-level element using a given namespace inside a
given annotation element.
- CORE_10403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10403:
Top-level elements within an annotation element cannot use any SBML namespace,
whether explicitly (by declaring the namespace to be one of the URIs
"http://www.sbml.org/sbml/level1", "http://www.sbml.org/sbml/level2",
"http://www.sbml.org/sbml/level2/version2", or
"http://www.sbml.org/sbml/level2/version3", or
"http://www.sbml.org/sbml/level2/version4", or
"http://www.sbml.org/sbml/level2/version5" or
"http://www.sbml.org/sbml/level3/version1/core"), or implicitly (by failing to
declare any namespace).
- CORE_10404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10404:
A given SBML object may contain at most one <annotation> element.
- CORE_10501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10501:
The units of the expressions used as arguments to a function call must match the units expected for
the arguments of that function.
- CORE_10503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10503:
The unit of measurement associated with the mathematical formula in the MathML
math element of every KineticLaw object in a model should be identical to all
KineticLaw objects in the model.
- CORE_10511 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10511:
When the 'variable' in an <assignmentRule> refers to a <compartment>, the units
of the rule's right-hand side are expected to be consistent with the units of
that compartment's size.
- CORE_10512 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10512:
When the 'variable' in an <assignmentRule> refers to a <species>, the units of
the rule's right-hand side are expected to be consistent with the units of the
species' quantity.
- CORE_10513 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10513:
When the 'variable' in an <assignmentRule> refers to a <parameter>, the units of
the rule's right-hand side are expected to be consistent with the units declared
for that parameter.
- CORE_10514 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10514:
When the value of the attribute variable in an AssignmentRule object refers to a
SpeciesReference object, the unit of measurement associated with the rule's
right-hand side should be consistent with the unit of stoichiometry, that is,
dimensionless.
- CORE_10521 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10521:
When the 'variable' in an <initialAssignment> refers to a <compartment>, the
units of the <initialAssignment>'s <math> expression are expected to be
consistent with the units of that compartment's size.
- CORE_10522 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10522:
When the 'variable' in an <initialAssignment> refers to a <species>, the units
of the <initialAssignment>'s <math> expression are expected to be consistent
with the units of that species' quantity.
- CORE_10523 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10523:
When the 'variable' in an <initialAssignment> refers to a <parameter>, the units
of the <initialAssignment>'s <math> expression are expected to be consistent
with the units declared for that parameter.
- CORE_10524 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10524:
When the value of the attribute variable in an InitialAssignment object refers
to a SpeciesReference object, the unit of measurement associated with the
InitialAssignment's math expression should be consistent with the unit of
stoichiometry, that is, dimensionless.
- CORE_10531 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10531:
When the 'variable' in a <rateRule> definition refers to a <compartment>, the
units of the rule's right-hand side are expected to be of the form _x per time_,
where _x_ is either the 'units' in that <compartment> definition, or (in the
absence of explicit units declared for the compartment size) the default units
for that compartment, and _time_ refers to the units of time for the model.
- CORE_10532 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10532:
When the 'variable' in a <rateRule> definition refers to a <species>, the units
of the rule's right-hand side are expected to be of the form _x per time_, where
_x_ is the units of that species' quantity, and _time_ refers to the units of
time for the model.
- CORE_10533 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10533:
When the 'variable' in a <rateRule> definition refers to a <parameter>, the
units of the rule's right-hand side are expected to be of the form _x per time_,
where _x_ is the 'units' in that <parameter> definition, and _time_ refers to
the units of time for the model.
- CORE_10534 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10534:
When the value of the attribute variable in a RateRule object refers to a
SpeciesReference object, the unit of measurement associated with the RateRule's
math expression should be consistent with {unit derived from
dimensionless}/{unit of time}.
- CORE_10541 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10541:
The units of the 'math' formula in a <kineticLaw> definition are expected to be
the equivalent of _substance per time_.
- CORE_10542 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10542:
For every Species object produced or consumed in a reaction (that is, referenced
by a SpeciesReference object), the unit of measurement of the species' substance
should be consistent with the unit of extent for the model times the unit of the
conversion factor for that species.
- CORE_10551 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10551:
When a value for <delay> is given in a <event> definition, the units of the
delay formula are expected to correspond to either the value of 'timeUnits' in
the <event> or (if no 'timeUnits' are given), the model's default units of time.
- CORE_10561 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10561:
When the 'variable' in an <eventAssignment> refers to a <compartment>, the units
of the <eventAssignment>'s <math> expression are expected to be consistent with
the units of that compartment's size.
- CORE_10562 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10562:
When the 'variable' in an <eventAssignment> refers to a <species>, the units of
the <eventAssignment>'s <math> expression are expected to be consistent with the
units of the species' quantity.
- CORE_10563 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10563:
When the 'variable' in an <eventAssignment> refers to a <parameter>, the units
of the <eventAssignment>'s <math> expression are expected to be consistent with
the units declared for that parameter.
- CORE_10564 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10564:
When the value of the attribute variable of an EventAssignment object is the
identifier of a SpeciesReference object, the unit of measurement associated with
the EventAssignment's math expression should be consistent with the unit of
stoichiometry, i.e., dimensionless.
- CORE_10565 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10565:
In an Event object, the unit of measurement associated with a Priority object's
<math> expression object should be 'dimensionless'.
- CORE_10599 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10599:
- CORE_10601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10601:
The system of equations created from an SBML model must not be overdetermined.
- CORE_10701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10701:
The value of the 'sboTerm' attribute on a <model> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/).
- CORE_10702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10702:
The value of the 'sboTerm' attribute on a <functionDefinition> is expected to be
an SBO identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10703:
The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter
defined in SBO (i.e., terms derived from SBO:0000002, "quantitative systems
description parameter").
- CORE_10704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10704:
The value of the 'sboTerm' attribute on an <initialAssignment> is expected to be
an SBO identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10705:
The value of the 'sboTerm' attribute on a rule is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10706:
The value of the 'sboTerm' attribute on a <constraint> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10707:
The value of the 'sboTerm' attribute on a <reaction> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to an occurring entity
representation defined in SBO (i.e., terms derived from SBO:0000231, "occurring
entity representation").
- CORE_10708 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10708:
The value of the 'sboTerm' attribute on a <speciesReference> or
<modifierSpeciesReference> is expected to be an SBO identifier
(http://www.biomodels.net/SBO/) referring to a participant role.
- CORE_10709 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10709:
The value of the 'sboTerm' attribute on a <kineticLaw> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring rate law defined in SBO
(i.e., terms derived from SBO:0000001, "rate law").
- CORE_10710 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10710:
The value of the 'sboTerm' attribute on an <event> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to an occurring entity
representation defined in SBO (i.e., terms derived from SBO:0000231, "occurring
entity representation").
- CORE_10711 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10711:
The value of the 'sboTerm' attribute on an <eventAssignment> is expected to be
an SBO identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10712 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10712:
The value of the 'sboTerm' attribute on a <compartment> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/).
- CORE_10713 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10713:
The value of the 'sboTerm' attribute on a <species> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/).
- CORE_10714 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10714:
The value of the 'sboTerm' attribute on a <compartmentType> is expected to be an
SBO identifier (http://www.biomodels.net/SBO/).
- CORE_10715 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10715:
The value of the 'sboTerm' attribute on a <speciesType> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/).
- CORE_10716 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10716:
The value of the 'sboTerm' attribute on a <trigger> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10717 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10717:
The value of the 'sboTerm' attribute on a <delay> is expected to be an SBO
identifier (http://www.biomodels.net/SBO/) referring to a mathematical
expression (i.e., terms derived from SBO:0000064, "mathematical expression").
- CORE_10718 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10718:
[Although SBML Level 3 Version 1 does not explicitly define the following as an
error, other Levels and/or Versions of SBML do.] The value of the 'sboTerm'
attribute on a <localParameter> is expected to be an SBO identifier
(http://www.biomodels.net/SBO/) referring to a quantitative parameter (i.e.,
terms derived from SBO:0000002, "quantitive systems description parameter").
- CORE_10801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10801:
The contents of the <notes> element must be explicitly placed in the XHTML XML
namespace.
- CORE_10802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10802:
The contents of the <notes> element must not contain an XML declaration (i.e., a
string of the form "<?xml version="1.0" encoding="UTF-8"?>" or similar).
