- 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
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParser.JJCalls
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2.JJCalls
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3.JJCalls
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2.JJCalls
-
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Generate ParseException.
- generateSubModel(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
Generates a sub-model containing the elements passed as argument and all
the necessary dependencies.
- generateSubModel(Model, String[], String[], String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
Generates a sub-model containing the elements passed as argument and all
the necessary dependencies.
- generateSubModel(Model, String[], String[], String[], String[], String[], boolean, boolean, boolean, boolean, boolean) - Static method in class org.sbml.jsbml.util.SubModel
-
Creates a sub-model with the option to ignore certain items.
- geq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode representing greater or equal for
the two given nodes.
- geq(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- geq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Greater equal.
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- geq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Greater equal.
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- get(int) - Method in class org.sbml.jsbml.ListOf
-
Returns the element at the specified position in this list or null if the index is negative or too big.
- get(String) - Method in class org.sbml.jsbml.ListOf
-
Gets the list element which has the id 'id'.
- getAbout() - Method in class org.sbml.jsbml.Annotation
-
Returns the about String of this object.
- getActivator() - Static method in class org.sbml.jsbml.SBO
-
- getAllostericActivator() - Static method in class org.sbml.jsbml.SBO
-
Describes an activator (ligand) which binds at a site other than the active site, resulting in a conformational change, enhancing the activity of the enzyme.
- getAllostericInhibitor() - Static method in class org.sbml.jsbml.SBO
-
An inhibitor whose binding to an enzyme results in a conformational change, resulting in a loss of enzymatic activity.
- getAllowsChildren() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getAllowsChildren() - Method in class org.sbml.jsbml.AbstractSBase
-
- getAllowsChildren() - Method in class org.sbml.jsbml.Annotation
-
- getAllowsChildren() - Method in class org.sbml.jsbml.ASTNode
-
- getAllowsChildren() - Method in class org.sbml.jsbml.Creator
-
- getAllowsChildren() - Method in class org.sbml.jsbml.CVTerm
-
- getAllowsChildren() - Method in class org.sbml.jsbml.Event
-
- getAllowsChildren() - Method in class org.sbml.jsbml.History
-
- getAllowsChildren() - Method in class org.sbml.jsbml.ListOf
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTFunction
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTNumber
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getAllowsChildren() - Method in class org.sbml.jsbml.Model
-
- getAllowsChildren() - Method in class org.sbml.jsbml.Reaction
-
- getAllowsChildren() - Method in class org.sbml.jsbml.SBMLDocument
-
- getAllowsChildren() - Method in class org.sbml.jsbml.SpeciesReference
-
- getAllowsChildren() - Method in class org.sbml.jsbml.UnitDefinition
-
- getAllowsChildren() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- getAllowsChildren() - Method in class org.sbml.jsbml.xml.XMLNode
-
- getAndReplacement() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
Gets the String that will be used to replace ' and ' (the mathML
<and> element) in the boolean expressions.
- getAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
-
- getAnnotation() - Method in interface org.sbml.jsbml.SBase
-
Returns the content of the 'annotation' sub-element of this object as an
Annotation instance.
- getAnnotationBuilder() - Method in class org.sbml.jsbml.Annotation
-
Deprecated.
- getAnnotationString() - Method in class org.sbml.jsbml.AbstractSBase
-
Returns the
Annotation of this SBML object as a
String.
- getAnnotationString() - Method in interface org.sbml.jsbml.SBase
-
Returns the content of the 'annotation' sub-element of this object as a
String.
- getAntisenseRNA() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id for antisense RNA.
- getAreaUnits() - Method in class org.sbml.jsbml.Model
-
Returns the area units ID of this
Model.
- getAreaUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getArgument(int) - Method in class org.sbml.jsbml.FunctionDefinition
-
Get the nth argument to this function.
- getArgument(String) - Method in class org.sbml.jsbml.FunctionDefinition
-
- getArgumentCount() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getAssignmentRuleByVariable(String) - Method in class org.sbml.jsbml.Model
-
- getAssociation() - Static method in class org.sbml.jsbml.SBO
-
Interaction between several biochemical entities that results in the
formation of a non-covalent complex
- getAttributes() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getAttributes() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the attributes of this element.
- getAttributesLength() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the number of attributes in the attributes set.
- getAttrIndex(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the index of an attribute with the given local name.
- getAttrIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the index of an attribute with the given local name and namespace URI.
- getAttrIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the index of an attribute with the given
XMLTriple.
- getAttrName(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the local name of an attribute in the attributes set in this
XMLToken (by position).
- getAttrPrefix(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the prefix of an attribute in the attribute set in this
XMLToken (by position).
- getAttrPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the prefixed name of an attribute in the attribute set in this
XMLToken (by position).
- getAttrURI(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the namespace URI of an attribute in the attribute set in this
XMLToken (by position).
- getAttrValue(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the value of an attribute in the attribute set in this
XMLToken
(by position).
- getAttrValue(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns a value of an attribute with the given local name.
- getAttrValue(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns a value of an attribute with the given local name and namespace URI.
- getAttrValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns a value of an attribute with the given
XMLTriple.
- getBase() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- getBasis() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- getBeginColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token beginning line number.
- getBeginLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token beginning line number.
- getBindingActivator() - Static method in class org.sbml.jsbml.SBO
-
An essential activator that affects the apparent value of the Michaelis
constant(s).
- getBiochemicalReaction() - Static method in class org.sbml.jsbml.SBO
-
An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.
- getBiologicalQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- getBody() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getBoundaryCondition() - Method in class org.sbml.jsbml.Species
-
- getBundle(String) - Static method in class org.sbml.jsbml.util.ResourceManager
-
Loads the ResourceBundle with the given name for the default
Locale.
- getBundle(String, Locale) - Static method in class org.sbml.jsbml.util.ResourceManager
-
Loads the ResourceBundle with the given name for the given
Locale.
- getBvarCount() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- getBytesFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource
-
Gets the byte data from a file at the given resource location.
- getBytesFromStream(InputStream) - Method in class org.sbml.jsbml.resources.Resource
-
Gets the byte data from a file.
- getCalculatedStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
-
This method computes the fraction of the stoichiometry and the
denominator.
- getCatalysis() - Static method in class org.sbml.jsbml.SBO
-
Modification of the velocity of a reaction by lowering the energy of the
transition state.
- getCatalyst() - Static method in class org.sbml.jsbml.SBO
-
Substance that accelerates the velocity of a chemical reaction without
itself being consumed or transformed.
- getCatalyticActivator() - Static method in class org.sbml.jsbml.SBO
-
- getCategory() - Method in exception org.sbml.jsbml.SBMLError
-
- getCategory() - Method in exception org.sbml.jsbml.SBMLException
-
- getCategory() - Method in class org.sbml.jsbml.util.Detail
-
- getCharacter() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of this node as a single character.
- getCharacters() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getCharacters() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the text of this element.
- getCharge() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- getCheckCategories() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Returns the list of all enabled check categories.
- getChild(int) - Method in class org.sbml.jsbml.ASTNode
-
Gets a child of this node according to an index number.
- getChild() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
Get the child of this node
- getChild(int) - Method in class org.sbml.jsbml.xml.XMLNode
-
Returns the child
XMLNode at index childIndex.
- getChildAt(int) - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getChildAt(int) - Method in class org.sbml.jsbml.AbstractSBase
-
- getChildAt(int) - Method in class org.sbml.jsbml.Annotation
-
- getChildAt(int) - Method in class org.sbml.jsbml.ASTNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.Constraint
-
- getChildAt(int) - Method in class org.sbml.jsbml.Creator
-
- getChildAt(int) - Method in class org.sbml.jsbml.CVTerm
-
- getChildAt(int) - Method in class org.sbml.jsbml.Event
-
- getChildAt(int) - Method in class org.sbml.jsbml.History
-
- getChildAt(int) - Method in class org.sbml.jsbml.KineticLaw
-
- getChildAt(int) - Method in class org.sbml.jsbml.ListOf
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTFunction
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTNumber
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getChildAt(int) - Method in class org.sbml.jsbml.Model
-
- getChildAt(int) - Method in class org.sbml.jsbml.Reaction
-
- getChildAt(int) - Method in class org.sbml.jsbml.SBMLDocument
-
- getChildAt(int) - Method in class org.sbml.jsbml.SpeciesReference
-
- getChildAt(int) - Method in class org.sbml.jsbml.UnitDefinition
-
- getChildAt(int) - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- getChildAt(int) - Method in class org.sbml.jsbml.xml.XMLNode
-
- getChildCount() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getChildCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getChildCount() - Method in class org.sbml.jsbml.Annotation
-
- getChildCount() - Method in class org.sbml.jsbml.ASTNode
-
- getChildCount() - Method in class org.sbml.jsbml.Constraint
-
- getChildCount() - Method in class org.sbml.jsbml.Creator
-
- getChildCount() - Method in class org.sbml.jsbml.CVTerm
-
- getChildCount() - Method in class org.sbml.jsbml.Event
-
- getChildCount() - Method in class org.sbml.jsbml.History
-
- getChildCount() - Method in class org.sbml.jsbml.KineticLaw
-
- getChildCount() - Method in class org.sbml.jsbml.ListOf
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTFunction
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTNumber
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getChildCount() - Method in class org.sbml.jsbml.Model
-
- getChildCount() - Method in class org.sbml.jsbml.Reaction
-
- getChildCount() - Method in class org.sbml.jsbml.SBMLDocument
-
- getChildCount() - Method in class org.sbml.jsbml.SpeciesReference
-
- getChildCount() - Method in class org.sbml.jsbml.UnitDefinition
-
- getChildCount() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- getChildCount() - Method in class org.sbml.jsbml.xml.XMLNode
-
- getChildElement(String, String) - Method in class org.sbml.jsbml.xml.XMLNode
-
Gets the first direct child element of this
XMLNode with the given local name and namespace.
- getChildElements(String, String) - Method in class org.sbml.jsbml.xml.XMLNode
-
Gets all the direct children of this
XMLNode with the given local
name and namespace.
- getChildren() - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of children of the current ASTNode.
- getChildren() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction.
- getChildren() - Method in class org.sbml.jsbml.ontology.Term
-
Returns a set of all the children Term.
- getClassName() - Method in class org.sbml.jsbml.ASTNode
-
Returns the class name of the mathML element represented by this ASTNode.
- getCode() - Method in exception org.sbml.jsbml.SBMLError
-
- getCode() - Method in exception org.sbml.jsbml.SBMLException
-
- getColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Deprecated.
- getColumn() - Method in exception org.sbml.jsbml.SBMLError
-
Returns the column where this
SBMLError happened.
- getColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Deprecated.
- getColumn() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the column at which this
XMLToken occurred in the input
document or data stream.
- getCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
Returns the value of the referenced compartment.
- getCompartment(int) - Method in class org.sbml.jsbml.Model
-
Gets the n
th Compartment instance of the
listOfCompartments.
- getCompartment(String) - Method in class org.sbml.jsbml.Model
-
Gets the
Compartment of the listOfCompartments which has 'id' as
id.
- getCompartment() - Method in class org.sbml.jsbml.Reaction
-
Only available if Level >= 3.
- getCompartment() - Static method in class org.sbml.jsbml.SBO
-
Physical compartment.
- getCompartment() - Method in class org.sbml.jsbml.Species
-
- getCompartmentCount() - Method in class org.sbml.jsbml.Model
-
- getCompartmentInstance() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- getCompartmentInstance() - Method in class org.sbml.jsbml.Reaction
-
- getCompartmentInstance() - Method in class org.sbml.jsbml.Species
-
- getCompartmentType() - Method in class org.sbml.jsbml.Compartment
-
- getCompartmentType(int) - Method in class org.sbml.jsbml.Model
-
- getCompartmentType(String) - Method in class org.sbml.jsbml.Model
-
- getCompartmentTypeCount() - Method in class org.sbml.jsbml.Model
-
- getCompartmentTypeInstance() - Method in class org.sbml.jsbml.Compartment
-
Deprecated.
- getCompetitiveInhibitor() - Static method in class org.sbml.jsbml.SBO
-
Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, by stericaly hindering the interaction between reactants.
- getCompleteInhibitor() - Static method in class org.sbml.jsbml.SBO
-
- getComplex() - Static method in class org.sbml.jsbml.SBO
-
- getComplexAssembly() - Static method in class org.sbml.jsbml.SBO
-
Interaction between several biochemical entities that results in the formation of a non-covalent complex
Also known as non-covalent binding
- getConservationLaw() - Static method in class org.sbml.jsbml.SBO
-
- getConstant() - Method in class org.sbml.jsbml.SpeciesReference
-
- getConstant() - Method in class org.sbml.jsbml.Symbol
-
- getConstant() - Method in interface org.sbml.jsbml.Variable
-
- getConstantAvogadro(String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getConstantAvogadro(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantE() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getConstantE() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantFalse() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getConstantFalse() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantPi() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getConstantPi() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getConstantPi() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantTrue() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getConstantTrue() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstraint(int) - Method in class org.sbml.jsbml.Model
-
Gets the nth Constraint object in this Model.
- getConstraintCount() - Method in class org.sbml.jsbml.Model
-
- getConstraints() - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
Returns the members of the group.
- getConstraintsCount() - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
Returns the number of constraints in this group
- getConstraintsForAttribute(Class<?>, String, int, int) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
Returns all constraints which
- getConstraintsForAttribute(Class<?>, String, int, int, Set<Class<?>>) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
Returns all constraints which
- getConstraintsForClass(Class<?>, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
- getConstraintsForClass(Class<?>, SBMLValidator.CHECK_CATEGORY[], int, int) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
- getConstraintsForClass(Class<?>, SBMLValidator.CHECK_CATEGORY[], int, int, Set<Class<?>>) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
- getConstraintType() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Gets the Class on which the root constraint is typed.
- getConsumption() - Static method in class org.sbml.jsbml.SBO
-
Decrease in amount of a material or conceptual entity.
- getContinuousFramework() - Static method in class org.sbml.jsbml.SBO
-
- getConversion() - Static method in class org.sbml.jsbml.SBO
-
Biochemical reaction that results in the modification of some covalent bonds.
- getConversionFactor() - Method in class org.sbml.jsbml.Model
-
Returns the conversionFactor ID of this
Model.
- getConversionFactor() - Method in class org.sbml.jsbml.Species
-
- getConversionFactorInstance() - Method in class org.sbml.jsbml.Model
-
Returns the Parameter instance which has the conversionFactorID of this
Model as id.
- getConversionFactorInstance() - Method in class org.sbml.jsbml.Species
-
- getCreatedDate() - Method in class org.sbml.jsbml.History
-
Returns the createdDate from the
History.
- getCreator(int) - Method in class org.sbml.jsbml.History
-
- getCreatorCount() - Method in class org.sbml.jsbml.History
-
- getCVTerm(int) - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTerm(int) - Method in class org.sbml.jsbml.Annotation
-
Returns the CVTerm at the ith position in the list of CVTerms.