- CORE_10803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10803:
The contents of the <notes> element must not contain an XML DOCTYPE declaration
(i.e., a string beginning with the characters "<!DOCTYPE".
- CORE_10804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10804:
The XHTML content inside a <notes> element can only take one of the following
general forms: (1) a complete XHTML document beginning with the element <html>
and ending with </html>; (2) the "body" portion of a document beginning with the
element <body> and ending with </body>; or (3) XHTML content that is permitted
within a <body> ...
- CORE_10805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 10805:
A given SBML object may contain at most one <notes> element.
- CORE_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20101:
The <sbml> container element must declare the XML Namespace for SBML, and this
declaration must be consistent with the values of the 'level' and 'version'
attributes on the <sbml> element.
- CORE_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20102:
The <sbml> container element must declare the SBML Level using the attribute
'level', and this declaration must be consistent with the XML Namespace declared
for the <sbml> element.
- CORE_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20103:
The <sbml> container element must declare the SBML Version using the attribute
'version', and this declaration must be consistent with the XML Namespace
declared for the <sbml> element.
- CORE_20104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20104:
The <sbml> container element must declare the XML Namespace for any SBML Level 3
packages used within the SBML document.
- CORE_20105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20105:
The attribute 'level' on the <sbml> container element must have a value of type
'positiveInteger'.
- CORE_20106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20106:
The attribute 'version' on the <sbml> container element must have a value of
type 'positiveInteger'.
- CORE_20108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20108:
The <sbml> object may only have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20109:
It is not possible to use SBML L3 packages with earlier levels of SBML.
- CORE_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20201:
An SBML document must contain a <model> element.
- CORE_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20202:
The order of subelements within a <model> element must be the following (where
any one may be optional, but the ordering must be maintained):
<listOfFunctionDefinitions>, <listOfUnitDefinitions>, <listOfCompartmentTypes>,
<listOfSpeciesTypes>, <listOfCompartments>, <listOfSpecies>, <listOfParameters>,
<listOfInitialAssignments>, <listOfRules>, <listOfConstraints>,
<listOfReactions> and <listOfEvents>.
- CORE_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20203:
The <listOf___> containers in a <model> are optional, but if present, the lists
cannot be empty.
- CORE_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20204:
If a model defines any species, then the model must also define at least one
compartment.
- CORE_20205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20205:
There may be at most one instance of each of the following kind of element in a
<model> object: ListOfFunctionDefinitions, ListOfUnitDefinitions,
ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments,
ListOfRules, ListOfConstraints, ListOfReactions and ListOfEvents.
- CORE_20206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20206:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfFunctionDefinitions container object may only contain
FunctionDefinition objects.
- CORE_20207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20207:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfUnitDefinitions container object may only contain
UnitDefinition objects.
- CORE_20208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20208:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfCompartments container object may only contain Compartment
objects.
- CORE_20209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20209:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfSpecies container object may only contain Species objects.
- CORE_20210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20210:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfParameters container object may only contain Parameter
objects.
- CORE_20211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20211:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfInitialAssignments container object may only contain
InitialAssignment objects.
- CORE_20212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20212:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfRules container object may only contain Rule objects.
- CORE_20213 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20213:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfConstraints container object may only contain Constraint
objects.
- CORE_20214 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20214:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfReactions container object may only contain Reaction
objects.
- CORE_20215 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20215:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfEvents container object may only contain Event objects.
- CORE_20216 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20216:
The value of the attribute 'conversionFactor' on a Model object must be the
identifier of an existing Parameter object defined in the Model object's
ListOfParameters.
- CORE_20217 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20217:
The value of the attribute 'timeUnits' on a Model object should be either the
units 'second', 'dimensionless', or the identifier of a UnitDefinition object
based on these units.
- CORE_20218 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20218:
The value of the attribute 'volumeUnits' on a Model object should be either the
units 'litre', 'dimensionless', or the identifier of a UnitDefinition object
based on these units or a unit derived from 'metre' (with an exponent of '3').
- CORE_20219 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20219:
The value of the attribute 'areaUnits' on a Model object should be either
'dimensionless' or the identifier of a UnitDefinition object based on
'dimensionless' or a unit derived from 'metre' (with an exponent of '2').
- CORE_20220 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20220:
The value of the attribute 'lengthUnits' on a Model object should be either the
units 'metre', 'dimensionless', or the identifier of a UnitDefinition object
based on these units.
- CORE_20221 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20221:
The value of the attribute extentUnits on a Model object should be either the
units 'mole', 'item', 'avogadro', 'dimensionless', 'kilogram', 'gram', or the
identifier of a UnitDefinition object based on these units.
- CORE_20222 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20222:
A Model object may only have the following attributes, all of which are
optional: 'metaid', 'sboTerm', 'id', 'name', 'substanceUnits', 'timeUnits',
'volumeUnits', 'areaUnits', 'lengthUnits', 'extentUnits' and 'conversionFactor'.
- CORE_20223 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20223:
A ListOfFunctionDefinitions object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20224 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20224:
A ListOfUnitDefinitions object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20225 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20225:
A ListOfCompartments object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20226 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20226:
A ListOfSpecies object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20227 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20227:
A ListOfParameters object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20228 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20228:
A ListOfInitialAssignments object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20229 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20229:
A ListOfRules object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20230 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20230:
A ListOfConstraints object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20231 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20231:
A ListOfReactions object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_20232 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20232:
A ListOfEvents object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20233 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20233:
[Although SBML Level 3 Version 1 does not explicitly define the following as an
error, other Levels and/or Versions of SBML do.] The value of the attribute
substanceUnits on a Model object should be either the units 'mole', 'item',
'avogadro', 'dimensionless', 'kilogram', 'gram', or the identifier of a
UnitDefinition object based on these units.
- CORE_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20301:
The top-level element within <math> in a <functionDefinition> is restricted.
- CORE_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20302:
Inside the <lambda> of a <functionDefinition>, if a <ci> element is the first
element within a MathML <apply>, then the <ci>'s value can only be chosen from
the set of identifiers of other SBML <functionDefinition>s defined prior to that
point in the SBML model.
- CORE_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20303:
Inside the <lambda> of a <functionDefinition>, the identifier of that
<functionDefinition> cannot appear as the value of a <ci> element.
- CORE_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20304:
Inside the <lambda> of a <functionDefinition>, if a <ci> element is not the
first element within a MathML <apply>, then the <ci>'s value can only be the
value of a <bvar> element declared in that <lambda>.
- CORE_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20305:
The value type returned by a <functionDefinition>'s <lambda> must be either
Boolean or numeric.
- CORE_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20306:
A FunctionDefinition object must contain exactly one MathML math element.
- CORE_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20307:
FunctionDefinition object must have the required attribute 'id', and may have
the optional attributes 'metaid', 'sboTerm' and 'name'.
- CORE_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20401:
The value of the 'id' attribute in a <unitDefinition> must be of type 'UnitSId'
and not be identical to any unit predefined in SBML.
- CORE_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20402:
Redefinitions of the built-in unit 'substance' are restricted.
- CORE_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20403:
Redefinitions of the built-in unit 'length' are restricted.
- CORE_20404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20404:
Redefinitions of the built-in unit 'area' are restricted.
- CORE_20405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20405:
Redefinitions of the built-in unit 'time' are restricted.
- CORE_20406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20406:
Redefinitions of the built-in unit 'volume' are restricted.
- CORE_20407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20407:
If a <unitDefinition> for 'volume' simplifies to a <unit> in which the 'kind'
attribute value is 'litre', then its 'exponent' attribute value must be '1'.
- CORE_20408 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20408:
If a <unitDefinition> for 'volume' simplifies to a <unit> in which the 'kind'
attribute value is 'metre', then its 'exponent' attribute value must be '3'.
- CORE_20409 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20409:
The <listOfUnits> container in a <unitDefinition> cannot be empty.
- CORE_20410 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20410:
The value of the 'kind' attribute of a <unit> can only be one of the base units
enumerated by 'UnitKind'; that is, the SBML unit system is not hierarchical and
user-defined units cannot be defined using other user-defined units.
- CORE_20411 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20411:
The 'offset' attribute on <unit> previously available in SBML Level 2 Version 1,
has been removed as of SBML Level 2 Version 2.
- CORE_20412 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20412:
The predefined unit 'Celsius', previously available in SBML Level 1 and Level 2
Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_20413 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20413:
The ListOfUnits container object in a UnitDefinition object is optional, but if
present, it must not be empty.
- CORE_20414 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20414:
There may be at most one ListOfUnits container objects in a UnitDefinition
object.
- CORE_20415 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20415:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfUnits container object may only contain Unit objects.
- CORE_20419 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20419:
A UnitDefinition object must have the required attribute 'id' and may have the
optional attributes 'metaid', 'sboTerm' and 'name'.
- CORE_20420 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20420:
A ListOfUnits object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20421 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20421:
A Unit object must have the required attributes 'kind', 'exponent', 'scale' and
'multiplier', and may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20501:
The size of a <compartment> must not be set if the compartment's
'spatialDimensions' attribute has value '0'.
- CORE_20502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20502:
If a <compartment> definition has a 'spatialDimensions' value of '0', then its
'units' attribute must not be set.
- CORE_20503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20503:
If a <compartment> definition has a 'spatialDimensions' value of '0', then its
'constant' attribute value must either default to or be set to 'true'.
- CORE_20504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20504:
The 'outside' attribute value of a <compartment> must be the identifier of
another <compartment> defined in the model.
- CORE_20505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20505:
A <compartment> may not enclose itself through a chain of references involving
the 'outside' field.
- CORE_20506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20506:
The 'outside' attribute value of a <compartment> cannot be a compartment whose
'spatialDimensions' value is '0', unless both compartments have
'spatialDimensions'='0'.
- CORE_20507 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20507:
The value of the 'units' attribute on a <compartment> having 'spatialDimensions'
of '1' is restricted.
- CORE_20508 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20508:
The value of the 'units' attribute on a <compartment> having 'spatialDimensions'
of '2' is restricted.
- CORE_20509 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20509:
The value of the 'units' attribute on a <compartment> having 'spatialDimensions'
of '3' is restricted.
- CORE_20510 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20510:
If the 'compartmentType' attribute is given a value in a <compartment>
definition, it must contain the identifier of an existing <compartmentType>.
- CORE_20511 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20511:
If the attribute 'units' on a Compartment object having a 'spatialDimensions'
attribute value of '1' has not been set, then the unit of measurement associated
with the compartment's size is determined by the value of the enclosing Model
object's 'lengthUnits' attribute.
- CORE_20512 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20512:
If the attribute 'units' on a Compartment object having a 'spatialDimensions'
attribute value of '2' has not been set, then the unit of measurement associated
with the compartment's size is determined by the value of the enclosing Model
object's 'areaUnits' attribute.
- CORE_20513 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20513:
If the attribute 'units' on a Compartment object having a 'spatialDimensions'
attribute value of '3' has not been set, then the unit of measurement associated
with the compartment's size is determined by the value of the enclosing Model
object's 'volumeUnits' attribute.
- CORE_20517 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20517:
A Compartment object must have the required attributes 'id' and 'constant', and
may have the optional attributes 'metaid', 'sboTerm', 'name',
'spatialDimensions', 'size' and 'units'.
- CORE_20518 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20518:
If neither the attribute 'units' nor the attribute 'spatialDimensions' on a
Compartment object is set, the unit associated with that compartment's size is
undefined.
- CORE_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20601:
The value of 'compartment' in a <species> definition must be the identifier of
an existing <compartment> defined in the model.
- CORE_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20602:
If a <species> definition sets 'hasOnlySubstanceUnits' to 'true', then it must
not have a value for 'spatialSizeUnits'.
- CORE_20603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20603:
A <species> definition must not set 'spatialSizeUnits' if the <compartment> in
which it is located has a 'spatialDimensions' value of '0'.
- CORE_20604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20604:
If a <species> located in a <compartment> whose 'spatialDimensions' is set to
'0', then that <species> definition cannot set 'initialConcentration'.
- CORE_20605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20605:
If a <species> is located in a <compartment> whose 'spatialDimensions' has value
'1', then that <species> definition can only set 'spatialSizeUnits' to a value
of 'length', 'metre', 'dimensionless', or the identifier of a <unitDefinition>
derived from 'metre' (with an 'exponent' value of '1') or 'dimensionless'.
- CORE_20606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20606:
If a <species> is located in a <compartment> whose 'spatialDimensions' has value
'2', then that <species> definition can only set 'spatialSizeUnits' to a value
of 'area', 'dimensionless', or the identifier of a <unitDefinition> derived from
either 'metre' (with an 'exponent' value of '2') or 'dimensionless'.
- CORE_20607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20607:
If a <species> is located in a <compartment> whose 'spatialDimensions' has value
'3', then that <species> definition can only set 'spatialSizeUnits' to a value
of 'volume', 'litre', 'dimensionless', or the identifier of a <unitDefinition>
derived from either 'litre', 'metre' (with an 'exponent' value of '3') or
'dimensionless'.
- CORE_20608 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20608:
The value of a <species>'s 'units' attribute is restricted.
- CORE_20609 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20609:
A <species> cannot set values for both 'initialConcentration' and
'initialAmount' because they are mutually exclusive.
- CORE_20610 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20610:
A <species>'s quantity cannot be determined simultaneously by both reactions and
rules.
- CORE_20611 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20611:
A <species> having boundaryCondition='false' cannot appear as a reactant or
product in any reaction if that Species also has constant='true'.
- CORE_20612 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20612:
The value of 'speciesType' in a <species> definition must be the identifier of
an existing <speciesType>.
- CORE_20613 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20613:
There cannot be more than one species of a given <speciesType> in the same
compartment of a model.
- CORE_20614 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20614:
The 'compartment' attribute in a <species> is mandatory.
- CORE_20615 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20615:
The 'spatialSizeUnits' attribute on <species>, previously available in SBML
Level 2 versions prior to Version 3, has been removed as of SBML Level 2 Version
3.
- CORE_20616 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20616:
If the attribute 'substanceUnits' in a Species object has not been set, then the
unit of measurement associated with the species' quantity is determined by the
value of the enclosing Model object's 'substanceUnits' attribute.
- CORE_20617 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20617:
The value of the attribute 'conversionFactor' on a Species object must be the
identifier of an existing Parameter object defined in the enclosing Model
object.
- CORE_20623 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20623:
A Species object must have the required attributes 'id', 'compartment',
'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant', and may have the
optional attributes 'metaid', 'sboTerm', 'name', 'initialAmount',
'initialConcentration', 'substanceUnits' and 'conversionFactor'.
- CORE_20701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20701:
The 'units' in a <Parameter> definition must be a value chosen from among the
following: a predefined unit (e.g., 'substance', 'time', etc.), the identifier
of a <UnitDefinition> in the model, or one of the base units in SBML (e.g.,
'litre', 'mole', 'metre', etc.) Reference: L3V1 Section 4.7.3
- CORE_20702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20702:
If the attribute 'units' on a given Parameter object has not been set, then the
unit of measurement associated with that parameter's value is undefined.
- CORE_20705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20705:
A Parameter object referenced by the attribute 'conversionFactor' on a Species
or Model object must have a value of 'true' for its attribute 'constant'.
- CORE_20706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20706:
A Parameter object must have the required attributes 'id' and 'constant', and
may have the optional attributes 'metaid', 'sboTerm', 'name', 'value' and
'units'.
- CORE_20801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20801:
The value of 'symbol' in an <initialAssignment> definition must be the
identifier of an existing <compartment>, <species>, or <parameter> defined in
the model or <speciesReference> in Level 3.
- CORE_20802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20802:
A given identifier cannot appear as the value of more than one 'symbol' field
across the set of <initialAssignment>s in a model.
- CORE_20803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20803:
The value of a 'symbol' field in any <initialAssignment> definition cannot also
appear as the value of a 'variable' field in an <assignmentRule>.
- CORE_20804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20804:
An InitialAssignment object must contain exactly one MathML <math> element.
- CORE_20805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20805:
An InitialAssignment object must have the required attribute 'symbol' and may
have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20806:
The identifier given as the value of a 'symbol' attribute in any
<initialAssignment> definition cannot be the identifier of a <compartment> with
a 'spatialDimensions' value of 0.
- CORE_20901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20901:
The value of an <assignmentRule>'s 'variable' must be the identifier of an
existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3)
<speciesReference>.
- CORE_20902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20902:
The value of a <rateRule>'s 'variable' must be the identifier of an existing
<compartment>, <species>, globally-defined <parameter>, or (in Level 3)
<speciesReference>.