- getCVTerm(int) - Method in interface org.sbml.jsbml.SBase
-
Returns the
CVTerm instance at the position 'index' in the list of
CVTerms of this object.
- getCVTermCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTermCount() - Method in class org.sbml.jsbml.Annotation
-
- getCVTermCount() - Method in interface org.sbml.jsbml.SBase
-
- getCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTerms() - Method in interface org.sbml.jsbml.SBase
-
Returns the list of
CVTerms of this object.
- getDataType(ASTNode) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
Returns the data type of an
ASTNode.
- getDeclaredNamespaces() - Method in class org.sbml.jsbml.AbstractSBase
-
- getDeclaredNamespaces() - Method in class org.sbml.jsbml.Annotation
-
- getDeclaredNamespaces() - Method in interface org.sbml.jsbml.SBase
-
Returns all the namespaces declared on this object.
- getDefaultIndentChar() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns the default symbol to be used to indent new elements in the XML
representation of SBML data structures.
- getDefaultIndentCount() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns the default number of indent symbols to be concatenated at the
beginning of a new block in an XML representation of SBML data
structures.
- getDefaultLevel() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the default SBML Level of new SBMLDocument objects.
- getDefaultPossibleEnzymes() - Static method in class org.sbml.jsbml.SBO
-
Creates and returns a list of molecule types accepted as an enzyme by
default.
- getDefaultVersion() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the default Version of new SBMLDocument objects.
- getDefinedSpecies(Reaction) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- getDefinition() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the definition of this
Term, which is stored in the
corresponding OBO file under the key
def.
- getDefinitionURIavogadro() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getDefinitionURIdelay() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getDefinitionURItime() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
-
Returns the definitionURL
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Returns the definitionURL of the MathML element represented by this ASTCiFunctionNode
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getDegradation() - Static method in class org.sbml.jsbml.SBO
-
Complete disappearance of a physical entity.
- getDelay() - Method in class org.sbml.jsbml.Event
-
- getDelayCount() - Method in class org.sbml.jsbml.Model
-
- getDenominator() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of the denominator of this node.
- getDenominator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Get the denominator value of this node.
- getDenominator() - Method in class org.sbml.jsbml.SpeciesReference
-
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Compartment
-
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Reaction
-
- getDerivedUnitDefinition() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit
-
Derives the unit of this quantity and tries to identify an
equivalent
UnitDefinition within the corresponding
Model.
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Species
-
- getDerivedUnitDefinition() - Method in class org.sbml.jsbml.SpeciesReference
-
- getDerivedUnits() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getDerivedUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- getDerivedUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getDerivedUnits() - Method in class org.sbml.jsbml.Reaction
-
- getDerivedUnits() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit
-
Derives the unit of this quantity.
- getDerivedUnits() - Method in class org.sbml.jsbml.Species
-
- getDerivedUnits() - Method in class org.sbml.jsbml.SpeciesReference
-
- getDerivedVariable() - Method in class org.sbml.jsbml.AlgebraicRule
-
Provides a convenient way to obtain the variable whose amount
is determined by this rule.
- getDetail() - Method in exception org.sbml.jsbml.SBMLError
-
- getDiscreteFramework() - Static method in class org.sbml.jsbml.SBO
-
- getDissociation() - Static method in class org.sbml.jsbml.SBO
-
Transformation of a non-covalent complex that results in the formation of
several independent biochemical entities.
- getDNA() - Static method in class org.sbml.jsbml.SBO
-
Polymer composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.
- getDNASegment() - Static method in class org.sbml.jsbml.SBO
-
Fragment or region of a DNA macromolecule.
- getDocument() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getDrug() - Static method in class org.sbml.jsbml.SBO
-
- getElementByMetaId(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getElementByMetaId(String) - Method in interface org.sbml.jsbml.SBase
-
Returns the first child element found that has the given metaid.
- getElementByMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- getElementBySId(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getElementBySId(String) - Method in class org.sbml.jsbml.Model
-
Returns an
SBase element of the model that has the given 'id'
as id or
null if no element is found.
- getElementBySId(String) - Method in interface org.sbml.jsbml.SBase
-
Returns the first child element found that has the given id.
- getElementName() - Method in class org.sbml.jsbml.AbstractSBase
-
- getElementName() - Method in class org.sbml.jsbml.AssignmentRule
-
- getElementName() - Method in class org.sbml.jsbml.ListOf
-
- getElementName() - Method in class org.sbml.jsbml.LocalParameter
-
- getElementName() - Method in interface org.sbml.jsbml.SBase
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.jsbml.SBMLDocument
-
- getElementName() - Method in class org.sbml.jsbml.Species
-
- getElementName() - Method in class org.sbml.jsbml.SpeciesReference
-
- getElementName() - Method in class org.sbml.jsbml.util.ListOfWithName
-
Deprecated.
- getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
-
Returns a name corresponding to this Qualifier Object.
- getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Type
-
Returns a name corresponding to this Type of qualifier Object.
- getElementNameEquivalentToQualifier(CVTerm.Qualifier) - Static method in class org.sbml.jsbml.Annotation
-
- getElementNamespace() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getElementNamespace() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getElementNamespace() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the XML namespace (URI) of the package extension of this plugin object.
- getElementNamespace() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the XML namespace (URI) of the package extension of this plugin object.
- getEmail() - Method in class org.sbml.jsbml.Creator
-
Returns the email from the
Creator.
- getEmptySet() - Static method in class org.sbml.jsbml.SBO
-
Empty set is used to represent the source of a creation process or the
result of a degradation process.
- getEnabledPackageNamespace(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Return the package namespace enabled on this SBMLDocument or null if the
package
is not enabled.
- getEncoding() - Method in class org.sbml.jsbml.ASTNode
-
Returns the encoding of the mathML element represented by this ASTNode.
- getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- getEncoding() - Method in interface org.sbml.jsbml.math.ASTCSymbolNode
-
Returns the encoding of the MathML element represented by
this
ASTCSymbolNode
- getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getEndColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token end column number.
- getEndColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token end column number.
- getEndLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token end line number.
- getEndLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token end line number.
- getEnthalpyChange() - Static method in class org.sbml.jsbml.SBO
-
Change in enthalpy observed in the constituents of a thermodynamic system when undergoing
a transformation or chemical reaction.
- getEntity() - Static method in class org.sbml.jsbml.SBO
-
- getEntropyChange() - Static method in class org.sbml.jsbml.SBO
-
The increase or decrease of the entropy of a system.
- getEnzymaticCatalysis() - Static method in class org.sbml.jsbml.SBO
-
- getEquilibriumConstant() - Static method in class org.sbml.jsbml.SBO
-
Quantity characterizing a chemical equilibrium in a chemical reaction, which is a useful tool to
determine the concentration of various reactants or products in a system where chemical equilibrium
occurs.
- getError(int) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the ith error or warning encountered during consistency
checking.
- getError(long) - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the
nth
SBMLError object in this log.
- getErrorCode() - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraint
-
- getErrorCode() - Method in interface org.sbml.jsbml.validator.offline.constraints.AnyConstraint
-
Returns the error code from this constraints.
- getErrorCount() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during consistency
checking.
- getErrorCount() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged.
- getErrorId() - Method in exception org.sbml.jsbml.xml.XMLException
-
- getErrorLog() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns a collection of all
SBMLErrors reflecting
problems in the overall data structure of this
SBMLDocument.
- getErrorLog() - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- getErrorsBySeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog
-
- getEssentialActivator() - Static method in class org.sbml.jsbml.SBO
-
- getEvent(int) - Method in class org.sbml.jsbml.Model
-
Gets the nth Event object in this Model.
- getEvent(String) - Method in class org.sbml.jsbml.Model
-
Gets the
Event which as the given
id as id.
- getEvent() - Static method in class org.sbml.jsbml.SBO
-
- getEventAssignment(int) - Method in class org.sbml.jsbml.Event
-
Gets an element from the listOfEventAssignments at the given index.
- getEventAssignment(String) - Method in class org.sbml.jsbml.Event
-
Gets an element from the listOfEventAssignments, with the given id.
- getEventAssignmentCount() - Method in class org.sbml.jsbml.Event
-
- getEventAssignmentCount() - Method in class org.sbml.jsbml.Model
-
- getEventCount() - Method in class org.sbml.jsbml.Model
-
- getExcerpt() - Method in exception org.sbml.jsbml.SBMLError
-
Returns a fragment of the original XML file that induced the error.
- getExponent() - Method in class org.sbml.jsbml.ASTNode
-
Gets the exponent value of this ASTNode.
- getExponent() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Get the exponent value of this node.
- getExponent() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- getExponent() - Method in class org.sbml.jsbml.Unit
-
- getExponentAsDouble() - Method in class org.sbml.jsbml.Unit
-
- getExtendedASTNode() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getExtendedASTNode() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the object that is extended by this plug-in.
- getExtendedSBase() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getExtendedSBase() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the SBase object that is extended by this plug-in.
- getExtension(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtension(String) - Method in class org.sbml.jsbml.ASTNode
-
Returns the
ASTNodePlugin object which matches this package
name or URI.
- getExtension(String) - Method in interface org.sbml.jsbml.SBase
-
Returns the
SBasePlugin extension object which matches this package
name or URI.
- getExtensionCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtensionCount() - Method in class org.sbml.jsbml.ASTNode
-
- getExtensionCount() - Method in interface org.sbml.jsbml.SBase
-
- getExtensionPackages() - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtensionPackages() - Method in class org.sbml.jsbml.ASTNode
-
- getExtensionPackages() - Method in interface org.sbml.jsbml.SBase
-
- getExtentUnits() - Method in class org.sbml.jsbml.Model
-
Returns the extent units ID of this
Model.
- getExtentUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns the
UnitDefinition instance which has the extent units ID
of this Model as id.
- getFamilyName() - Method in class org.sbml.jsbml.Creator
-
Returns the familyName from the
Creator.
- getFast() - Method in class org.sbml.jsbml.Reaction
-
Deprecated.
- getFile() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the file containing the xml error log representation.
- getFilters() - Method in class org.sbml.jsbml.util.filters.AndFilter
-
- getFirst() - Method in class org.sbml.jsbml.ListOf
-
Returns the first element in this list.
- getFirstElementIndex(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
-
Return the index of the first child of type 'Element' for the given
XMLNode.
- getFormats(String) - Method in class org.sbml.jsbml.util.XMLResourceBundleControl
-
- getFormula() - Method in class org.sbml.jsbml.AbstractMathContainer
-
Deprecated.
- getFormula() - Method in interface org.sbml.jsbml.MathContainer
-
- getFromCache(int) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- getFullAnnotation() - Method in class org.sbml.jsbml.Annotation
-
- getFullAnnotationString() - Method in class org.sbml.jsbml.Annotation
-
- getFunctionalCompartment() - Static method in class org.sbml.jsbml.SBO
-
- getFunctionalEntity() - Static method in class org.sbml.jsbml.SBO
-
- getFunctionDefinition(int) - Method in class org.sbml.jsbml.Model
-
- getFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
- getFunctionDefinitionCount() - Method in class org.sbml.jsbml.Model
-
- getGene() - Static method in class org.sbml.jsbml.SBO
-
A gene is an informational molecule segment.
- getGeneCodingRegion() - Static method in class org.sbml.jsbml.SBO
-
- getGeneric() - Static method in class org.sbml.jsbml.SBO
-
- getGeneticInteraction() - Static method in class org.sbml.jsbml.SBO
-
A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone.
- getGibbsFreeEnergyChange() - Static method in class org.sbml.jsbml.SBO
-
The increase or decrease of the Gibbs free energy of a system.
- getGivenName() - Method in class org.sbml.jsbml.Creator
-
Returns the givenName from the
Creator.
- getHashMap() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Constraints can use this HashMap to store additional
information.
- getHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
-
- getHillEquation() - Static method in class org.sbml.jsbml.SBO
-
- getHistory() - Method in class org.sbml.jsbml.AbstractSBase
-
- getHistory() - Method in class org.sbml.jsbml.Annotation
-
Returns the
History of the Annotation.
- getHistory() - Method in interface org.sbml.jsbml.SBase
-
Returns the
History instance of this object.
- getId() - Method in class org.sbml.jsbml.AbstractSBase
-
- getId() - Method in class org.sbml.jsbml.ASTNode
-
Returns the id of the mathML element represented by this ASTNode.
- getId() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getId() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Get the id of this node
- getId() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getId() - Method in interface org.sbml.jsbml.NamedSBase
-
Returns the id of the element if it is set, an empty string otherwise.
- getId() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the SBO identifier of this
Term, for instance:
SBO:0000031.
- getId() - Method in interface org.sbml.jsbml.SBase
-
Returns the id of the element if it is set, an empty string otherwise.
- getId() - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
-
- getId() - Method in class org.sbml.jsbml.util.filters.IdFilter
-
Returns the id that will be searched for by the filter.
- getId() - Method in class org.sbml.jsbml.util.filters.NameFilter
-
Returns the id.
- getId() - Method in class org.sbml.jsbml.util.filters.SIdFilter
-
Returns the id that will be searched for by the filter.
- getIdManager(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
- getIdOrName(NamedSBase) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- GetImage() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token literal value.
- GetImage() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token literal value.
- getIndent() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getIndent() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
Returns the indent
- getIndentationChar() - Method in class org.sbml.jsbml.SBMLWriter
-
Gives the symbol that is used to indent the SBML output for a better
structure and to improve human-readability.
- getIndentationChar() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Gives the symbol that is used to indent the SBML output for a better
structure and to improve human-readability.
- getIndentationCount() - Method in class org.sbml.jsbml.SBMLWriter
-
Gives the number of indent symbols that are inserted in a line to better
structure the SBML output.
- getIndentationCount() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Gives the number of indent symbols that are inserted in a line to better structure the SBML output.
- getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
Returns true if indenting
- getIndex(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getIndex(TreeNode) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getIndex(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the index of an attribute with the given name.
- getIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the index of an attribute with the given local name and namespace URI.
- getIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the index of an attribute with the given
XMLTriple.
- getIndex(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the index of an XML namespace declaration by URI.
- getIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the index of an XML namespace declaration by prefix.
- getInhibition() - Static method in class org.sbml.jsbml.SBO
-
Negative modulation of the execution of a process.
- getInhibitor() - Static method in class org.sbml.jsbml.SBO
-
Substance that decreases the probability of a chemical reaction without
itself being consumed or transformed by the reaction.
- getInitialAmount() - Method in class org.sbml.jsbml.Species
-
- getInitialAssignment(int) - Method in class org.sbml.jsbml.Model
-
- getInitialAssignment(String) - Method in class org.sbml.jsbml.Model
-
- getInitialAssignmentById(String) - Method in class org.sbml.jsbml.Model
-
- getInitialAssignmentBySymbol(String) - Method in class org.sbml.jsbml.Model
-
- getInitialAssignmentCount() - Method in class org.sbml.jsbml.Model
-
- getInitialConcentration() - Method in class org.sbml.jsbml.Species
-
- getInitialValue() - Method in class org.sbml.jsbml.Trigger
-
- getInstance() - Static method in class org.sbml.jsbml.math.ASTUnknown
-
- getInstance() - Static method in class org.sbml.jsbml.resources.Resource
-
- getInstance() - Static method in class org.sbml.jsbml.util.JAXPFacade
-
Creates and returns a new JAXPFacade.