- CORE_20903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20903:
Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference>
whose identifier is the value of a 'variable' attribute in an <assignmentRule>,
must have a value of 'false' for 'constant'.
- CORE_20904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20904:
Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference>
whose identifier is the value of a 'variable' attribute in an <rateRule>, must
have a value of 'false' for 'constant'.
- CORE_20905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20905:
- CORE_20906 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20906:
There must not be circular dependencies in the combined set of
<initialAssignment>, <assignmentRule> and <kineticLaw> definitions in a model.
- CORE_20907 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20907:
Every AssignmentRule, RateRule and AlgebraicRule object must contain exactly one
MathML <math> element.
- CORE_20908 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20908:
An AssignmentRule object must have the required attribute 'variable' and may
have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20909 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20909:
A RateRule object must have the required attribute 'variable' and may have the
optional attributes 'metaid' and 'sboTerm'.
- CORE_20910 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20910:
An AlgebraicRule object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_20911 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 20911:
The value of a <rateRule> or <assignmentRule>'s 'variable' attribute must not be
the identifier of a <compartment> with a 'spatialDimensions' value of 0.
- CORE_21001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21001:
A <constraint>'s <math> expression must evaluate to a value of type Boolean.
- CORE_21002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21002:
The order of subelements within <constraint> must be the following: <math>,
<message>.
- CORE_21003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21003:
The contents of the <message> element in a <constraint> must be explicitly
placed in the XHTML XML namespace.
- CORE_21004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21004:
The contents of the <message> element must not contain an XML declaration (i.e.,
a string of the form "<?xml version="1.0" encoding="UTF-8"?>" or similar).
- CORE_21005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21005:
The contents of the <message> element must not contain an XML DOCTYPE
declaration (i.e., a string beginning with the characters "<!DOCTYPE".
- CORE_21006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21006:
The XHTML content inside a <constraint>'s <message> element can only take one of
the following general forms: (1) a complete XHTML document beginning with the
element <html> and ending with </html>; (2) the "body" portion of a document
beginning with the element <body> and ending with </body>; or (3) XHTML content
that is permitted within a <body> ...
- CORE_21007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21007:
A <constraint> object must contain exactly one MathML <math> element.
- CORE_21008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21008:
A <constraint> object may contain at most one <message> subobject.
- CORE_21009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21009:
A <constraint> object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_21101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21101:
A <reaction> definition must contain at least one <speciesReference>, either in
its <listOfReactants> or its <listOfProducts>.
- CORE_21102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21102:
The order of subelements within <reaction> must be the following:
<listOfReactants> (optional), <listOfProducts> (optional), <listOfModifiers>
(optional), <kineticLaw>.
- CORE_21103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21103:
The following containers are all optional in a <reaction>, but if any is
present, it must not be empty: <listOfReactants>, <listOfProducts>,
<listOfModifiers>, <kineticLaw>.
- CORE_21104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21104:
The list of reactants (<listOfReactants>) and list of products
(<listOfProducts>) in a <reaction> can only contain <speciesReference> elements.
- CORE_21105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21105:
The list of modifiers (<listOfModifiers>) in a <reaction> can only contain
<modifierSpeciesReference> elements.
- CORE_21106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21106:
A <reaction> object may contain at most one of each of the following elements:
<listOfReactants>, <listOfProducts>, <listOfModifiers>, and <kineticLaw>.
- CORE_21107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21107:
The value of the attribute 'compartment' in a <reaction> object is optional, but
if present, must be the identifier of an existing Compartment object defined in
the model.
- CORE_21110 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21110:
A <reaction> object must have the required attributes 'id', 'reversible' and
'fast', and may have the optional attributes 'metaid', 'sboTerm', 'name' and
'compartment'.
- CORE_21111 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21111:
The value of a <speciesReference> 'species' attribute must be the identifier of
an existing <species> in the model.
- CORE_21112 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21112:
- CORE_21113 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21113:
A <speciesReference> must not have a value for both 'stoichiometry' and
'stoichiometryMath'; they are mutually exclusive.
- CORE_21116 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21116:
A <speciesReference> object must have the required attributes 'species' and
'constant', and may have the optional attributes 'metaid', 'sboTerm', 'name'
'id' and 'stoichiometry'.
- CORE_21117 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21117:
A <modifierSpeciesReference> object must have the required attribute 'species'
and may have the optional attributes 'metaid', 'sboTerm', 'id' and 'name'.
- CORE_21121 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21121:
All species referenced in the <kineticLaw> formula of a given reaction must
first be declared using <speciesReference> or <modifierSpeciesReference>.
- CORE_21122 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21122:
The order of subelements within <kineticLaw> must be the following: <math>,
<listOfParameters>.
- CORE_21123 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21123:
If present, the <listOfParameters> in a <kineticLaw> must not be an empty list.
- CORE_21124 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21124:
The 'constant' attribute on a <parameter> local to a <kineticLaw> cannot have a
value other than 'true'.
- CORE_21125 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21125:
The 'substanceUnits' attribute on <kineticLaw>, previously available in SBML
Level 1 and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_21126 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21126:
The 'timeUnits' attribute on <kineticLaw>, previously available in SBML Level 1
and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_21127 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21127:
A KineticLaw object may contain at most one ListOfLocalParameters container
object.
- CORE_21128 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21128:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfLocalParameters container object may only contain
LocalParameter objects.
- CORE_21129 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21129:
A ListOfLocalParameters object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_21130 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21130:
A KineticLaw object must contain exactly one MathML <math> element.
- CORE_21131 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21131:
All species referenced in the <stoichiometryMath> formula of a given reaction
must first be declared using <speciesReference> or <modifierSpeciesReference>.
- CORE_21132 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21132:
A KineticLaw object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_21150 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21150:
A ListOfSpeciesReferences object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_21151 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21151:
A ListOfModifierSpeciesReferences object may have the optional attributes
'metaid' and 'sboTerm'.
- CORE_21152 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21152:
The value of the 'fast' attribute should be 'false', as the attribute has been
deprecated.
- CORE_21172 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21172:
A LocalParameter object must have the required attribute 'id' and may have the
optional attributes 'metaid', 'sboTerm', 'name', 'value' and 'units'.
- CORE_21201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21201:
An <event> object must have a 'trigger'.
- CORE_21202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21202:
An <event>'s <trigger> expression must evaluate to a value of type Boolean.
- CORE_21203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21203:
An <event> object must have at least one <eventAssignment> object in its
<listOfEventAssignments>.
- CORE_21204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21204:
The value of an <event>'s 'timeUnits' attribute must be 'time', 'second',
'dimensionless', or the identifier of a <unitDefinition> derived from either
'second' (with an 'exponent' value of '1') or 'dimensionless'.
- CORE_21205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21205:
The order of subelements within <event> must be the following: <trigger>,
<delay>, <listOfEventAssignments>.
- CORE_21206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21206:
If an <event>'s 'useValuesFromTriggerTime' attribute has the value 'false', then
the <event> must contain a <delay> element.
- CORE_21207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21207:
If an Event object contains a Delay subobject, then the Event must have a value
for the attribute 'useValuesFromTriggerTime'.
- CORE_21209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21209:
A Trigger object must contain exactly one MathML <math> element.
- CORE_21210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21210:
A Delay object must contain exactly one MathML <math> element.
- CORE_21211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21211:
The value of the attribute 'variable' in an <eventAssignment> can only be the
identifier of a <compartment>, <species>, model-wide <parameter> definition, or
<speciesReference> in Level 3.
- CORE_21212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21212:
Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference>
definition whose identifier is used as the value of 'variable' in an
<eventAssignment> must have a value of 'false' for its 'constant' attribute.
- CORE_21213 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21213:
An EventAssignment object must contain exactly one MathML <math> element.
- CORE_21214 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21214:
An EventAssignment object must have the required attribute 'variable' and may
have the optional attributes 'metaid' and 'sboTerm'.
- CORE_21221 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21221:
An Event object may contain at most one Delay object.
- CORE_21222 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21222:
An Event object may contain at most one ListOfEventAssignments object.
- CORE_21223 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21223:
Apart from the general Notes and Annotation subobjects permitted on all SBML
components, a ListOfEventAssignments container object may only contain
EventAssignment objects.
- CORE_21224 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21224:
A ListOfEventAssignments object may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_21225 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21225:
An Event object must have the required attribute 'useValuesFromTriggerTime' and
in addition may have the optional attributes 'metaid', 'sboTerm', 'id', and
'name'.
- CORE_21226 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21226:
A Trigger object must have the required attributes 'persistent' and
'initialValue', and in addition, may have the optional attributes 'metaid' and
'sboTerm'.
- CORE_21227 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21227:
A Delay object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_21228 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21228:
The attribute 'persistent' on a Trigger object must have a value of type
Boolean.
- CORE_21229 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21229:
The attribute 'initialValue' on a Trigger object must have a value of type
Boolean.
- CORE_21230 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21230:
An Event object may contain at most one Priority object.
- CORE_21231 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21231:
An Priority object must contain exactly one MathML <math> element.
- CORE_21232 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 21232:
A Priority object may have the optional attributes 'metaid' and 'sboTerm'.
- CORE_29999 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 29999:
- CORE_80501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 80501:
As a principle of best modeling practice, the size of a <compartment> should be
set to a value rather than be left undefined.
- CORE_80601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 80601:
As a principle of best modeling practice, the <species> should set an initial
value (amount or concentration) rather than be left undefined.
- CORE_80701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 80701:
As a principle of best modeling practice, the units of a <parameter> should be
declared rather than be left undefined.
- CORE_80702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 80702:
As a principle of best modeling practice, the <parameter> should set an initial
value rather than be left undefined.
- CORE_81121 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 81121:
In SBML's simple symbol system, there is no separation of symbols by class of
object; consequently, inside the kinetic law mathematical formula, the value of
a local parameter having the same identifier as a species or compartment or
other global model entity will override the global value.
- CORE_90000 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 90000:
- CORE_90001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 90001:
Use of SBML Level 1 Version 1 is not recommended and conversion is not supported
by libSBML.
- CORE_91001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91001:
A model with <event> definitions cannot be represented in SBML Level 1.
- CORE_91002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91002:
SBML Level 1 does not have <functionDefinitions>.
- CORE_91003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91003:
Conversion of a model with <constraint>s to SBML Level 1 may result in loss of
information.
- CORE_91004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91004:
SBML Level 1 does not have <initialAssignments>.
- CORE_91005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91005:
<speciesType> definitions cannot be represented in SBML Level 1.
- CORE_91006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91006:
<compartmentType> definitions cannot be represented in SBML Level 1.
- CORE_91007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91007:
A <compartment> with 'spatialDimensions' not equal to 3 cannot be represented in
SBML Level 1.
- CORE_91008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91008:
A <speciesReference> containing a non-integer or non-rational
<stoichiometryMath> subelement cannot be represented in SBML Level 1.
- CORE_91009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91009:
A <speciesReference> containing a non-integer 'stoichiometry' attribute value
cannot be represented in SBML Level 1.
- CORE_91010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91010:
A <unit> containing multipliers or offsets cannot be represented in SBML Level
1.
- CORE_91011 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91011:
A <species> that does not identify its compartment cannot be represented in SBML
Level 1.
- CORE_91012 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91012:
The information represented by the value of a 'spatialSizeUnit' attribute on a
<species> definition cannot be represented in SBML Level 1.
- CORE_91013 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91013:
SBO terms cannot be represented directly in SBML Level 1.
- CORE_91014 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91014:
SBML Level 2 Version 4 removed the requirement that all units be consistent.
- CORE_91015 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91015:
This model contains conversion factors and thus conversion to earlier levels is
not supported.
- CORE_91016 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91016:
SBML Level 1/2 do not have the 'compartment' attribute on a Reaction.
- CORE_91017 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91017:
Conversion to SBML Level 1 requires that 'extent' units be a variant of
substance
- CORE_91018 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91018:
Conversion to SBML Levels 1 and 2 requires that any global units must refer to a
valid unit kind or the id of a valid unitDefinition.
- CORE_91019 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91019:
The concept of a Species having only substance units and not units of
concentration cannot be correctly interpreted in SBML Level 1 without alteration
of any mathematical formula.
- CORE_91020 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 91020:
Conversion of the csymbol avogadro is not yet supported.
- CORE_92001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92001:
Conversion of a model with <constraints> to SBML Level 2 Version 1 may result in
loss of information.
- CORE_92002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92002:
SBML Level 2 Version 1 does not have <initialAssignments>.
- CORE_92003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92003:
<speciesType> definitions cannot be represented in SBML Level 2 Version 1.
- CORE_92004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92004:
<compartmentType> definitions cannot be represented in SBML Level 2 Version 1.
- CORE_92005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92005:
SBO terms cannot be represented directly in SBML Level 2 Version 1.
- CORE_92006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92006:
The 'id' attribute value of a <speciesReference> cannot be represented directly
in SBML Level 2 Version 1.
- CORE_92007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92007:
The implication of 'useValuesFromTriggerTime=false' is that there is a delay
between the time of trigger and the time of value assignments performed by the
<event>.
- CORE_92008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92008:
SBML Level 2 Version 4 removed the requirement that all units be consistent.
- CORE_92009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92009:
Models in SBML Level 2 Versions 1-4 can only represent compartments with integer
values 0, 1, 2, or 3 as spatial dimensions.
- CORE_92010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92010:
Conversion of a varying stoichiometry to an SBML L2 StoichiometryMath element is
not yet supported.
- CORE_92011 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92011:
Event priority is not supported in SBML Level 2.
- CORE_92012 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92012:
Non persistent events are not supported in SBML Level 2.
- CORE_92013 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 92013:
Initialvalue of event Triggers was assumed true in L2.
- CORE_93001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93001:
In SBML Level 2 Version 2, an 'sboTerm' attribute is only permitted on the
following elements: <model>, <functionDefinition>, <parameter>,
<initialAssignment>, <rule>, <constraint>, <reaction>, <speciesReference>,
<kineticLaw>, <event> and <eventAssignment>.
- CORE_93002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93002:
The 'offset' attribute on <unit> previously available in SBML Level 2 Version 1,
has been removed as of SBML Level 2 Version 2.
- CORE_93003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93003:
The 'timeUnits' attribute on <kineticLaw>, previously available in SBML Level 1
and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_93004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93004:
The 'substanceUnits' attribute on <kineticLaw>, previously available in SBML
Level 1 and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_93005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93005:
The implication of 'useValuesFromTriggerTime=false' is that there is a delay
between the time of trigger and the time of value assignments performed by the
<event>.
- CORE_93006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93006:
In SBML Level 2 prior to Version 4 the value of the 'sboTerm' attribute on a
<model> is expected to be a term derived from SBO:0000004, "modeling framework";
in Version 4 and above it is expected to be a term derived from SBO:0000231
"interaction".
- CORE_93007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93007:
SBML Level 2 Version 4 removed the requirement that all units be consistent.
- CORE_93008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93008:
SBML Level 2 Version 4 removed the requirement that all sboTerms be drawn from a
given branch of SBO (http://www.biomodels.net/SBO/).
- CORE_93009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 93009:
In SBML prior to Level 2 Version 1 annotations it was permissible to have
multiple top level elements using the same namespace.
- CORE_94001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94001:
The 'offset' attribute on <unit> previously available in SBML Level 2 Version 1,
has been removed as of SBML Level 2 Version 2.
- CORE_94002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94002:
The 'timeUnits' attribute on <kineticLaw>, previously available in SBML Level 1
and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_94003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94003:
The 'substanceUnits' attribute on <kineticLaw>, previously available in SBML
Level 1 and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_94004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94004:
The 'spatialSizeUnits' attribute on <species>, previously available in SBML
Level 2 versions prior to Version 3, has been removed as of SBML Level 2 Version
3.
- CORE_94005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94005:
The 'timeUnits' attribute on <event>, previously available in SBML Level 2
versions prior to Version 3, has been removed as of SBML Level 2 Version 3.
- CORE_94006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94006:
The implication of 'useValuesFromTriggerTime=false' is that there is a delay
between the time of trigger and the time of value assignments performed by the
<event>.
- CORE_94007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94007:
In SBML Level 2 prior to Version 4 the value of the 'sboTerm' attribute on a
<model> is expected to be a term derived from SBO:0000004, "modeling framework";
in Version 4 and above it is expected to be a term derived from SBO:0000231
"interaction".
- CORE_94008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94008:
SBML Level 2 Version 4 removed the requirement that all units be consistent.