- getInstance(String) - Static method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- getInstance() - Static method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
- getInteger() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of this node as an integer.
- getInteger() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
Get the integer value of this node.
- getInteger(ASTNode) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- getInteraction() - Static method in class org.sbml.jsbml.SBO
-
- getIon() - Static method in class org.sbml.jsbml.SBO
-
- getIonChannel() - Static method in class org.sbml.jsbml.SBO
-
- getIonicStrength() - Static method in class org.sbml.jsbml.SBO
-
A combined (weighted) measure of the concentration of all electrolytes present in a
solution.
- getIrreversibleInhibitor() - Static method in class org.sbml.jsbml.SBO
-
An inhibitor which binds irreversibly with the enzyme such that it cannot be removed, and abolishes enzymatic function.
- getJSBMLDottedVersion() - Static method in class org.sbml.jsbml.JSBML
-
Returns the JSBML version as a string of the form '1.2.3'.
- getJSBMLVersion() - Static method in class org.sbml.jsbml.JSBML
-
Returns the JSBML version as an integer: version 1.2.3 becomes 123.
- getJSBMLVersionString() - Static method in class org.sbml.jsbml.JSBML
-
Returns the JSBML version as a string: version 1.2.3 becomes '123'.
- getKey() - Method in class org.sbml.jsbml.util.Pair
-
- getKeys() - Method in class org.sbml.jsbml.util.XMLResourceBundleControl.XMLResourceBundle
-
- getKind() - Method in class org.sbml.jsbml.Unit
-
- getKineticConstant() - Static method in class org.sbml.jsbml.SBO
-
- getKineticLaw() - Method in class org.sbml.jsbml.Reaction
-
- getKineticLawCount() - Method in class org.sbml.jsbml.Model
-
- getL() - Method in class org.sbml.jsbml.util.ValuePair
-
- getLang() - Method in class org.sbml.jsbml.util.Message
-
- getLast() - Method in class org.sbml.jsbml.ListOf
-
Returns the last element in this list.
- getLastElementOf(ListOf<? extends T>) - Method in class org.sbml.jsbml.Model
-
Returns the last element added in the given list.
- getLastIndexOf(XMLNode, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getLeftChild() - Method in class org.sbml.jsbml.ASTNode
-
Gets the left child of this node.
- getLeftChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- getLength() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the number of attributes in the set.
- getLength() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Returns the total number of URI-and-prefix pairs stored in this
particular
XMLNamespaces instance.
- getLengthUnits() - Method in class org.sbml.jsbml.Model
-
Returns the length units ID of this
Model.
- getLengthUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getLevel() - Method in class org.sbml.jsbml.AbstractSBase
-
- getLevel() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getLevel() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getLevel() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the SBML level of this plugin object.
- getLevel() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the SBML level of this plugin object.
- getLevel() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Returns the level of the SBML document that was the basis to create this
ASTNode2Value.
- getLevel() - Method in interface org.sbml.jsbml.SBase
-
Returns the SBML Level of the overall SBML document.
- getLevel() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
Returns the level of the SBML document that was the basis to create this
ASTNodeValue.
- getLevel() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getLevel() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Returns the used level of SBML
- getLevelAndVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- getLevelAndVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the Level and Version combination of this
SBase.
- getLevelAndVersion() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
This value determines which constraints will be loaded and in which way
broken constraints will be logged.
- getLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Deprecated.
- getLine() - Method in exception org.sbml.jsbml.SBMLError
-
Returns the line where this
SBMLError happened.
- getLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Deprecated.
- getLine() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the line at which this
XMLToken occurred in the input document
or data stream.
- getListOfCompartments() - Method in class org.sbml.jsbml.Model
-
Returns the listOfCompartments of this
Model.
- getListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
- getListOfConstraints() - Method in class org.sbml.jsbml.Model
-
Returns the listOfConstraints of this
Model.
- getListOfCount() - Method in class org.sbml.jsbml.Model
-
- getListOfCreators() - Method in class org.sbml.jsbml.History
-
- getListOfCVTerms() - Method in class org.sbml.jsbml.Annotation
-
Returns the list of CVTerms.
- getListOfErrors() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns a collection of all
SBMLErrors reflecting
problems in the overall data structure of this
SBMLDocument.
- getListOfEventAssignments() - Method in class org.sbml.jsbml.Event
-
Returns the listOfEventAssignments.
- getListOfEvents() - Method in class org.sbml.jsbml.Model
-
Returns the listOfEvents of this
Model.
- getListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model
-
Returns the listOfFunctionDefinitions of this
Model.
- getListOfInitialAssignments() - Method in class org.sbml.jsbml.Model
-
Returns the listOfInitialAssignments of this
Model.
- getListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getListOfModifiedDates() - Method in class org.sbml.jsbml.History
-
Get the list of modifiedDate objects in this
History.
- getListOfModifiers() - Method in class org.sbml.jsbml.Reaction
-
- getListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- getListOfNodes() - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of children of the current ASTNode.
- getListOfNodes(Filter) - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of children of the current ASTNode that satisfy the
given filter.
- getListOfNodes() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction.
- getListOfNodes(Filter) - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction that satisfy the
given filter.
- getListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getListOfParameters() - Method in class org.sbml.jsbml.Model
-
- getListOfPredefinedUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
- getListOfProducts() - Method in class org.sbml.jsbml.Reaction
-
- getListOfReactants() - Method in class org.sbml.jsbml.Reaction
-
- getListOfReactions() - Method in class org.sbml.jsbml.Model
-
Returns the listOfReactions of this
Model.
- getListOfRules() - Method in class org.sbml.jsbml.Model
-
Returns the listOfRules of this
Model.
- getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- getListOfSBMLElementsToWrite(Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
-
Returns the list of children of the objectToWrite.
- getListOfSemanticsAnnotations() - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of semantics annotations of this node.
- getListOfSpecies() - Method in class org.sbml.jsbml.Model
-
- getListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
-
- getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getListOfTreeNodeChangeListeners() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
Returns the listOfUnitDefinitions of this
Model.
- getListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
- getLocalParameter(int) - Method in class org.sbml.jsbml.KineticLaw
-
- getLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
-
- getLocalParameterCount() - Method in class org.sbml.jsbml.KineticLaw
-
- getLocalParameterCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of parameters that are contained within kineticLaws in
the reactions of this model.
- getLogger() - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
-
- getLogicalFramework() - Static method in class org.sbml.jsbml.SBO
-
- getMacromolecule() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO term id for macromolecule.
- getManager() - Static method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- getMantissa() - Method in class org.sbml.jsbml.ASTNode
-
Gets the mantissa value of this node.
- getMantissa() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Get the mantissa value of this node.
- getMatching() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
-
Returns the determined matching
- getMaterialEntity() - Static method in class org.sbml.jsbml.SBO
-
- getMath() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getMath() - Method in interface org.sbml.jsbml.MathContainer
-
- getMathContainerCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of elements that can contain math in the
Model .
- getMathematicalExpression() - Static method in class org.sbml.jsbml.SBO
-
- getMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns the class of the MathML element represented by
this
ASTNode2
- getMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getMathMLString() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getMathMLString() - Method in interface org.sbml.jsbml.MathContainer
-
If
MathContainer.isSetMath() returns true, this method returns the
corresponding MathML
String, otherwise an empty
String
will be returned.
- getMessage() - Method in class org.sbml.jsbml.Constraint
-
- getMessage() - Method in error org.sbml.jsbml.math.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMessage() - Method in exception org.sbml.jsbml.SBMLError
-
- getMessage() - Method in error org.sbml.jsbml.text.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMessage() - Method in class org.sbml.jsbml.util.Message
-
- getMessageInstance() - Method in exception org.sbml.jsbml.SBMLError
-
- getMessageString() - Method in class org.sbml.jsbml.Constraint
-
Returns the message of this
Constraint as an XML
String.
- getMessengerRNA() - Static method in class org.sbml.jsbml.SBO
-
- getMetaId() - Method in class org.sbml.jsbml.AbstractSBase
-
- getMetaId() - Method in interface org.sbml.jsbml.SBase
-
Returns the metaid of this element.
- getMetaId() - Method in class org.sbml.jsbml.util.filters.MetaIdFilter
-
Returns the metaid that will be searched for by the filter.
- getModel() - Method in class org.sbml.jsbml.AbstractSBase
-
- getModel() - Method in interface org.sbml.jsbml.SBase
-
Returns the
Model object in which the current
SBase is
located.
- getModel() - Method in class org.sbml.jsbml.SBMLDocument
-
- getModel() - Method in class org.sbml.jsbml.util.ModelBuilder
-
- getModelHistory() - Method in class org.sbml.jsbml.Model
-
- getModellingFramework() - Static method in class org.sbml.jsbml.SBO
-
- getModelQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- getModifiedDate() - Method in class org.sbml.jsbml.History
-
Returns the modifiedDate from the
History.
- getModifiedDate(int) - Method in class org.sbml.jsbml.History
-
Get the nth
Date object in the list of ModifiedDates in this
History.
- getModifiedDateCount() - Method in class org.sbml.jsbml.History
-
Get the number of ModifiedDate objects in this
History.
- getModifier(int) - Method in class org.sbml.jsbml.Reaction
-
- getModifier(String) - Method in class org.sbml.jsbml.Reaction
-
- getModifier() - Static method in class org.sbml.jsbml.SBO
-
Substance that changes the velocity of a process without itself being
consumed or transformed by the reaction.
- getModifierCount() - Method in class org.sbml.jsbml.Reaction
-
- getModifierForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getModifierSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model
-
- getModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model
-
- getModifierUnknownActivity() - Static method in class org.sbml.jsbml.SBO
-
A modifier whose activity is not known or has not been specified.
- getModulation() - Static method in class org.sbml.jsbml.SBO
-
Modification of the execution of an event or a process.
- getMolecularInteraction() - Static method in class org.sbml.jsbml.SBO
-
Relationship between molecular entities, based on contacts, direct or indirect.
- getMultiplier() - Method in class org.sbml.jsbml.Unit
-
- getName() - Method in class org.sbml.jsbml.AbstractSBase
-
- getName() - Method in class org.sbml.jsbml.ASTNode
-
Gets the name of this node.
- getName() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Deprecated.
- getName() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getName() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- getName() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getName() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the name of the MathML element represented by
this
ASTFunction
- getName() - Method in interface org.sbml.jsbml.NamedSBase
-
Returns the name of the element if it is set, an empty string otherwise.
- getName() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the name of this
Term, i.e., a very short characterization.
- getName() - Method in interface org.sbml.jsbml.SBase
-
Returns the name of the element if it is set, an empty string otherwise.
- getName() - Method in enum org.sbml.jsbml.Unit.Kind
-
Returns the name of this unit kind.
- getName() - Method in class org.sbml.jsbml.util.filters.NameFilter
-
Returns the name.
- getName() - Method in class org.sbml.jsbml.util.Option
-
- getName() - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-
- getName() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the local name of an attribute in this
XMLAttributes set (by position).
- getName() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the (unqualified) name of this XML element.
- getName() - Method in class org.sbml.jsbml.xml.XMLTriple
-
- getNamedSBaseCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of
NamedSBases in the
Model, so elements
that can have a name in SBML L3V1 or below.
- getNamedSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model
-
- getNameOrID(NamedSBase) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
If the field printNameIfAvailable is false this method returns a the id
of the given SBase.
- getNameOrID(NamedSBase) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
If the field printNameIfAvailable is false this method returns a the id
of the given SBase.
- getNameOrId(NamedSBase) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- getNamespace() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNamespace() - Method in interface org.sbml.jsbml.SBase
-
Returns the namespace to which this
SBase belong to.
- getNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getNamespaceFor(int, int, int) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Gets the namespace for this package that correspond to the given SBML level, version
and the package version.
- getNamespaceFor(int, int, int, String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Gets the namespace for the given package name that correspond to the SBML level, version
and package version.
- getNamespaceFrom(int, int) - Static method in class org.sbml.jsbml.JSBML
-
- getNamespaceIndex(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the index of an XML namespace declaration by URI.
- getNamespaceIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the index of an XML namespace declaration by prefix.
- getNamespacePrefix(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the prefix of an XML namespace declaration by position.
- getNamespacePrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the prefix of an XML namespace declaration by its URI.
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- getNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Returns a List of all the namespaces that this parser is handling.
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- getNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
-
Returns a List of all the namespaces that this parser is handling
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- getNamespaces() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
- getNamespaces() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the XML namespace declarations for this XML element.
- getNamespacesLength() - Method in class org.sbml.jsbml.xml.XMLToken
-
- getNamespaceURI() - Method in enum org.sbml.jsbml.CVTerm.Type
-
- getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
Return the namespace URI of the namespace parsed by this class.
- getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- getNamespaceURI() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the URI of an XML namespace declaration for the empty prefix.
- getNamespaceURI(int) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the URI of an XML namespace declaration by its position.
- getNamespaceURI(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the URI of an XML namespace declaration by its prefix.
- getNecessaryStimulation() - Static method in class org.sbml.jsbml.SBO
-
Control that is necessary to the execution of a process.
- getNegativeInfinity() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getNegativeInfinity() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getNestedCVTerm(int) - Method in class org.sbml.jsbml.CVTerm
-
- getNestedCVTermCount() - Method in class org.sbml.jsbml.CVTerm
-
- getNextNode() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
-
- getNextNode() - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
-
Returns the next node in the list of nodes
- getNextNode() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
-
- getNextNode() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
-
- getNextObject(ValidationContext, T, int) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UniqueValidation
-
Returns the n-th object that should be tested.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Get the next Token.
- getNode(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
-
- getNode(int) - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
-
Returns the i-th node in the list of nodes
- getNode(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
-
- getNode(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
-
- getNodes() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
-
- getNodes() - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
-
Returns the list of adjacent nodes
- getNodes() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
-
- getNodes() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
-
- getNonAllostericActivator() - Static method in class org.sbml.jsbml.SBO
-
Describes an activator (ligand) which binds to the enzyme, which does not result in a conformational change, but which enhances the enzyme's activity.
- getNonCompetitiveInhibitor() - Static method in class org.sbml.jsbml.SBO
-
Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants.
- getNonCovalentComplex() - Static method in class org.sbml.jsbml.SBO
-
Entity composed of several independant components that are not linked by covalent bonds.
- getNonEssentialActivator() - Static method in class org.sbml.jsbml.SBO
-
An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity.
- getNonRDFannotation() - Method in class org.sbml.jsbml.Annotation
-
Returns the
XMLNode containing annotations other than
the official RDF annotation, as defined in the SBML specifications.