- CORE_94009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94009:
SBML Level 2 Version 4 removed the requirement that all sboTerms be drawn from a
given branch of SBO (http://www.biomodels.net/SBO/).
- CORE_94010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 94010:
In SBML prior to Level 2 Version 1 annotations it was permissible to have
multiple top level elements using the same namespace.
- CORE_95001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95001:
The 'offset' attribute on <unit> previously available in SBML Level 2 Version 1,
has been removed as of SBML Level 2 Version 2.
- CORE_95002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95002:
The 'timeUnits' attribute on <kineticLaw>, previously available in SBML Level 1
and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_95003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95003:
The 'substanceUnits' attribute on <kineticLaw>, previously available in SBML
Level 1 and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_95004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95004:
The 'spatialSizeUnits' attribute on <species>, previously available in SBML
Level 2 versions prior to Version 3, has been removed as of SBML Level 2 Version
3.
- CORE_95005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95005:
The 'timeUnits' attribute on <event>, previously available in SBML Level 2
versions prior to Version 3, has been removed as of SBML Level 2 Version 3.
- CORE_95006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95006:
In SBML Level 2 prior to Version 4 the value of the 'sboTerm' attribute on a
<model> is expected to be a term derived from SBO:0000004, "modeling framework";
in Version 4 and above it is expected to be a term derived from SBO:0000231
"interaction".
- CORE_95007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 95007:
In SBML prior to Level 2 Version 1 annotations it was permissible to have
multiple top level elements using the same namespace.
- CORE_96001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96001:
<speciesType> definitions cannot be represented in SBML Level 3 Version 1.
- CORE_96002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96002:
<compartmentType> definitions cannot be represented in SBML Level 3 Version 1.
- CORE_96003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96003:
The 'offset' attribute on <unit> previously available in SBML Level 2 Version 1,
has been removed as of SBML Level 2 Version 2.
- CORE_96004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96004:
The 'timeUnits' attribute on <kineticLaw>, previously available in SBML Level 1
and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_96005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96005:
The 'substanceUnits' attribute on <kineticLaw>, previously available in SBML
Level 1 and Level 2 Version 1, has been removed as of SBML Level 2 Version 2.
- CORE_96006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96006:
The 'spatialSizeUnits' attribute on <species>, previously available in SBML
Level 2 versions prior to Version 3, has been removed as of SBML Level 2 Version
3.
- CORE_96007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96007:
The 'timeUnits' attribute on <event>, previously available in SBML Level 2
versions prior to Version 3, has been removed as of SBML Level 2 Version 3.
- CORE_96008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96008:
In SBML Level 2 prior to Version 4 the value of the 'sboTerm' attribute on a
<model> is expected to be a term derived from SBO:0000004, "modeling framework";
in Version 4 and above it is expected to be a term derived from SBO:0000231
"interaction".
- CORE_96009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96009:
In SBML prior to Level 2 Version 1 annotations it was permissible to have
multiple top level elements using the same namespace.
- CORE_96010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96010:
The 'outside' attribute on <compartment>, previously available in SBML Level 2
has been removed as of SBML Level 3 Version 1.
- CORE_96011 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 96011:
Conversion of a model with <stoichiometryMath> to SBML Level 3 is not yet
supported.
- CORE_99101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99101:
The level and version specified for the document must be consistent with a valid
published SBML specification.
- CORE_99104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99104:
The <sbml> container element cannot contain <notes> or <annotations> in an SBML
Level 1 document.
- CORE_99106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99106:
The math field of an assignment rule structure can contain any identifier in a
MathML <ci> element except for the following: (a) identifiers for which there
exists a subsequent assignment rule, and (b) the identifier for which the rule
is defined.
- CORE_99107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99107:
Every SBML Level 3 package is identified uniquely by an XML namespace URI and
defines the attribute named 'required'.
- CORE_99108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99108:
Every SBML Level 3 package is identified uniquely by an XML namespace URI and
defines the attribute named 'required'.
- CORE_99109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99109:
The 'required' attribute for this package is expected to be 'false' as there is
no way to change the mathematical interpretation of the model using the
constructs in this package.
- CORE_99127 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99127:
A KineticLaw's substanceUnits must be 'substance', 'item', 'mole', or the id of
a UnitDefinition that defines a variant of 'item' or 'mole' (L2v1 Section
4.9.7).
- CORE_99128 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99128:
A KineticLaw's timeUnits must be 'time', 'second', or the id of a UnitDefnition
that defines a variant of 'second' with exponent='1' (L2v1 Section 4.9.7).
- CORE_99129 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99129:
In a Level 1 model, only predefined functions are permitted within the formula.
- CORE_99130 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99130:
The value of the attribute substanceUnits on a Model object should be either the
units 'mole', 'item', 'avogadro', 'dimensionless', 'kilogram', 'gram', or the
identifier of a UnitDefinition object based on these units.
- CORE_99206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99206:
The 'timeUnits' attribute on <event>, previously available in SBML Level 2
versions prior to Version 3, has been removed as of SBML Level 2 Version 3.
- CORE_99219 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99219:
Invalid MathML.
- CORE_99220 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99220:
Failed to read a valid double value from MathML.
- CORE_99221 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99221:
Failed to read a valid integer value from MathML.
- CORE_99222 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99222:
Failed to read a valid exponential value from MathML.
- CORE_99223 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99223:
Failed to read a valid rational value from MathML.
- CORE_99224 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99224:
Invalid MathML.
- CORE_99225 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99225:
An invalid MathML attribute has been encountered.
- CORE_99301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99301:
The csymbol 'time' should not be used within the <math> element of a
<functionDefinition>.
- CORE_99302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99302:
The <lambda> element of a FunctionDefinition object must contain a function body
in addition to zero or more arguments.
- CORE_99303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99303:
Where a component has an attribute that refers to a unit identifier, that
attribute must refer to a unit defined in SBML or be the id of a UnitDefinition
in the model.
- CORE_99401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99401:
In order to follow the general syntax for a standard SBML RDF annotation the
first element of RDF element must be a Description element with an 'about'
attribute.
- CORE_99402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99402:
In order to follow the general syntax for a standard SBML RDF annotation, the
'about' attribute of the Description element must be of the form #string.
- CORE_99403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99403:
In order to follow the general syntax for a standard SBML RDF annotation, the
'about' attribute of the Description element must be of the form #string, where
the string component is equal to the value of the metaid attribute of the
containing SBML element.
- CORE_99404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99404:
LibSBML expected to read the annotation into a ModelHistory object.
- CORE_99405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99405:
LibSBML expected to read the annotation into a ModelHistory object.
- CORE_99406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99406:
An annotation must contain elements; with each top-level element placed in a
unique namespace.
- CORE_99407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99407:
The specified annotation RELATION element does not permit nested elements.
- CORE_99505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99505:
In situations where a mathematical expression contains literal numbers or
parameters whose units have not been declared, it is not possible to verify
accurately the consistency of the units in the expression.
- CORE_99506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99506:
In situations where a mathematical expression refers to time, the units of time
should be consistent with the global time units of the model.
- CORE_99507 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99507:
In situations where a mathematical expression refers to extent, the units of
extent should be consistent with the global extent units of the model.
- CORE_99508 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99508:
In situations where a mathematical expression refers to a compartment, species
or parameter, it is necessary to know the units of the object to establish unit
consistency.
- CORE_99701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99701:
The SBOTerm used is not recognized by libSBML and therefore the correct
parentage cannot be checked.
- CORE_99702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99702:
The SBOTerm value used is considered obsolete.
- CORE_99901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99901:
The 'spatialDimensions' attribute on <compartment> was not available in SBML
Level 1.
- CORE_99902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99902:
The 'compartmentType' attribute on <compartment> was not available in SBML Level
1 or SBML Level 2 Version 1.
- CORE_99903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99903:
The 'constant' attribute on <compartment> and <parameter> was not available in
SBML Level 1.
- CORE_99904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99904:
The 'metaid' attribute on all <SBase> objects was not available in SBML Level 1.
- CORE_99905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99905:
The 'sboTerm' attribute on <compartment>, <compartmentType> <delay>, <species>,
<speciesType>, <stoichiometryMath>, <trigger> <unit> and <unitDefinition> was
not available before SBML Level 2 Version 3.
- CORE_99906 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99906:
The value of the 'units' attribute on a <compartment> must be either 'volume',
'litre', 'liter' or the identifier of a <unitDefinition> based on either
'litre'/'liter' or 'metre'/'meter' (with 'exponent' equal to '3').
- CORE_99907 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99907:
A value for the compartment 'volume' attribute must be specified in this
Level+Version of SBML.
- CORE_99908 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99908:
The <compartmentType> component was introduced in SBML Level 2 Version 2.
- CORE_99909 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99909:
The <constraint> component was introduced in SBML Level 2 Version 2.
- CORE_99910 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99910:
The <event> component was introduced in SBML Level 2 Version 1.
- CORE_99911 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99911:
The 'sboTerm' attribute on <event>, <eventAssignment> <functionDefinition>,
<kineticLaw>, <model>, <parameter>, <reaction> <rule> and <speciesReferenece>
was not available before SBML Level 2 Version 2.
- CORE_99912 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99912:
The <functionDefinition> component was introduced in SBML Level 2 Version 1.
- CORE_99913 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99913:
The <initialAssignment> component was introduced in SBML Level 2 Version 2.
- CORE_99914 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99914:
An <algebraicRule> does not assign a value to a particular variable and does not
carry an attribute named 'variable'.
- CORE_99915 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99915:
The 'units' attribute on <rule> was only applicable to a <parameterRule> in SBML
Level 1.
- CORE_99916 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99916:
The 'constant' attribute on <species> was not available in SBML Level 1.
- CORE_99917 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99917:
The 'spatialSizeUnits' attribute on <species> was not available in SBML Level 1.
- CORE_99918 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99918:
The 'speciesType' attribute on <species> was not available in SBML Level 1 or
SBML Level 2 Version 1.
- CORE_99919 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99919:
The 'hasOnlySubstanceUnits' attribute on <species> was not available in SBML
Level 1.
- CORE_99920 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99920:
The 'id' attribute on <speciesReference> was not available in SBML Level 1 or
SBML Level 2 Version 1.
- CORE_99921 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99921:
The 'name' attribute on <speciesReference> was not available in SBML Level 1 or
SBML Level 2 Version 1.
- CORE_99922 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99922:
The <speciesType> component was introduced in SBML Level 2 Version 2.
- CORE_99923 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99923:
The <stoichiometryMath> component on a <speciesReference> was introduced in SBML
Level 2.
- CORE_99924 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99924:
The 'multiplier' attribute on <unit> was not available in SBML Level 1.
- CORE_99925 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99925:
The 'offset' attribute on <unit> was only available in SBML Level 2 Version 1.
- CORE_99926 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99926:
The 'spatialDimensions' attribute on <compartment> was left unset on the SBML
Level 3 model.
- CORE_99994 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99994:
- CORE_99995 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99995:
- CORE_99996 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99996:
Conversion of SBML Level 3 package information is not yet supported.
- CORE_99997 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99997:
Conversion is only possible to an existing SBML Level and Version.
- CORE_99998 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99998:
Validation of or conversion from L3 documents/models is not yet supported.
- CORE_99999 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 99999:
- CoreSpecialErrorCodes - Interface in org.sbml.jsbml.validator.offline.constraints
-
Some ErrorCodes which are not officially part of SBML and only are used for
offline validation.
- cos(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- cos(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- cosh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- cosh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- cot(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- cot(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- cot(double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the cot of n
- coth(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- coth(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- coth(double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the coth of n
- COULD_NOT_CREATE_ELEMENT_MSG - Static variable in class org.sbml.jsbml.Model
-
Error message to indicate that an element could not be created.
- countType(ASTNode2, ASTNode.Type) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Counts the number of nodes that have
ASTNode.Type type
in the tree rooted at node.
- create(InputStream, boolean) - Method in interface org.sbml.jsbml.util.DocumentFactory
-
Creates an XML DOM document by parsing the content of the specified byte
stream as XML, using a nonvalidating parser.
- create(InputStream, Object[], ErrorHandler) - Method in interface org.sbml.jsbml.util.DocumentFactory
-
Creates an XML DOM document by parsing the content of the specified byte
stream as XML, using a validating parser.
- create(Reader, boolean) - Method in interface org.sbml.jsbml.util.DocumentFactory
-
Creates an XML DOM document by parsing the content of the specified
character stream as XML, using a nonvalidating parser.
- create(Reader, Object[], ErrorHandler) - Method in interface org.sbml.jsbml.util.DocumentFactory
-
Creates an XML DOM document by parsing the content of the specified
character stream as XML, using a validating parser.
- create(InputStream, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Creates an XML DOM document by parsing the content of the specified byte
stream as XML, using a nonvalidating parser.
- create(InputStream, Object[], ErrorHandler) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Creates an XML DOM document by parsing the content of the specified byte
stream as XML, using a validating parser.
- create(Reader, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Creates an XML DOM document by parsing the content of the specified
character stream as XML, using a nonvalidating parser.
- create(Reader, Object[], ErrorHandler) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Creates an XML DOM document by parsing the content of the specified
character stream as XML, using a validating parser.
- createAlgebraicRule() - Method in class org.sbml.jsbml.Model
-
- createApplyNode(Node, ASTNodeValue...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createApplyNode(Node, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
Creates an apply
Node with the given tag
Node as its
child and
ASTNodeValues on the same level as the tag
Node
.
- createApplyNode(String, ASTNode...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createApplyNode(String, ASTNodeValue...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createApplyNode(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
Creates a Node with the tag "apply" and adds the given
Node as its child.
- createAssignmentRule() - Method in class org.sbml.jsbml.Model
-
- createCiElement(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createCnElement(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createCnElement(Number, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createCompartment() - Method in class org.sbml.jsbml.Model
-
- createCompartment(String) - Method in class org.sbml.jsbml.Model
-
- createCompartmentType() - Method in class org.sbml.jsbml.Model
-
- createCompartmentType(String) - Method in class org.sbml.jsbml.Model
-
- createConstant(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
Creates an
ASTNodeValue with the single node as defined by the
tagName.
- createConstraint() - Method in class org.sbml.jsbml.Model
-
- createConstraint(int) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- createConstraint(int) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Tries to create the constraint with the given error code
- createConstraints(int[]) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- createConstraints(int, int, SBMLValidator.CHECK_CATEGORY) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- createConstraints(int, int, String) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- createConstraints(int, int, SBMLValidator.CHECK_CATEGORY[]) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- createConstraints(int, int, SBMLValidator.CHECK_CATEGORY[]) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Creates all the constraints which are needed to validate the categories
in the given level and version of SBML.
- createConstraints(int, int, SBMLValidator.CHECK_CATEGORY) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Creates all the constraints which are needed to validate this category
in the given level and version of SBML.
- createConstraints(int, int, String) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Creates all the constraints which are needed to validate the attribute
in the given level and version of SBML.
- createConstraints(int[]) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Tries to create the constraints with the given error codes
- createCSymbol(String, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createdDate - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- createDelay() - Method in class org.sbml.jsbml.Event
-
Creates a new
Delay instance and sets it to this
Event.
- createDelay(ASTNode) - Method in class org.sbml.jsbml.Event
-
Creates a new
Delay instance and sets it to this
Event.
- createDelay() - Method in class org.sbml.jsbml.Model
-
Creates a new
Delay inside the last
Event object created in
this
Model, and returns a pointer to it.
- createError(int, int, int) - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory
-
- createEvent() - Method in class org.sbml.jsbml.Model
-
Creates a new
Event inside this
Model and returns it.
- createEvent(String) - Method in class org.sbml.jsbml.Model
-
Creates a new
Event inside this
Model and returns it.
- createEventAssignment() - Method in class org.sbml.jsbml.Event
-
Creates a new
EventAssignment element and adds it to the ListOfEventAssignments list.
- createEventAssignment(String, ASTNode) - Method in class org.sbml.jsbml.Event
-
Creates a new
EventAssignment element and adds it to the ListOfEventAssignments list.
- createEventAssignment(Variable, ASTNode) - Method in class org.sbml.jsbml.Event
-
Creates a new
EventAssignment element and adds it to the ListOfEventAssignments list.
- createEventAssignment() - Method in class org.sbml.jsbml.Model
-
- createFunctionDefinition() - Method in class org.sbml.jsbml.Model
-
- createFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
- createHistory() - Method in class org.sbml.jsbml.AbstractSBase
-
Creates a new
History and associates it with the annotation of
this element.