- getNonRDFannotationAsString() - Method in class org.sbml.jsbml.Annotation
-
Returns the String containing annotations other than RDF
annotation.
- getNotes() - Method in class org.sbml.jsbml.AbstractSBase
-
Returns an XMLNode object that represent the notes of this element.
- getNotes() - Method in interface org.sbml.jsbml.SBase
-
Returns the XMLNode containing the notes sub-element of
this object.
- getNotesString() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNotesString() - Method in interface org.sbml.jsbml.SBase
-
Returns the notes sub-element of this object as a String.
- getNumArguments() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getNumber() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Get the numerical base of MathML element.
- getNumbering(long) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getNumbering(long) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getNumberOfNonEmptyChildElement(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Returns the number of child XMLNode, excluding text XMLNode that
contains only spaces.
- getNumChildren() - Method in class org.sbml.jsbml.AbstractTreeNode
-
Returns the number of child elements of this TreeNode.
- getNumCompartments() - Method in class org.sbml.jsbml.Model
-
- getNumCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
Deprecated.
- getNumConstraints() - Method in class org.sbml.jsbml.Model
-
- getNumCreators() - Method in class org.sbml.jsbml.History
-
- getNumCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNumCVTerms() - Method in class org.sbml.jsbml.Annotation
-
- getNumCVTerms() - Method in interface org.sbml.jsbml.SBase
-
- getNumDelays() - Method in class org.sbml.jsbml.Model
-
- getNumerator() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of the numerator of this node.
- getNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Get the numerator value of this node.
- getNumErrors() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during consistency
checking.
- getNumErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged.
- getNumEventAssignments() - Method in class org.sbml.jsbml.Event
-
- getNumEventAssignments() - Method in class org.sbml.jsbml.Model
-
- getNumEvents() - Method in class org.sbml.jsbml.Model
-
- getNumFailsWithSeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged with the given
severity code.
- getNumFunctionDefinitions() - Method in class org.sbml.jsbml.Model
-
- getNumInitialAssignments() - Method in class org.sbml.jsbml.Model
-
- getNumKineticLaws() - Method in class org.sbml.jsbml.Model
-
- getNumListsOf() - Method in class org.sbml.jsbml.Model
-
- getNumLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getNumLocalParameters() - Method in class org.sbml.jsbml.Model
-
Returns the number of parameters that are contained within kineticLaws in
the reactions of this model.
- getNumMathContainers() - Method in class org.sbml.jsbml.Model
-
Returns the number of elements that can contain math in the
Model .
- getNumModifiedDates() - Method in class org.sbml.jsbml.History
-
Get the number of ModifiedDate objects in this
History.
- getNumModifiers() - Method in class org.sbml.jsbml.Reaction
-
- getNumModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model
-
- getNumNamedSBases() - Method in class org.sbml.jsbml.Model
-
Returns the number of
NamedSBases in the
Model, so elements
that can have a name.
- getNumNamedSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
-
- getNumNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- getNumObjects(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UniqueValidation
-
Returns the total number of objects which should be tested.
- getNumParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getNumParameters() - Method in class org.sbml.jsbml.Model
-
- getNumPlugins() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNumPlugins() - Method in class org.sbml.jsbml.ASTNode
-
- getNumPlugins() - Method in interface org.sbml.jsbml.SBase
-
- getNumProducts() - Method in class org.sbml.jsbml.Reaction
-
- getNumQuantities() - Method in class org.sbml.jsbml.Model
-
- getNumQuantitiesWithUnit() - Method in class org.sbml.jsbml.Model
-
- getNumReactants() - Method in class org.sbml.jsbml.Reaction
-
- getNumReactions() - Method in class org.sbml.jsbml.Model
-
- getNumResources() - Method in class org.sbml.jsbml.CVTerm
-
Returns the number of resources for this
CVTerm.
- getNumRules() - Method in class org.sbml.jsbml.Model
-
- getNumSBases() - Method in class org.sbml.jsbml.Model
-
- getNumSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
-
- getNumSemanticsAnnotations() - Method in class org.sbml.jsbml.ASTNode
-
Gets the number of semantic annotation elements inside this node.
- getNumSpecies() - Method in class org.sbml.jsbml.Model
-
- getNumSpeciesReferences() - Method in class org.sbml.jsbml.Model
-
- getNumSpeciesTypes() - Method in class org.sbml.jsbml.Model
-
Deprecated.
- getNumSpeciesWithBoundaryCondition() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Species whose boundary condition is set to
true.
- getNumStoichiometryMath() - Method in class org.sbml.jsbml.Model
-
- getNumSymbols() - Method in class org.sbml.jsbml.Model
-
Returns the number of all instances of
Symbol referenced within the
model.
- getNumTriggers() - Method in class org.sbml.jsbml.Model
-
- getNumUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
- getNumUnits() - Method in class org.sbml.jsbml.Model
-
- getNumUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
- getNumVariables() - Method in class org.sbml.jsbml.Model
-
- getObject() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the object of this
Triple.
- getOffset() - Method in class org.sbml.jsbml.Unit
-
Deprecated.
- getOmitXMLDeclaration() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getOmitXMLDeclaration() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
Returns true if we need to omit the XML declaration.
- getOntology() - Static method in class org.sbml.jsbml.SBO
-
Grants access to the underlying Ontology form BioJava.
- getOptions() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the list of options.
- getOrCreate(XMLNode, String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreate(XMLNode, int, String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreateAfter(XMLNode, String, String, String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreateDescription(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreateWithCustomRDF(XMLNode, int, String, String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrganisation() - Method in class org.sbml.jsbml.Creator
-
Returns the organisation from the
Creator.
- getOrganization() - Method in class org.sbml.jsbml.Creator
-
Returns the organisation from the
Creator.
- getOriginalModel() - Method in interface org.sbml.jsbml.SBMLInputConverter
-
- getOrReplacement() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
Gets the String that will be used to replace ' or ' (the mathML
<or> element) in the boolean expressions.
- getOtherAttribute(String) - Method in class org.sbml.jsbml.Creator
-
- getOtherAttributes() - Method in class org.sbml.jsbml.Creator
-
- getOtherListName() - Method in class org.sbml.jsbml.ListOf
-
- getOutside() - Method in class org.sbml.jsbml.Compartment
-
Returns the outside id of this compartment.
- getOutsideInstance() - Method in class org.sbml.jsbml.Compartment
-
Returns the compartment instance which matches the outside id in Model.
- getPackage() - Method in exception org.sbml.jsbml.SBMLError
-
- getPackageInfo(SBase, String, int, String, Map<String, PackageInfo>, Map<String, PackageInfo>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
- getPackageName() - Method in class org.sbml.jsbml.AbstractSBase
-
- getPackageName() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the package name of this plugin object.
- getPackageName() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the package name of this plugin object.
- getPackageName() - Method in interface org.sbml.jsbml.SBase
-
- getPackageName() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Returns the short name of this package.
- getPackageName(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the name of the SBML package corresponding to the given namespace URI.
- getPackageNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Returns a List of all the valid namespaces for the package.
- getPackageParser(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the
PackageParser corresponding to the given name or namespace.
- getPackageRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the required attribute of the given package extension.
- getPackageRequired(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the required attribute corresponding to the given name or namespace.
- getPackageVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- getPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getPackageVersion() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the package version of the package extension of this plugin object.
- getPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the package version of the package extension of this plugin object.
- getPackageVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the version of the SBML Level 3 package to which this element belongs.
- getParameter(int) - Method in class org.sbml.jsbml.KineticLaw
-
- getParameter(String) - Method in class org.sbml.jsbml.KineticLaw
-
- getParameter(int) - Method in class org.sbml.jsbml.Model
-
- getParameter(String) - Method in class org.sbml.jsbml.Model
-
- getParameterCount() - Method in class org.sbml.jsbml.Model
-
- getParent() - Method in class org.sbml.jsbml.AbstractSBase
-
- getParent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getParent() - Method in class org.sbml.jsbml.ASTNode
-
- getParent() - Method in class org.sbml.jsbml.CompartmentType
-
Deprecated.
- getParent() - Method in class org.sbml.jsbml.Constraint
-
- getParent() - Method in class org.sbml.jsbml.Delay
-
- getParent() - Method in class org.sbml.jsbml.Event
-
- getParent() - Method in class org.sbml.jsbml.EventAssignment
-
- getParent() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getParent() - Method in class org.sbml.jsbml.InitialAssignment
-
- getParent() - Method in class org.sbml.jsbml.KineticLaw
-
- getParent() - Method in class org.sbml.jsbml.LocalParameter
-
- getParent() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getParent() - Method in class org.sbml.jsbml.Priority
-
- getParent() - Method in class org.sbml.jsbml.Reaction
-
- getParent() - Method in class org.sbml.jsbml.Rule
-
- getParent() - Method in class org.sbml.jsbml.SpeciesType
-
Deprecated.
- getParent() - Method in class org.sbml.jsbml.StoichiometryMath
-
Deprecated.
- getParent() - Method in class org.sbml.jsbml.Trigger
-
- getParent() - Method in class org.sbml.jsbml.Unit
-
- getParent() - Method in class org.sbml.jsbml.UnitDefinition
-
- getParents() - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-
- getParentSBMLObject() - Method in class org.sbml.jsbml.AbstractSBase
-
- getParentSBMLObject() - Method in class org.sbml.jsbml.ASTNode
-
This method is convenient when holding an object nested inside other
objects in an SBML model.
- getParentSBMLObject() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getParentSBMLObject() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getParentSBMLObject() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the parent
SBase object to which this plugin object is connected.
- getParentSBMLObject() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the parent
SBase object to which this plugin object connected.
- getParentSBMLObject() - Method in class org.sbml.jsbml.KineticLaw
-
This method is convenient when holding an object nested inside other
objects in an SBML model.
- getParentSBMLObject() - Method in class org.sbml.jsbml.LocalParameter
-
- getParentSBMLObject() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getParentSBMLObject() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Return the parentSBMLObject of this
ASTNode2
- getParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getParentSBMLObject() - Method in interface org.sbml.jsbml.SBase
-
Returns the parent of this
SBase.
- getParentTerms() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the parent Terms.
- getPartialInhibitor() - Static method in class org.sbml.jsbml.SBO
-
- getParticipant() - Static method in class org.sbml.jsbml.SBO
-
- getParticipantRole() - Static method in class org.sbml.jsbml.SBO
-
The function of a physical or conceptual entity, that is its role, in the
execution of an event or process.
- getPattern() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- getPersistent() - Method in class org.sbml.jsbml.Trigger
-
- getPertubingAgent() - Static method in class org.sbml.jsbml.SBO
-
Perturbing agent.
- getpH() - Static method in class org.sbml.jsbml.SBO
-
"A measure of acidity and alkalinity of a solution that is a number on a scale on
which a value of 7 represents neutrality and lower numbers indicate increasing acidity
and higher numbers increasing alkalinity and on which each unit of change represents a
tenfold change in acidity or alkalinity and that is the negative logarithm of the
effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per
liter of the solution.
- getPhenotype() - Static method in class org.sbml.jsbml.SBO
-
- getPhysicalCompartment() - Static method in class org.sbml.jsbml.SBO
-
- getPhysicalParticipant() - Static method in class org.sbml.jsbml.SBO
-
- getPieceCount() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- getPiecewiseMap() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
Gets a Map of the piecewise expressions that have been
transformed.
- getPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- getPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getPlugin(String) - Method in class org.sbml.jsbml.ASTNode
-
Returns an
ASTNodePlugin for an SBML Level 3 package extension
with the given package name or URI.
- getPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Returns an
SBasePlugin for an SBML Level 3 package extension
with the given package name or URI.
- getPMg() - Static method in class org.sbml.jsbml.SBO
-
An enumeration of the concentration of magnesium (Mg) in solution (pMg = -log10[Mg2+]).
- getPositiveInfinity() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getPositiveInfinity() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getPossibleEnzymes(String...) - Static method in class org.sbml.jsbml.SBO
-
Creates and returns a list of molecule types that are accepted as an
enzyme for the given type names.
- getPotentiator() - Static method in class org.sbml.jsbml.SBO
-
Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction.
- getPredefinedUnit(String, int, int) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns the predefined unit with the given identifier for the
specified level and version combination or null if either for the given
combination of level and version there is no such predefined unit or the
identifier is not one of those belonging to the group of predefined unit
definitions.
- getPredefinedUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
Returns a
UnitDefinition representing one of the predefined units
of SBML,
returns
null if the given unit kind is not a valid one for the SBML
level
and version of this
Model.
- getPredefinedUnitID() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
Returns the predefined unit identifier for this data type with the
current level/version combination.
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Compartment
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Event
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.LocalParameter
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Parameter
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Species
-
- getPredicate() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the predicate of this
Triple.
- getPrefix() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the prefix of the package extension of this plugin object.
- getPrefix() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the prefix of the package extension of this plugin object.
- getPrefix() - Method in class org.sbml.jsbml.Unit
-
- getPrefix() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the prefix of an attribute in this
XMLAttributes set (by position).
- getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the prefix of an XML namespace declaration by its position.
- getPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the prefix of an XML namespace declaration by its URI.
- getPrefix() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the namespace prefix of this XML element.
- getPrefix() - Method in class org.sbml.jsbml.xml.XMLTriple
-
Returns the
prefix portion of this
XMLTriple.
- getPrefixAsWord() - Method in class org.sbml.jsbml.Unit
-
- getPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the prefixed name of an attribute in this
XMLAttributes set (by position).
- getPrefixedName() - Method in class org.sbml.jsbml.xml.XMLTriple
-
Returns the prefixed name from this
XMLTriple.
- getPreviousParent() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
-
Access the pointer to the previous parent node of the removed node, may be
null.
- getPriority() - Method in class org.sbml.jsbml.Event
-
- getProcess() - Static method in class org.sbml.jsbml.SBO
-
- getProduct(int) - Method in class org.sbml.jsbml.Reaction
-
- getProduct(String) - Method in class org.sbml.jsbml.Reaction
-
- getProduct() - Static method in class org.sbml.jsbml.SBO
-
Substance that is produced in a reaction.
- getProductCount() - Method in class org.sbml.jsbml.Reaction
-
- getProductForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getProduction() - Static method in class org.sbml.jsbml.SBO
-
Generation of a material or conceptual entity.
- getProgramName() - Method in class org.sbml.jsbml.SBMLWriter
-
- getProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter
-
- getProtein() - Static method in class org.sbml.jsbml.SBO
-
- getQualifier() - Method in class org.sbml.jsbml.CVTerm
-
- getQualifier() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- getQualifierFor(String, String, CVTerm.Qualifier) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- getQuantitativeParameter() - Static method in class org.sbml.jsbml.SBO
-
- getQuantityCount() - Method in class org.sbml.jsbml.Model
-
- getQuantityWithUnitCount() - Method in class org.sbml.jsbml.Model
-
- getRadicand() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- getRateLaw() - Static method in class org.sbml.jsbml.SBO
-
- getRateOf(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getRateOf(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getRateOf(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getRateOf(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getRateOf(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getRateOf(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getRateRuleByVariable(String) - Method in class org.sbml.jsbml.Model
-
Searches for the first instance of
RateRule within this
Model's
Model.listOfRules, whose variable attribute is set to
the value passed to this method.
- getReactant(int) - Method in class org.sbml.jsbml.Reaction
-
- getReactant(String) - Method in class org.sbml.jsbml.Reaction
-
- getReactant() - Static method in class org.sbml.jsbml.SBO
-
Substance consumed by a chemical reaction.
- getReactantCount() - Method in class org.sbml.jsbml.Reaction
-
- getReactantForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getReaction(int) - Method in class org.sbml.jsbml.Model
-
Gets the n-th
Reaction object in this Model.
- getReaction(String) - Method in class org.sbml.jsbml.Model
-
- getReactionCount() - Method in class org.sbml.jsbml.Model
-
- getReadingParsers() - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- getReal() - Method in class org.sbml.jsbml.ASTNode
-
Gets the real-numbered value of this node.
- getReal() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Get the real value of this node.
- getReceptor() - Static method in class org.sbml.jsbml.SBO
-
- getReferencedNamedSBases() - Method in class org.sbml.jsbml.ASTNode
-
Returns a set of all the
NamedSBase referenced on this node and
all his descendant.
- getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- getRefId() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Get refId attribute
- getRefId() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Get refId attribute
- getRelatedCompartments(Model, String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
- getRelatedEvents(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
- getRelatedFunctions(Set<String>, Set<String>, ASTNode) - Static method in class org.sbml.jsbml.util.SubModel
-
- getRelatedFunctionsId(Set<String>, Set<String>, ASTNode) - Static method in class org.sbml.jsbml.util.SubModel
-
- getRelatedId(SBase) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
Returns an id depending of the type of SBase given.
- getRelatedReactions(Model, String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
Returns an array of reaction id related to the reactsIds or speciesIds.
- getRelatedRules(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
- getRelatedSpecies(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
-
- getReservedNamesL1V1() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
- getResource(int) - Method in class org.sbml.jsbml.CVTerm
-
- getResourceCount() - Method in class org.sbml.jsbml.CVTerm
-
Returns the number of resources for this
CVTerm.
- getResources() - Method in class org.sbml.jsbml.CVTerm
-
Returns the resources for this CVTerm.
- getResourceURI(int) - Method in class org.sbml.jsbml.CVTerm
-
Returns the value of the nth resource for this CVTerm.
- getReversible() - Method in class org.sbml.jsbml.Reaction
-
- getRightChild() - Method in class org.sbml.jsbml.ASTNode
-
Returns the last child in the list of children of this node.
- getRightChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- getRNA() - Static method in class org.sbml.jsbml.SBO
-
- getRNASegment() - Static method in class org.sbml.jsbml.SBO
-
Fragment or region of an RNA macromolecule.
- getRoot() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getRoot() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getRoot() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getRootConstraint() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Returns the root constraint from this context.
- getRootExponent() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- getRule(int) - Method in class org.sbml.jsbml.Model
-
Gets the n
th Rule of the listOfRules.
- getRule(String) - Method in class org.sbml.jsbml.Model
-
- getRuleById(String) - Method in class org.sbml.jsbml.Model
-
Searches for the first instance of
Rule within this
Model's
Model.listOfRules, whose id attribute is set to
the value passed to this method.
- getRuleByVariable(String) - Method in class org.sbml.jsbml.Model
-
- getRuleCount() - Method in class org.sbml.jsbml.Model
-
- getSBaseById(String) - Method in class org.sbml.jsbml.Model
-
Returns an
SBase element of the model that has the given 'id'
as id or
null if no element is found.
- getSBaseCount() - Method in class org.sbml.jsbml.Model
-
- getSBaseListType() - Method in class org.sbml.jsbml.ListOf
-
Returns the SBaseListType of this ListOf instance.
- getSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model
-
- getSBMLDocument() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBMLDocument() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getSBMLDocument() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.SBase
-
- getSBMLDocument() - Method in class org.sbml.jsbml.util.ModelBuilder
-
- getSBMLDocumentAttributes() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the map of attribute names and values of this SBMLDocument.
- getSBMLDocumentNamespaces() - Method in class org.sbml.jsbml.SBMLDocument
-
- getSBMLNSAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getSBMLUnitsAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getSBORoot() - Static method in class org.sbml.jsbml.SBO
-
Returns the root element of the SBO Ontology (SBO:0000000).
- getSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBOTerm() - Method in interface org.sbml.jsbml.SBase
-
Grants access to the Systems Biology Ontology (SBO) term associated with
this
SBase.
- getSBOTermID() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBOTermID() - Method in interface org.sbml.jsbml.SBase
-
Grants access to the Systems Biology Ontology (SBO) term associated with
this
SBase.
- getScale() - Method in class org.sbml.jsbml.Unit
-
- getSemanticsAnnotation(int) - Method in class org.sbml.jsbml.ASTNode
-
Gets the nth <semantics> annotation of this node.
- getSeverity() - Method in exception org.sbml.jsbml.SBMLError
-
- getSeverity() - Method in class org.sbml.jsbml.util.Detail
-
- getSeverityKey(int, int) - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory
-
- getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
Returns the shortLabel of the namespace parsed by this class.
- getShortMessage() - Method in exception org.sbml.jsbml.SBMLError
-
- getShortMessage() - Method in exception org.sbml.jsbml.SBMLException
-
- getSideProduct() - Static method in class org.sbml.jsbml.SBO
-
Returns the side product SBO term
- getSideSubstrate() - Static method in class org.sbml.jsbml.SBO
-
Returns the side substrate SBO term
- getSimpleMolecule() - Static method in class org.sbml.jsbml.SBO
-
- getSize() - Method in class org.sbml.jsbml.Compartment
-
Returns the size of this compartment.
- getSmallMolecule() - Static method in class org.sbml.jsbml.SBO
-
Simple, non-repetitive chemical entity.
- getSource() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- getSource() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
-
- getSpatialDimensions() - Method in class org.sbml.jsbml.Compartment
-
- getSpatialDimensionsAsDouble() - Method in class org.sbml.jsbml.Compartment
-
- getSpatialSizeUnits() - Method in class org.sbml.jsbml.Species
-
- getSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- getSpecies(SpeciesReference) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the id of a PluginSpeciesReference object's belonging species as
an object of type StringBuffer.
- getSpecies(int) - Method in class org.sbml.jsbml.Model
-
Gets the n-th
Species object in this Model.
- getSpecies(String) - Method in class org.sbml.jsbml.Model
-
- getSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- getSpecies(SpeciesReference) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Returns the id of a PluginSpeciesReference object's belonging species as
an object of type StringBuffer.
- getSpeciesCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- getSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesType(int) - Method in class org.sbml.jsbml.Model
-
- getSpeciesType(String) - Method in class org.sbml.jsbml.Model
-
- getSpeciesType() - Method in class org.sbml.jsbml.Species
-
- getSpeciesTypeCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
-
- getSpeciesWithBoundaryConditionCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Species whose boundary condition is set to
true.
- getSpecificActivator() - Static method in class org.sbml.jsbml.SBO
-
- getStateTransition() - Static method in class org.sbml.jsbml.SBO
-
- getStatus() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the status of the error log.
- getStatus() - Method in class org.sbml.jsbml.util.Option
-
- getSteadyStateExpression() - Static method in class org.sbml.jsbml.SBO
-
- getStimulation() - Static method in class org.sbml.jsbml.SBO
-
Positive modulation of the execution of a process.
- getStimulator() - Static method in class org.sbml.jsbml.SBO
-
- getStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
-
- getStoichiometry(SpeciesReference) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Returns the value of a PluginSpeciesReference object's stoichiometry
either as a double or, if the stoichiometry has an integer value, as an
int object.
- getStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference
-
- getStoichiometryMathCount() - Method in class org.sbml.jsbml.Model
-
- getStreamFromFile(String) - Method in class org.sbml.jsbml.resources.Resource
-
Gets the byte data from a file.
- getStreamFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource
-
Gets the byte data from a file at the given resource location.
- getStyle() - Method in class org.sbml.jsbml.ASTNode
-
Returns the style of the mathML element represented by this ASTNode.
- getStyle() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getStyle() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Return the style of this node
- getStyle() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getSubject() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the subject of this
Triple.
- getSubstanceUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getSubstanceUnits() - Method in class org.sbml.jsbml.Model
-
Returns the substance units ID of this model.
- getSubstanceUnits() - Method in class org.sbml.jsbml.Species
-
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- GetSuffix(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get the suffix.
- GetSuffix(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get the suffix.
- getSymbol() - Method in class org.sbml.jsbml.InitialAssignment
-
- getSymbol() - Method in enum org.sbml.jsbml.Unit.Kind
-
- getSymbolCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of all instances of
Symbol referenced within the
model.
- getSynonyms() - Method in class org.sbml.jsbml.ontology.Term
-
Returns all
Synonyms of this
Term.
- getTabSize(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- getTabSize(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- getTemplateReaction() - Static method in class org.sbml.jsbml.SBO
-
A composite biochemical process through which a gene sequence is fully converted into
mature gene products.
- getTemplateReactionRegulation() - Static method in class org.sbml.jsbml.SBO
-
A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone.
- getTerm() - Method in class org.sbml.jsbml.ontology.Term
-
Grants access to the underlying BioJava
org.biojava3.ontology.Term.
- getTerm(int) - Static method in class org.sbml.jsbml.SBO
-
Gets the SBO term with the id 'sboTerm'.
- getTerm(String) - Static method in class org.sbml.jsbml.SBO
-
Gets the SBO term with the id 'sboTerm'.
- getTerms() - Static method in class org.sbml.jsbml.SBO
-
Return the set of terms of the SBO Ontology.
- getTerms() - Method in class org.sbml.jsbml.util.filters.SBOFilter
-
- getThermodynamicTemperature() - Static method in class org.sbml.jsbml.SBO
-
Temperature is the physical property of a system which underlies the common notions of
"hot" and "cold"; the material with the higher temperature is said to be hotter.
- getTimeUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getTimeUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getTimeUnits() - Method in class org.sbml.jsbml.Model
-
Returns the time units ID of this
Model.
- getTimeUnitsID() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getTimeUnitsInstance() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getTimeUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getTimeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Get the specific Token.
- getTranscription() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSCRIPTION'
- getTranscriptionalActivation() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_ACTIVATION'
- getTranscriptionalInhibitor() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_INHIBITION'
- getTransitionOmitted() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'KNOWN_TRANSITION_OMITTED'
- getTranslation() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSLATION'
- getTranslationalActivation() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSLATIONAL_ACTIVATION'
- getTranslationalInhibitor() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSLATIONAL_INHIBITION'
- getTransport() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRANSPORT'
- getTransportWithBiochemicalReaction() - Static method in class org.sbml.jsbml.SBO
-
An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants.
- getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getTreeNodeChangeListenerCount() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getTrigger() - Method in class org.sbml.jsbml.Event
-
- getTrigger() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRIGGER'
- getTriggerCount() - Method in class org.sbml.jsbml.Model
-
- getTriple() - Method in class org.sbml.jsbml.ontology.Triple
-
Grants access to the original BioJava
org.biojava.nbio.ontology.Triple.
- getTriples(Term, Term, Term) - Static method in class org.sbml.jsbml.SBO
-
Returns a set of Triple which match the supplied subject, predicate and object.
- getTrueIndexOf(XMLNode, String, String, int) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getTruncated() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRUNCATED'
- getType() - Method in class org.sbml.jsbml.ASTNode
-
Returns the type of this node.
- getType() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getType() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns the type of this ASTNode2.
- getType() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getType() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getType() - Method in exception org.sbml.jsbml.SBMLException
-
- getType() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- getType() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
-
- getTypeFor(String) - Static method in enum org.sbml.jsbml.ASTNode.Type
-
- getTypeOfNotes() - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- getUncompetitiveInhibitor() - Static method in class org.sbml.jsbml.SBO
-
An inhibitor which binds only to the complex formed between the enzyme and substrate (E-S complex).
- getUnit(int) - Method in class org.sbml.jsbml.UnitDefinition
-
Returns a specific Unit instance belonging to this UnitDefinition.
- getUnitCount() - Method in class org.sbml.jsbml.Model
-
- getUnitCount() - Method in class org.sbml.jsbml.UnitDefinition
-
- getUnitDefinition(int) - Method in class org.sbml.jsbml.Model
-
- getUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- getUnitDefinitionById(String) - Method in class org.sbml.jsbml.Model
-
Returns a
UnitDefinition element that has the given 'id' within
this
Model or
null if no such element can be found.
- getUnitDefinitionCount() - Method in class org.sbml.jsbml.Model
-
- getUnitKindsDefinedIn(int, int) - Static method in enum org.sbml.jsbml.Unit.Kind
-
Returns a set of
Unit.Kind objects for the given level/version
combination of SBML.
- getUnitOntologyIdentifier() - Method in enum org.sbml.jsbml.Unit.Kind
-
Creates a unit ontology identifier for this
Unit.Kind if possible
and returns it.
- getUnitOntologyNumber() - Method in enum org.sbml.jsbml.Unit.Kind
-
Looks for the corresponding unit ontology resource for this
Unit.Kind.
- getUnitOntologyResource() - Method in enum org.sbml.jsbml.Unit.Kind
-
Creates a MIRIAM resource pointing to the entry in the unit ontology
corresponding to this
Unit.Kind.
- getUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- getUnits() - Method in class org.sbml.jsbml.ASTNode
-
Returns the units attribute.
- getUnits() - Method in class org.sbml.jsbml.Compartment
-
- getUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getUnits() - Method in class org.sbml.jsbml.ExplicitRule
-
- getUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getUnits() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns the units of the MathML element represented by this ASTCnNumberNode
- getUnits() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- getUnits() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- getUnitsInstance() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- getUnitsInstance() - Method in class org.sbml.jsbml.ASTNode
-
Creates or obtains a
UnitDefinition corresponding to the unit
that has been set for this
ASTNode and returns a pointer to it.
- getUnitsInstance() - Method in class org.sbml.jsbml.Compartment
-
- getUnitsInstance() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getUnitsInstance() - Method in class org.sbml.jsbml.ExplicitRule
-
- getUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getUnitsInstance() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- getUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- getUnknownMolecule() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'UNKNOWN'
- getUnknownQualifierName() - Method in class org.sbml.jsbml.CVTerm
-
Gets a name corresponding to the Qualifier of this
CVTerm.
- getUnknownTransition() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'UNKNOWN_TRANSITION'
- getURI() - Method in class org.sbml.jsbml.AbstractSBase
-
- getURI() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Gets the URI to which this element belongs to.
- getURI() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Gets the URI to which this element belongs to.
- getURI() - Method in interface org.sbml.jsbml.SBase
-
Returns the namespace to which this
SBase belong to.