- createHistory() - Method in class org.sbml.jsbml.Annotation
-
- createIndentationString(int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Creates the necessary number of white spaces at the beginning
of an entry in the SBML file.
- createInitialAssignment() - Method in class org.sbml.jsbml.Model
-
- createInvalidUnit() - Method in class org.sbml.jsbml.UnitDefinition
-
- createKineticLaw() - Method in class org.sbml.jsbml.Model
-
- createKineticLaw() - Method in class org.sbml.jsbml.Reaction
-
Creates a new
KineticLaw object, installs it as this
Reaction's 'kineticLaw' sub-element, and returns it.
- createKineticLawParameter() - Method in class org.sbml.jsbml.Model
-
- createKineticParameter(String) - Method in class org.sbml.jsbml.Model
-
- createListOfChild(ListOf<?>, String) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
Creates a new object instance using reflection on the listOf parent.
- createLocalParameter() - Method in class org.sbml.jsbml.KineticLaw
-
- createLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
-
- createMathMLDocumentFor(Node, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- createMessage(String, String, SBase) - Static method in exception org.sbml.jsbml.PropertyException
-
Creates an error message pointing out that the property of the given name is not defined
in the Level/Version combination of the given
SBase.
- createMessage(String, String, SBasePlugin) - Static method in exception org.sbml.jsbml.PropertyException
-
- createMessage(String, String, TreeNode) - Static method in exception org.sbml.jsbml.PropertyException
-
Creates an error message pointing out that the property of the given name
is not defined in the Level/Version combination of the given
TreeNode.
- createModel() - Method in class org.sbml.jsbml.SBMLDocument
-
Creates a new Model inside this
SBMLDocument, and returns a
pointer to it.
- createModel(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Creates a new instance of Model from id and the level and version of this
SBMLDocument.
- createModifier() - Method in class org.sbml.jsbml.Model
-
- createModifier(String) - Method in class org.sbml.jsbml.Model
-
- createModifier() - Method in class org.sbml.jsbml.Reaction
-
- createModifier(Species) - Method in class org.sbml.jsbml.Reaction
-
- createModifier(String) - Method in class org.sbml.jsbml.Reaction
-
- createModifier(String, Species) - Method in class org.sbml.jsbml.Reaction
-
- createModifier(String, String) - Method in class org.sbml.jsbml.Reaction
-
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Returns a piecewise
ASTNode representing the modulo operation between the left and right child given.
- createModulo(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Returns a piecewise
ASTNode representing the modulo operation between the left and right child given.
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Returns a piecewise
ASTNode representing the modulo operation between the left and right child given.
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Returns a piecewise
ASTNode representing the modulo operation between the left and right child given.
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Returns a piecewise
ASTNode representing the modulo operation between the left and right child given.
- createModulo(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Returns a piecewise
ASTNode representing the modulo operation between the left and right child given.
- createNestedCVTerm() - Method in class org.sbml.jsbml.CVTerm
-
- createParameter() - Method in class org.sbml.jsbml.Model
-
- createParameter(String) - Method in class org.sbml.jsbml.Model
-
- createPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- createPlugin(String) - Method in class org.sbml.jsbml.ASTNode
-
- createPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Creates a new
SBasePlugin for the given package name or URI
and adds it to this
SBase.
- createPluginFor(SBase) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
- createPluginFor(ASTNode) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
- createPriority() - Method in class org.sbml.jsbml.Event
-
- createPriority(ASTNode) - Method in class org.sbml.jsbml.Event
-
- createProduct() - Method in class org.sbml.jsbml.Model
-
- createProduct(String) - Method in class org.sbml.jsbml.Model
-
- createProduct() - Method in class org.sbml.jsbml.Reaction
-
- createProduct(Species) - Method in class org.sbml.jsbml.Reaction
-
- createProduct(String) - Method in class org.sbml.jsbml.Reaction
-
- createProduct(String, Species) - Method in class org.sbml.jsbml.Reaction
-
- createProduct(String, String) - Method in class org.sbml.jsbml.Reaction
-
- createRateRule() - Method in class org.sbml.jsbml.Model
-
- createReactant() - Method in class org.sbml.jsbml.Model
-
- createReactant(String) - Method in class org.sbml.jsbml.Model
-
Creates a new
SpeciesReference object, with the specified 'id', for
a reactant inside the last
Reaction object in this
Model,
and returns a pointer to it.
- createReactant() - Method in class org.sbml.jsbml.Reaction
-
- createReactant(Species) - Method in class org.sbml.jsbml.Reaction
-
- createReactant(String) - Method in class org.sbml.jsbml.Reaction
-
- createReactant(String, Species) - Method in class org.sbml.jsbml.Reaction
-
- createReactant(String, String) - Method in class org.sbml.jsbml.Reaction
-
- createReaction() - Method in class org.sbml.jsbml.Model
-
- createReaction(String) - Method in class org.sbml.jsbml.Model
-
- createSpecies() - Method in class org.sbml.jsbml.Model
-
- createSpecies(String) - Method in class org.sbml.jsbml.Model
-
- createSpecies(String, Compartment) - Method in class org.sbml.jsbml.Model
-
- createSpecies(String, String, Compartment) - Method in class org.sbml.jsbml.Model
-
- createSpeciesType() - Method in class org.sbml.jsbml.Model
-
- createSpeciesType(String) - Method in class org.sbml.jsbml.Model
-
- createStoichiometryMath(ASTNode) - Method in class org.sbml.jsbml.SpeciesReference
-
- createTrigger() - Method in class org.sbml.jsbml.Event
-
- createTrigger(boolean, boolean) - Method in class org.sbml.jsbml.Event
-
- createTrigger(boolean, boolean, ASTNode) - Method in class org.sbml.jsbml.Event
-
- createTrigger(ASTNode) - Method in class org.sbml.jsbml.Event
-
- createTrigger() - Method in class org.sbml.jsbml.Model
-
Creates a new
Trigger inside the last
Event object created
in this
Model, and returns a pointer to it.
- createUnit() - Method in class org.sbml.jsbml.Model
-
Creates a new
Unit object within the last
UnitDefinition
object created in this model and returns a pointer to it.
- createUnit(Unit.Kind) - Method in class org.sbml.jsbml.Model
-
Creates a new
Unit object within the last
UnitDefinition
object created in this model and returns a pointer to it.
- createUnit() - Method in class org.sbml.jsbml.UnitDefinition
-
- createUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition
-
- createUnitDefinition() - Method in class org.sbml.jsbml.Model
-
- createUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- creation - Variable in class org.sbml.jsbml.History
-
Date of creation
- Creator - Class in org.sbml.jsbml
-
Contains all the information about a creator of a
Model (or other
SBase in level 3).
- Creator() - Constructor for class org.sbml.jsbml.Creator
-
- Creator(Creator) - Constructor for class org.sbml.jsbml.Creator
-
- Creator(String, String, String, String) - Constructor for class org.sbml.jsbml.Creator
-
- creator - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- csc(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- csc(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- csc(double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the csc of n
- csch(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- csch(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- csch(double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the csch of n
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- currentToken - Variable in exception org.sbml.jsbml.math.parser.ParseException
-
This is the last token that has been consumed successfully.
- currentToken - Variable in exception org.sbml.jsbml.text.parser.ParseException
-
This is the last token that has been consumed successfully.
- CUSTOM_RDF - Static variable in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
A Constant String that is used to store any remaining children
or attributes after having removed the standard SBML RDF elements and attributes.
- CVTerm - Class in org.sbml.jsbml
-
Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
of a SBML component.
- CVTerm() - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm(CVTerm) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm(CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm(CVTerm.Type, CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm(XMLNode) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm.Qualifier - Enum in org.sbml.jsbml
-
This enum list all the possible MIRIAM qualifiers.
- CVTerm.Type - Enum in org.sbml.jsbml
-
This enum list all the possible MIRIAM qualifiers type.
- CVTermFilter - Class in org.sbml.jsbml.util.filters
-
This filter accepts only instances of
CVTerm with a certain content
or instances of
SBase that are annotated with appropriate
CVTerm objects.
- CVTermFilter() - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
-
- CVTermFilter(CVTerm.Qualifier) - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
-
- CVTermFilter(CVTerm.Qualifier, String) - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
-
- CycleDetectionTreeNode - Class in org.sbml.jsbml.validator.offline.constraints.helper
-
- CycleDetectionTreeNode(String) - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-