- getURI(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the namespace URI of an attribute in this
XMLAttributes set (by position).
- getURI(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the URI of an XML namespace declaration by its position.
- getURI(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the URI of an XML namespace declaration by its prefix.
- getURI() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the URI of an XML namespace declaration by the empty prefix.
- getURI() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the namespace URI of this XML element.
- getURI() - Method in class org.sbml.jsbml.xml.XMLTriple
-
- getUserObject(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getUserObject(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- getUserObject(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
-
- getV() - Method in class org.sbml.jsbml.util.ValuePair
-
- getValidateRecursivly() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Returns true if the validation also validate every child of a
TreeNode
- getValidationErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.DelayConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.EventConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionDefinitionConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.KineticLawConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.RateRuleConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.RuleConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitConstraints
-
- getValidationFunction(int) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitDefinitionConstraints
-
- getValue() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- getValue() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- getValue() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getValue() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- getValue() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getValue() - Method in class org.sbml.jsbml.math.parser.Token
-
An optional attribute value of the Token.
- getValue() - Method in interface org.sbml.jsbml.Quantity
-
- getValue() - Method in class org.sbml.jsbml.QuantityWithUnit
-
- getValue() - Method in class org.sbml.jsbml.SpeciesReference
-
- getValue() - Method in class org.sbml.jsbml.text.parser.Token
-
An optional attribute value of the Token.
- getValue() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- getValue() - Method in class org.sbml.jsbml.util.Pair
-
- getValue() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
-
- getValue() - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
-
Returns the value of this node
- getValue() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
-
- getValue() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
-
- getValue(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the value of an attribute in this
XMLAttributes set (by position).
- getValue(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns an attribute's value by name.
- getValue(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns a value of an attribute with the given local name and namespace URI.
- getValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns a value of an attribute with the given
XMLTriple.
- getVariable() - Method in interface org.sbml.jsbml.Assignment
-
- getVariable() - Method in class org.sbml.jsbml.ASTNode
-
Returns the variable of this node.
- getVariable() - Method in class org.sbml.jsbml.EventAssignment
-
- getVariable() - Method in class org.sbml.jsbml.ExplicitRule
-
- getVariable() - Method in class org.sbml.jsbml.InitialAssignment
-
- getVariable() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- getVariableCount() - Method in class org.sbml.jsbml.Model
-
- getVariableInstance() - Method in interface org.sbml.jsbml.Assignment
-
- getVariableInstance() - Method in class org.sbml.jsbml.EventAssignment
-
- getVariableInstance() - Method in class org.sbml.jsbml.ExplicitRule
-
- getVariableInstance() - Method in class org.sbml.jsbml.InitialAssignment
-
- getVariables(ListOf<LocalParameter>, ASTNode, List<SBase>, int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
-
Returns the variables in a MathML object without local parameter
- getVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- getVersion() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- getVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getVersion() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns the SBML version of this plugin object.
- getVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the SBML version of this plugin object.
- getVersion() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the Version within the SBML Level of the overall SBML document.
- getVersion() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- getVersion() - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Returns the used version of SBML
- getVolume() - Method in class org.sbml.jsbml.Compartment
-
- getVolumeUnits() - Method in class org.sbml.jsbml.Model
-
Returns the volume units ID of this
Model.
- getVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getWarnings() - Method in interface org.sbml.jsbml.SBMLInputConverter
-
Creates an SBML error report and returns the list of errors.
- getWordForNumber(long) - Static method in class org.sbml.jsbml.util.StringTools
-
Returns the number as an English word.
- getWriteWarnings(T) - Method in interface org.sbml.jsbml.SBMLOutputConverter
-
- getWritingParsers() - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- getWritingParsers(Object, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Gets all the writing parsers necessary to write the given object.
- getXMLnamespaceSBML() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
The additional MathML name space for units to numbers.
- getXMLNode() - Method in class org.sbml.jsbml.Annotation
-
- givenName - Variable in class org.sbml.jsbml.Creator
-
Given name of the creator
- givenName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- GROUPS_10100 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4010100:
- GROUPS_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4010101:
To conform to the Groups Package specification for SBML Level 3 Version 1, an
SBML document must declare
'http://www.sbml.org/sbml/level3/version1/groups/version1' as the XMLNamespaceto
use for elements of this package.
- GROUPS_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4010102:
Wherever they appear in an SBML document, elements and attributes from the
Groups Package must use the
'http://www.sbml.org/sbml/level3/version1/groups/version1' namespace, declaring
so either explicitly or implicitly.
- GROUPS_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4010301:
(Extends validation rule #10301 in the SBML Level 3 Core specification.
- GROUPS_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4010302:
The value of a 'groups:id' must conform to the syntax of the <sbml> data type
'SId' Reference: L3V1 Groups V1 Section 3.3.1
- GROUPS_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020101:
In all SBML documents using the Groups Package, the <sbml> object must have the
'groups:required' attribute.
- GROUPS_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020102:
The value of attribute 'groups:required' on the <sbml> object must be of data
type 'boolean'.
- GROUPS_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020103:
The value of attribute 'groups:required' on the <sbml> object must be set to
'false'.
- GROUPS_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020201:
A <model> object may contain one and only one instance of the <listOfGroups>
element.
- GROUPS_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020202:
The <listOfGroups> subobject on a <model> object is optional, but if present,
this container object must not be empty.
- GROUPS_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020203:
Apart from the general notes and annotations subobjects permitted on all SBML
objects, a <listOfGroups> container object may only contain <group> objects.
- GROUPS_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020204:
A <listOfGroups> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- GROUPS_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020301:
A <group> object may have the optional SBML Level 3 Core attributes 'metaid' and
'sboTerm'.
- GROUPS_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020302:
A <group> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- GROUPS_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020303:
A <group> object must have the required attribute 'groups:kind', and may have
the optional attributes 'groups:id' and 'groups:name'.
- GROUPS_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020304:
A <group> object may contain one and only one instance of the <listOfMembers>
element.
- GROUPS_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020305:
The value of the attribute 'groups:kind' of a <group> object must conform to the
syntax of SBML data type 'groupKind' and may only take on the allowed values of
'groupKind' defined in SBML; that is, the value must be one of the following:
'classification', 'partonomy' or 'collection'.
- GROUPS_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020306:
The attribute 'groups:name' on a <group> must have a value of data type
'string'.
- GROUPS_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020307:
The <listOfMembers> subobject on a <group> object is optional, but if present,
this container object must not be empty.
- GROUPS_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020308:
Apart from the general notes and annotations subobjects permitted on all SBML
objects, a <listOfMembers> container object may only contain <member> objects.
- GROUPS_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020309:
A <listOfMembers> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- GROUPS_20310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020310:
A <listOfMembers> object may have the optional attributes 'groups:id' and
'groups:name'.
- GROUPS_20311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020311:
The attribute 'groups:name' on a <listOfMembers> must have a value of data type
'string'.
- GROUPS_20312 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020312:
If <listOfMembers> objects from different <group> objects contain <member>
elements that reference the same SBase object, the 'sboTerm' attribute and any
child <notes> or <annotation> elements set for those <listOfMembers> should be
consistent, as they should all apply to the same referenced object.
- GROUPS_20313 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020313:
Member references may not be circular: no <member>'s 'idRef' or 'metaIdRef' may
reference itself, its parent <listOfMembers>, nor its parent <group>.
- GROUPS_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020401:
A <member> object may have the optional SBML Level 3 Core attributes 'metaid'
and 'sboTerm'.
- GROUPS_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020402:
A <member> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- GROUPS_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020403:
A <member> object may have the optional attributes 'groups:id' and 'groups:name'
and must have a value for one (and exactly one) of the attributes 'groups:idRef'
and 'groups:metaIdRef'.
- GROUPS_20404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020404:
The attribute 'groups:name' on a <member> must have a value of data type
'string'.
- GROUPS_20405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020405:
The value of the attribute 'groups:idRef' of a <member> object must be the
identifier of an existing <SBase> object defined in the enclosing <model>
object.
- GROUPS_20406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020406:
The value of the attribute 'groups:metaIdRef' of a <member> object must be the
'metaid' of an existing <SBase> object defined in the enclosing <model> object.
- GROUPS_20407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020407:
The value of the attribute 'groups:idRef' of a <member> object must conform to
the syntax of the SBML data type 'SId'.
- GROUPS_20408 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 4020408:
The value of the attribute 'groups:metaIdRef' of a <member> object must conform
to the syntax of the SBML data type 'ID'.
- gt(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode representing greater than for
the two given left and right child.
- gt(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- gt(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Greater than.
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- gt(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Greater than.
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- id - Variable in class org.sbml.jsbml.AbstractSBase
-
id of the SBML component (can be optional depending on the level and
version).
- id - Variable in class org.sbml.jsbml.ASTNode
-
Possible attributes for a MathML element
- id - Variable in class org.sbml.jsbml.math.AbstractASTNode
-
The style of this MathML element
- id - Variable in class org.sbml.jsbml.ontology.Term
-
The base properties of this
Term.
- id - Variable in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
-
The desired identifier for NamedSBases to be acceptable.
- id - Variable in class org.sbml.jsbml.util.filters.IdFilter
-
The desired identifier for SBases to be acceptable.
- id - Variable in class org.sbml.jsbml.util.filters.NameFilter
-
The desired identifier.
- id - Variable in class org.sbml.jsbml.util.filters.SIdFilter
-
The desired identifier for SBases to be acceptable.
- id - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- ID_GROUP - Static variable in interface org.sbml.jsbml.validator.offline.constraints.CoreSpecialErrorCodes
-
- ID_VALIDATE_TREE_NODE - Static variable in interface org.sbml.jsbml.validator.offline.constraints.CoreSpecialErrorCodes
-
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- IdenticalUnitDefinitionFilter - Class in org.sbml.jsbml.util.filters
-
- IdenticalUnitDefinitionFilter(UnitDefinition) - Constructor for class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter
-
- IdentifierException - Exception in org.sbml.jsbml
-
This exception is thrown when trying to set or add an identifier to an
instance of
NamedSBase but if the given identifier is already
registered in the containing
Model.
- IdentifierException(NamedSBase, String) - Constructor for exception org.sbml.jsbml.IdentifierException
-
- IdentifierException(SBase, String) - Constructor for exception org.sbml.jsbml.IdentifierException
-
- IdFilter - Class in org.sbml.jsbml.util.filters
-
This filter only accepts instances of
SBase with the id as
given in the constructor of this object.
- IdFilter() - Constructor for class org.sbml.jsbml.util.filters.IdFilter
-
- IdFilter(String) - Constructor for class org.sbml.jsbml.util.filters.IdFilter
-
- IdManager - Interface in org.sbml.jsbml.util
-
Manages an id namespace.
- ids - Variable in class org.sbml.jsbml.validator.offline.constraints.helper.UniqueValidation
-
- IFormulaParser - Interface in org.sbml.jsbml.math.parser
-
An interface for the FormulaParser generated by JavaCC to parse infix math formula.
- IFormulaParser - Interface in org.sbml.jsbml.text.parser
-
An interface for the FormulaParser generated by JavaCC to parse infix math formula.
- ignoreCase - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- ignoreCase - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- ignoreCase - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- ignoreCase - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- ignoreCase - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- ignoredExtensions - Variable in class org.sbml.jsbml.AbstractSBase
-
Map containing the ignored package objects.
- ignoredXMLElements - Variable in class org.sbml.jsbml.AbstractSBase
-
Contains the unknown XML attributes or elements.
- ILLEGAL_ASTNODE_TYPE_MSG - Static variable in class org.sbml.jsbml.FunctionDefinition
-
Error message to indicate that an incorrect
ASTNode.Type has been passed
to a method.
- ILLEGAL_STOCHIOMETRY_VALUE - Static variable in class org.sbml.jsbml.SpeciesReference
-
Message to be displayed in case that an illegal stoichiometric value has been set.
- ILLEGAL_UNIT_EXCEPTION_MSG - Static variable in class org.sbml.jsbml.JSBML
-
Error message for the case that an invalid unit identifier is to be added
to this object.
- ILLEGAL_UNIT_KIND_EXCEPTION_MSG - Static variable in class org.sbml.jsbml.KineticLaw
-
Exception to be displayed in case that an illegal variant of unit is to
be set for this
SBaseWithUnit.
- image - Variable in class org.sbml.jsbml.math.parser.Token
-
The string image of the token.
- image - Variable in class org.sbml.jsbml.text.parser.Token
-
The string image of the token.
- IMPLEMENTATION_ASTNODE2 - Static variable in class org.sbml.jsbml.ASTNode
-
The String representing the facade implementation for the new
ASTNode2 implementation.
- IMPLEMENTATION_HISTORIC - Static variable in class org.sbml.jsbml.ASTNode
-
The String representing the first implementation of the ASTNode, since 0.8.
- IMPLEMENTATION_VERSION - Static variable in class org.sbml.jsbml.ASTNode
-
- implies(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Returns the logical implies between two
ASTNode.
- implies(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- implies(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- implies - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- implies(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- implies(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- implies(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- inBuf - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- inBuf - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- indent - Variable in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- indent - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- indent - Variable in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
The number of white spaces for the indent if this is to be used.
- indent - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
The number of white spaces for the indent if this is to be used.
- indentChar - Variable in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
-
- indentChar - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
-
The symbol for indentation.
- indentCount - Variable in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
-
- indentCount - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
-
The number of indentation symbols.
- indenting - Variable in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
Decides whether or not the content of the MathML string should be
indented.
- indenting - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
Decides whether or not the content of the MathML string should be
indented.
- INDEX_EXCEEDS_SIZE - Static variable in class org.sbml.jsbml.JSBML
-
- indexOf(TreeNode, TreeNode) - Static method in class org.sbml.jsbml.AbstractTreeNode
-
Searches the given child in the list of sub-nodes of the parent element.
- indexOf(Object) - Method in class org.sbml.jsbml.ListOf
-
- info(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
-
- init() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
Re-initializes the Document object belonging to this class.
- init() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
-
Initializes the Converter
- init() - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- initChemicalFormulaPattern() - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
- initDefaults() - Method in class org.sbml.jsbml.ASTNode
-
Initializes the default values/attributes of the node.
- initDefaults() - Method in class org.sbml.jsbml.Compartment
-
Initializes the default values using the current Level/Version
configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Compartment
-
Initializes the default values using the current Level/Version
configuration.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Compartment
-
- initDefaults() - Method in class org.sbml.jsbml.CompartmentType
-
Deprecated.
Initializes the default settings of this class.
- initDefaults() - Method in class org.sbml.jsbml.Event
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Event
-
Initializes the default values of this
Event.
- initDefaults() - Method in class org.sbml.jsbml.ExplicitRule
-
- initDefaults() - Method in class org.sbml.jsbml.KineticLaw
-
- initDefaults() - Method in class org.sbml.jsbml.math.ASTFunction
-
Initializes the default values/attributes of the node.
- initDefaults() - Method in class org.sbml.jsbml.Model
-
Initializes the default values using the current Level/Version
configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Model
-
Initializes the default values of the attributes of the
Model
- initDefaults(int, int) - Method in class org.sbml.jsbml.Parameter
-
Initializes the default values of this
Parameter, i.e., sets it to
a constant variable with a
Double.NaN value.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Parameter
-
- initDefaults() - Method in class org.sbml.jsbml.Parameter
-
Initializes the default values using the current Level/Version configuration.
- initDefaults() - Method in class org.sbml.jsbml.Reaction
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Reaction
-
Initializes the default variables of this Reaction.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Reaction
-
- initDefaults() - Method in class org.sbml.jsbml.SBMLDocument
-
- initDefaults() - Method in class org.sbml.jsbml.Species
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Species
-
Initializes the default values of this Species.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Species
-
- initDefaults() - Method in class org.sbml.jsbml.SpeciesReference
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.SpeciesReference
-
Initializes the default values of this SpeciesReference.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.SpeciesReference
-
- initDefaults() - Method in class org.sbml.jsbml.SpeciesType
-
Deprecated.
Initializes the default settings of this class.
- initDefaults() - Method in class org.sbml.jsbml.Trigger
-
- initDefaults() - Method in class org.sbml.jsbml.Unit
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Unit
-
Initializes the attributes of this Unit (except for 'kind') to their
defaults values.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Unit
-
- initialAmount - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- InitialAssignment - Class in org.sbml.jsbml
-
Represents the initialAssignment XML element of a SBML file.
- InitialAssignment() - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment instance.
- InitialAssignment(InitialAssignment) - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment instance from a given InitialAssignment.
- InitialAssignment(int, int) - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment from level and version.
- InitialAssignment(Variable) - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment instance from a
Variable.
- InitialAssignment(Variable, ASTNode, int, int) - Constructor for class org.sbml.jsbml.InitialAssignment
-
- InitialAssignmentConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- InitialAssignmentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints
-
- initialise(Token, int[][], String[]) - Static method in exception org.sbml.jsbml.math.parser.ParseException
-
It uses "currentToken" and "expectedTokenSequences" to generate a parse
error message and returns it.
- initialise(Token, int[][], String[]) - Static method in exception org.sbml.jsbml.text.parser.ParseException
-
It uses "currentToken" and "expectedTokenSequences" to generate a parse
error message and returns it.
- initializeAnnotationParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Initializes the packageParser HashMap of this class.
- initializedParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLReader
-
Contains all the initialized parsers.
- initializePackageParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Creates the ReadingParser instances and stores them in a
HashMap.
- initializePackageParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Creates the ReadingParser instances and stores them in a HashMap.
- initialValue - Variable in class org.sbml.jsbml.Trigger
-
- initialValue - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- initL1V1SNamePattern() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
Initializes the pattern for the type SName (described in SBML L1V1
specification, p.
- initL1V2SNamePattern() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
Creates the pattern for SName as defined in SBML specification for L1V2
page 7.
- initListOf(SBase, ListOf<T>, ListOf.Type) - Static method in class org.sbml.jsbml.ListOf
-
Initializes newly created lists.
- initMetaIdPatterns() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
Build the pattern for metaIds according to the definition in SBML
L2V2R1 p.
- initReservedNamesL1V1() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
These reserved words can occur in case of
UnitDefinitions:
"substance",
"time",
"volume".
- initReservedNamesL1V2() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
- initSIdL2Pattern() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
- InnerNode(T) - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
-
Creates a new inner node
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- inputStream - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- inputStream - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- insertChild(int, ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Inserts the given
ASTNode at point n in the list of children of this
ASTNode.
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- insertChild(int, XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
-
Inserts a node as the
nth child of this
XMLNode.
- instance - Static variable in class org.sbml.jsbml.math.ASTUnknown
-
- instance - Static variable in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
Shared singleton instance
- instance - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
-
- instance_ - Static variable in class org.sbml.jsbml.util.JAXPFacade
-
- instances_ - Static variable in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- instantiatedSBMLParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
-
contains the WritingParser instances of this class.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- intToString(int) - Static method in class org.sbml.jsbml.SBO
-
Returns the integer as a correctly formatted SBO string.
- invalid() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
Creates an invalid unit definition encapsulated in an ASTNode2Value.
- invalid() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
Creates an invalid unit definition encapsulated in an ASTNodeValue.
- INVALID_ATTRIBUTE_VALUE - Static variable in class org.sbml.jsbml.JSBML
-
- INVALID_LEXICAL_STATE - Static variable in error org.sbml.jsbml.math.parser.TokenMgrError
-
Tried to change to an invalid lexical state.
- INVALID_LEXICAL_STATE - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
-
Tried to change to an invalid lexical state.
- INVALID_OBJECT - Static variable in class org.sbml.jsbml.JSBML
-
- INVALID_XML_OPERATION - Static variable in class org.sbml.jsbml.JSBML
-
- INVERSE_TRIGONOMETRIC_PREFIX - Variable in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
All inverse trigonometric functions may be defined in the infix either using 'arc' as a prefix or simply 'a'
- involves(Species) - Method in class org.sbml.jsbml.Reaction
-
Convenient test if the given species takes part in this reaction as a
reactant, product, or modifier.
- isAlgebraic() - Method in class org.sbml.jsbml.Rule
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTDivideNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTFunction
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTMinusNode
-
- isAllowableType(ASTNode.Type) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns
true iff type is allowed in this
ASTNode2
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTPlusNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTQualifierNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTRootNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTTimesNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isAmpere() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind ampere.
- isAncestor(CycleDetectionTreeNode) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-
- isAntisenseRNA(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isAssignment() - Method in class org.sbml.jsbml.Rule
-
- isAssociation(int) - Static method in class org.sbml.jsbml.SBO
-
- isAttributesEmpty() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
the attribute set in this
XMLToken set is empty.
- isAvailable(JSONObject, int, int) - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory
-
- isAvogadro() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind avogadro.
- isBecquerel() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind becquerel.
- isBigLetter(char) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A big letter is a ASCII symbol between 'A' and 'Z'.
- isBindingActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isBiologicalQualifier() - Method in class org.sbml.jsbml.CVTerm
-
Returns true if this qualifier is a biological qualifier.
- isBiologicalQualifier() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
-
Returns true if this qualifier is a biological qualifier.
- isBoolean() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node has a boolean type (a logical operator, a
relational operator, or the constants true or false).
- isBoolean() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isBoolean() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isBoundaryCondition() - Method in class org.sbml.jsbml.Species
-
- isBuiltIn(String, int) - Static method in class org.sbml.jsbml.Unit
-
- isBuiltIn(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
- isBuiltIn() - Method in class org.sbml.jsbml.UnitDefinition
-
- isCallableSBase() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isCallableSBase() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isCandela() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind candela
- isCatalyst(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isCatalyticActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isCelsius() - Method in class org.sbml.jsbml.Unit
-
- isChildOf(int, int) - Static method in class org.sbml.jsbml.SBO
-
Checks whether the given sboTerm is a member of the SBO subgraph rooted
at parent.
- isChildOf(Term, Term) - Static method in class org.sbml.jsbml.SBO
-
Traverses the systems biology ontology starting at
Term subject until
either the root (SBO:0000000) or the
Term object is reached.
- isCompartmentMandatory() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- isCompartmentMandatory() - Method in class org.sbml.jsbml.Reaction
-
- isCompartmentMandatory() - Method in class org.sbml.jsbml.Species
-
- isCompartmentVolume() - Method in class org.sbml.jsbml.AlgebraicRule
-
- isCompartmentVolume() - Method in class org.sbml.jsbml.ExplicitRule
-
- isCompartmentVolume() - Method in class org.sbml.jsbml.Rule
-
(SBML Level 1 only) Predicate returning true or false depending on
whether this Rule is an CompartmentVolumeRule.
- isCompetetiveInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isCompleteInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isComplex(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isConservationLaw(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the term is-a conservation law, false otherwise
- isConstant() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents a MathML constant (e.g., true, Pi).
- isConstant() - Method in class org.sbml.jsbml.SpeciesReference
-
- isConstant() - Method in class org.sbml.jsbml.Symbol
-
- isConstant() - Method in interface org.sbml.jsbml.Variable
-
- isContinuousFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the term is-a continuous framework, false otherwise
- isCoulomb() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind coulomb.
- isDebugEnabled - Static variable in class org.sbml.jsbml.ASTNode
-
- isDebugEnabled - Static variable in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
-
- isDebugEnabled - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
A static boolean to avoid many unnecessary calls to Category.isDebugEnabled().
- isDebugEnabled - Static variable in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints
-
- isDebugMode() - Static method in class org.sbml.jsbml.ListOf
-
- isDefinedIn(int, int) - Method in enum org.sbml.jsbml.ASTNode.Type
-
Checks whether this type is valid for the given SBML
Level/Version combination.
- isDefinedIn(int, int) - Method in enum org.sbml.jsbml.Unit.Kind
-
Tests whether this kind of unit is defined in the given level and
version of SBML.
- isDifference() - Method in class org.sbml.jsbml.ASTNode
-
Checks if this
ASTNode represents a difference.
- isDifference() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isDifference() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isDigit(char) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A digit is a ASCII symbol between '0' and '9'.
- isDimensionless() - Method in class org.sbml.jsbml.Unit
-
- isDiscreteFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the term is-a discrete framework, false otherwise
- isDissociation(int) - Static method in class org.sbml.jsbml.SBO
-
- isDrug(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isElement() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
this
XMLToken is an XML element.
- isEmpty() - Method in class org.sbml.jsbml.Annotation
-
- isEmpty() - Method in class org.sbml.jsbml.History
-
Checks whether at least one attribute has been set for this
History.
- isEmpty() - Method in class org.sbml.jsbml.ListOf
-
- isEmpty() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns
true or
false depending on whether
this
XMLAttributes set is empty.
- isEmpty() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Returns
true or
false depending on whether this
XMLNamespaces list is empty.
- isEmpty() - Method in class org.sbml.jsbml.xml.XMLTriple
-
- isEmptyListOf(Object) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns
true if the given
Object is an empty
ListOf,
false otherwise.
- isEmptySet(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isEnd() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
this
XMLToken is an XML end element.
- isEndElement - Variable in class org.sbml.jsbml.xml.XMLToken
-
- isEndFor(XMLToken) - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
this
XMLToken is an XML end element for the given start element.
- isEntity(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the term is-a Entity, false otherwise
- isEnzymaticCatalysis(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isEOF - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isEOF - Variable in class org.sbml.jsbml.xml.XMLToken
-
- isEOF() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
this
XMLToken is an end of file marker.
- isError() - Method in exception org.sbml.jsbml.SBMLError
-
- isError() - Method in exception org.sbml.jsbml.SBMLException
-
- isEssentialActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isEvent(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isExplicitlySetConstant - Variable in class org.sbml.jsbml.LocalParameter
-
This field memorizes whether this
LocalParameter has been
explicitly set to be constant.
- isExplicitlySetConstant() - Method in class org.sbml.jsbml.LocalParameter
-
In SBML prior to Level 3 it was possible to explicitly state that a local
parameter represents a constant
Quantity.
- isExplicitlySetConstant - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isExtendedByOtherPackages() - Method in class org.sbml.jsbml.AbstractSBase
-
- isExtendedByOtherPackages() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this object is extended by other packages.
- isExtendedByOtherPackages() - Method in interface org.sbml.jsbml.SBase
-
Returns true if this object is extended by other packages.
- isFarad() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind farad
- isFast() - Method in class org.sbml.jsbml.Reaction
-
Deprecated.
- isFatal() - Method in exception org.sbml.jsbml.SBMLError
-
- isFatal() - Method in exception org.sbml.jsbml.SBMLException
-
- isFilterForSpecies() - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
-
- isFunction() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents a function.
- isFunctionalCompartment(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isFunctionalEntity(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isFunctionDefinition - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- isGene(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isGeneCodingRegion(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the sboTerm stands for a gene coding region, false
otherwise
- isGeneOrGeneCodingRegion(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the sboTerm stands for a gene coding region or a gene,
false otherwise
- isGeneric(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isGram() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind gram
- isGray() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind gray
- isHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
-
- isHenry() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind henry
- isHertz() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind hertz
- isHillEquation(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isId(String, int, int) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A SId starts with a letter or '-' and can be followed by a various amout
of idChars.
- isIdChar(char) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A idChar is a letter, digit or '-'.
- isIdMandatory() - Method in class org.sbml.jsbml.AbstractSBase
-
- isIdMandatory() - Method in class org.sbml.jsbml.CompartmentType
-
Deprecated.
- isIdMandatory() - Method in class org.sbml.jsbml.Event
-
- isIdMandatory() - Method in class org.sbml.jsbml.FunctionDefinition
-
- isIdMandatory() - Method in class org.sbml.jsbml.Model
-
- isIdMandatory() - Method in interface org.sbml.jsbml.NamedSBase
-
Returns
true if the identifier of this
NamedSBase is required to be defined (i.e., not
null)
in the definition of SBML.
- isIdMandatory() - Method in class org.sbml.jsbml.QuantityWithUnit
-
- isIdMandatory() - Method in class org.sbml.jsbml.Reaction
-
- isIdMandatory() - Method in interface org.sbml.jsbml.SBase
-
Returns
true if the identifier of this
SBase is required to be defined (i.e., not
null)
in the definition of SBML.
- isIdMandatory() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- isIdMandatory() - Method in class org.sbml.jsbml.SpeciesType
-
Deprecated.
- isIdMandatory() - Method in class org.sbml.jsbml.UnitDefinition
-
- isIgnoredPackage(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns true if the given package extension is one of an ignored
packages, otherwise returns false.
- isIgnoredPkg(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isInfinity() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents the special IEEE 754 value infinity,
false otherwise.
- isInfinity() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns
true if this
ASTCnRealNode represents the special IEEE 754 value infinity,
false otherwise.
- isInfo() - Method in exception org.sbml.jsbml.SBMLError
-
- isInfo() - Method in exception org.sbml.jsbml.SBMLException
-
- isInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isInitialValue() - Method in class org.sbml.jsbml.Trigger
-
- isInt(double) - Static method in class org.sbml.jsbml.util.Maths
-
Checks if the given argument represents an integer number, i.e., if it can
be casted to int without loosing information.
- isInteger() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node contains an integer value, false otherwise.
- isInteraction(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isInteraction - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Interaction'.
- isInternal() - Method in exception org.sbml.jsbml.SBMLError
-
Returns
true is the
SBMLError category is of type
internal
- isInternal() - Method in exception org.sbml.jsbml.SBMLException
-
- isInvalid() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind invalid.
- isInvalid() - Method in class org.sbml.jsbml.UnitDefinition
-
Checks if this UnitDefinition is invalid.
- isIon(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isIonChannel(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isItem() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind item
- isJoule() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind Joule
- isKatal() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind katal
- isKelvin() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind kelvin
- isKilogram() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind kilogram
- isKineticConstant(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isLambda() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is a MathML <lambda>, false otherwise.
- isLeaf() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- isLeaf() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isLetter(char) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A letter is either a small letter or big letter.
- isLevelAndVersionEqualTo(int, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Checks if the level and version of this context are both the same as the
given values.
- isLevelAndVersionGreaterEqualThan(int, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Checks if the level and version of this context is greater or equal to the
given values.
- isLevelAndVersionGreaterThan(int, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Checks if the level and version of this context is greater than the given
level and version.
- isLevelAndVersionLesserEqualThan(int, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Checks if the level and version of this context is lesser or equal to the
given values.
- isLevelAndVersionLessThan(int, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Checks if the level and version of this context is less then the given
level and version.
- isListOfCompartmentsEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfCompartments is != null, but has no
children.
- isListOfCompartmentTypesEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfCompartmentTypes is != null, but has no
children.
- isListOfConstraintsEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfConstraints is != null, but has no
children.
- isListOfEventAssignmentEmpty() - Method in class org.sbml.jsbml.Event
-
Returns true, if listOfEventAssignments is not null.
- isListOfEventsEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfEvents is != null, but has no
children.
- isListOfFunctionDefinitionsEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfFunctionDefinitions is != null, but has no
children.
- isListOfInitialAssignmentsEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfInitialAssignments is != null, but has no
children.
- isListOfLocalParametersEmpty() - Method in class org.sbml.jsbml.KineticLaw
-
Returns true, if the list of local parameters is not null.
- isListOfModifiersEmpty() - Method in class org.sbml.jsbml.Reaction
-
Returns true if the listOfModifiers of this Reaction is empty.
- isListOfParametersEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfParameters is != null, but has no
children.
- isListOfProductsEmpty() - Method in class org.sbml.jsbml.Reaction
-
Returns true if the listOfProducts of this reaction is empty.
- isListOfReactantsEmpty() - Method in class org.sbml.jsbml.Reaction
-
Returns true if the listOfReactants of this Reaction is empty.
- isListOfReactionsEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfReactions is != null, but has no
children.
- isListOfRulesEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfRules is != null, but has no
children.
- isListOfSpeciesEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfSpecies is != null, but has no
children.
- isListOfSpeciesTypesEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfSpeciesTypes is != null, but has no
children.
- isListOfUnitDefinitionEmpty() - Method in class org.sbml.jsbml.Model
-
Checks if the listOfUnitDefinitions is != null, but has no
children.
- isListOfUnitsEmpty() - Method in class org.sbml.jsbml.UnitDefinition
-
Returns true if the listOfUnits is empty.
- isLiteral() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is constant or of type INTEGER, REAL or RATIONAL, false otherwise.
- isLitre() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind litre.
- isLocalParameter(ASTNode, String) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- isLog10() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents a log10() function, false otherwise.
- isLogical() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is a MathML logical operator (i.e., and, or,
not, xor).
- isLogicalFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isLumen() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind lumen
- isLux() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind lux
- isMaterialEntity(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isMaterialEntity - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Material Entity'.
- isMathematicalExpression(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isMathematicalExpression - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Mathematical Expression'.
- isMessengerRNA(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isMetre() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind metre
- isMinusOne() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this astnode represents the number minus one (either as
integer or as real value).
- isModellingFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isModellingFramework - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Modelling Framework'.
- isModelQualifier() - Method in class org.sbml.jsbml.CVTerm
-
Returns true if this qualifier is a model qualifier.
- isModelQualifier() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
-
Returns true if this qualifier is a model qualifier.
- isModifier(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isMole() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind mole.
- isName() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if this node is a user-defined
Variable name in SBML L1, L2
(MathML), or the special symbols time, Avogadro or rateOf.
- isNameChar(char) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A NameChar (defined in the XML Schema 1.0) can be a letter, a digit, '.',
'-', '_', ':', a CombiningChar or Extender.
- isNamespacesEmpty() - Method in class org.sbml.jsbml.xml.XMLToken
-
- isNaN() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is a type Real and represents the special IEEE
754 value 'not a number' Double.NaN, false otherwise.
- isNegInfinity() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents the special IEEE 754 value 'negative
infinity' Double.NEGATIVE_INFINITY, false otherwise.
- isNegInfinity() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns
true if this
ASTCnRealNode represents the special IEEE 754 value 'negative
infinity'
Double.NEGATIVE_INFINITY,
false otherwise.
- isNewton() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind newton
- isNode() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Checks whether the value encapsulated in this
ASTNodeValue is an
instance of
Node.
- isNode() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
Checks whether the value encapsulated in this
ASTNodeValue is an
instance of
Node.
- isNonCompetetiveInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isNonEssentialActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isNumber() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node contains a number, false otherwise.
- isNumber() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isNumber() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ISO_8601_DATE_FORMAT - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
-
ISO 8601 [W3CDTF] date format for GMT
- isObsolete() - Method in class org.sbml.jsbml.ontology.Term
-
Checks whether or not this
Term is obsolete.
- isObsolete(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking whether the SBO term is obsolete.
- isObsolete - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is obsolete.
- isOhm() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind ohm
- isOne() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if this
ASTNode represents the number one (either as
integer or as real value).
- isOperator() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is a mathematical operator, meaning, +, -, *, /
or ^ (power).
- isOverdetermined() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
-
Returns a boolean that indicates whether the given model is over
determined or not.
- isPackageEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isPackageEnabled(String) - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if the given SBML Level 3 package is enabled within
the containing
SBMLDocument.
- isPackageEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true if the given SBML Level 3 package is enabled within
the containing
SBMLDocument.
- isPackageEnabled(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns
true if the given SBML Level 3 package is enabled within
the
SBMLDocument.
- isPackageEnabledOrDisabled(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isPackageURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isPackageURIEnabled(String) - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if the given SBML Level 3 package is enabled within
the containing
SBMLDocument.
- isPackageURIEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true if the given SBML Level 3 package is enabled within
the containing
SBMLDocument.
- isParameter() - Method in class org.sbml.jsbml.AlgebraicRule
-
- isParameter() - Method in class org.sbml.jsbml.ExplicitRule
-
- isParameter() - Method in class org.sbml.jsbml.Rule
-
(SBML Level 1 only) Predicate returning true or false depending on
whether this Rule is an ParameterRule.
- isPartialInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isParticipant(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isParticipantRole(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isParticipantRole - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Participant Role'.
- isPascal() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind pascal
- isPersistent() - Method in class org.sbml.jsbml.Trigger
-
- isPhenotype(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isPhysicalCompartment(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isPhysicalParticipant(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isPiecewise() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if this node is the MathML <piecewise> construct,
false otherwise.
- isPkgEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- isPkgEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
- isPkgURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- isPkgURIEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
- isPredefined(String, int) - Static method in class org.sbml.jsbml.Unit
-
Predicate to test whether a given string is the name of a predefined SBML
unit.
- isPredefined(UnitDefinition) - Static method in class org.sbml.jsbml.Unit
-
Tests whether the given
UnitDefinition belongs to the predefined
SBML units.
- isPredefined(String, int) - Static method in class org.sbml.jsbml.UnitDefinition
-
Tests if the given String is a predefined unit, meaning it is one of the five SBML predefined
unit identifiers ('substance', 'volume', 'area', 'length' or 'time').
- isPredefined(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
Tests if the given unit is a predefined unit, meaning it is one of the five SBML predefined
unit identifiers ('substance', 'volume', 'area', 'length' or 'time').
- isPredefined() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if this unit definition is a predefined unit.
- isPredefinedUnitsID(String) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
Checks whether or not a given identifier for a
Unit.Kind or
UnitDefinition equals a predefined unit identifier for this type.
- isPrefixNotationInLogicalOperations() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- isPrintNameIfAvailable() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- isPrintNameIfAvailable() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- isProcess(int) - Static method in class org.sbml.jsbml.SBO
-
- isProduct(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isProtein(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isQuantitativeParameter(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isQuantitativeParameter - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Quantitative Parameter'.
- isRadian() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind radian
- isRate() - Method in class org.sbml.jsbml.Rule
-
- isRateLaw(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isRateLaw - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
-
Checks if the SBO of the SBase is part of the branch 'Rate Law'.
- isRational() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents a rational number, false otherwise.
- isReactant(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isReadingInProgress() - Method in class org.sbml.jsbml.AbstractTreeNode
-
Returns true if JSBML is in the process of reading a model through the
SBMLReader
methods.
- isReal() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node can represent a real number, false otherwise.
- isReceptor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isRelational() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is a MathML relational operator, meaning ==,
>=, >, <, <=, and !=.
- isRequired() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Returns the value of the required attribute for this package.
- isReversible() - Method in class org.sbml.jsbml.Reaction
-
- isRNA(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isRNAOrMessengerRNA(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isRoot() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- isRoot() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isRoot() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- isSBMLNamespaceNeeded(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- isSBMLNamespaceNeeded(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- isSboTerm(String) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A SBOTerm begins with 'SBO:' followed by exactly 7 digits
- isScalar() - Method in class org.sbml.jsbml.AssignmentRule
-
- isScalar() - Method in class org.sbml.jsbml.ExplicitRule
-
Predicate returning true or false depending on whether this Rule is an
AssignmentRule (SBML Level 2) or has a 'type' attribute value of 'scalar'
(SBML Level 1).
- isScalar() - Method in class org.sbml.jsbml.RateRule
-
- isScalar() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
-
- isSecond() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind second
- isSemantics() - Method in class org.sbml.jsbml.ASTNode
-
Return true if this node contain some semantics annotations.
- isSetAbout() - Method in class org.sbml.jsbml.Annotation
-
Checks whether the 'about' element has been initialized.
- isSetAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetAnnotation() - Method in class org.sbml.jsbml.Annotation
-
- isSetAnnotation() - Method in interface org.sbml.jsbml.SBase
-
Returns true or false depending on whether this object's
'annotation' sub-elements exists and have some content.
- isSetAreaUnits() - Method in class org.sbml.jsbml.Model
-
Returns
true if the area units ID of this
Model is not
null.
- isSetAreaUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns
true if the
UnitDefinition which has the area units
ID of this
Model as id is not
null.
- isSetAttributes() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- isSetBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- isSetBoundaryCondition - Variable in class org.sbml.jsbml.Species
-
- isSetBoundaryCondition() - Method in class org.sbml.jsbml.Species
-
- isSetCharacters() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- isSetCharge - Variable in class org.sbml.jsbml.Species
-
Boolean value to test if the charge has been set.
- isSetCharge() - Method in class org.sbml.jsbml.Species
-
- isSetChild() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
Returns true iff the child of this node has been set
- isSetClassName() - Method in class org.sbml.jsbml.ASTNode
-
- isSetCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- isSetCompartment() - Method in class org.sbml.jsbml.Reaction
-
- isSetCompartment() - Method in class org.sbml.jsbml.Species
-
- isSetCompartmentInstance() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- isSetCompartmentInstance() - Method in class org.sbml.jsbml.Reaction
-
- isSetCompartmentInstance() - Method in class org.sbml.jsbml.Species
-
- isSetCompartmentType() - Method in class org.sbml.jsbml.Compartment
-
Returns true if the compartmentID of this compartment is not
null.
- isSetCompartmentTypeInstance() - Method in class org.sbml.jsbml.Compartment
-
Deprecated.
- isSetConstant - Variable in class org.sbml.jsbml.SpeciesReference
-
- isSetConstant() - Method in class org.sbml.jsbml.SpeciesReference
-
- isSetConstant - Variable in class org.sbml.jsbml.Symbol
-
- isSetConstant() - Method in class org.sbml.jsbml.Symbol
-
- isSetConstant() - Method in interface org.sbml.jsbml.Variable
-
- isSetConversionFactor() - Method in class org.sbml.jsbml.Model
-
- isSetConversionFactor() - Method in class org.sbml.jsbml.Species
-
- isSetConversionFactorInstance() - Method in class org.sbml.jsbml.Model
-
Returns true if the Parameter which has the conversionFactorID of
this
Model as id is not null.
- isSetConversionFactorInstance() - Method in class org.sbml.jsbml.Species
-
- isSetCreatedDate() - Method in class org.sbml.jsbml.History
-
Predicate returning true or false depending on whether this
History's createdDate has been set.
- isSetDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
Returns True iff definitionURL has been set
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetDelay() - Method in class org.sbml.jsbml.Event
-
- isSetDenominator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Returns true iff denominator has been set
- isSetDenominator - Variable in class org.sbml.jsbml.SpeciesReference
-
Boolean value to know if the SpeciesReference denominator has been set.
- isSetDenominator() - Method in class org.sbml.jsbml.SpeciesReference
-
- isSetEmail() - Method in class org.sbml.jsbml.Creator
-
Returns
true or false depending on whether this
Creator's email has been set.
- isSetEncoding() - Method in class org.sbml.jsbml.ASTNode
-
- isSetEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isSetEncoding() - Method in interface org.sbml.jsbml.math.ASTCSymbolNode
-
Returns true iff encoding has been set
- isSetEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetExponent() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Returns True iff exponent has been set
- isSetExponent - Variable in class org.sbml.jsbml.Unit
-
- isSetExponent() - Method in class org.sbml.jsbml.Unit
-
- isSetExtendedASTNode() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- isSetExtendedASTNode() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Checks whether an extended TreeNode has been set.
- isSetExtendedSBase() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- isSetExtendedSBase() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Check whether an extended SBase has been set.
- isSetExtentUnits() - Method in class org.sbml.jsbml.Model
-
Returns true if the extentUnitsID of this Model is not null
.
- isSetExtentUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns true if the UnitDefinition which has the extentUnitsID of
this
Model as id is not null.
- isSetFamilyName() - Method in class org.sbml.jsbml.Creator
-
Returns
true or false depending on whether this
Creator's familyName has been set.
- isSetFast - Variable in class org.sbml.jsbml.Reaction
-
Checks whether the
Reaction.fast attribute has been set by using a default or
by changing its value.
- isSetFast() - Method in class org.sbml.jsbml.Reaction
-
- isSetGivenName() - Method in class org.sbml.jsbml.Creator
-
Returns
true or false depending on whether this
Creator's givenName has been set.
- isSetHasOnlySubstanceUnits - Variable in class org.sbml.jsbml.Species
-
- isSetHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
-
- isSetHistory() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetHistory() - Method in class org.sbml.jsbml.Annotation
-
Checks if the
History is initialized
- isSetHistory() - Method in interface org.sbml.jsbml.SBase
-
Returns
true if the
History instance of this object is set.
- isSetId() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetId() - Method in class org.sbml.jsbml.ASTNode
-
- isSetId() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetId() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff id has been set
- isSetId() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetId() - Method in interface org.sbml.jsbml.NamedSBase
-
Returns true if the id is not null.
- isSetId() - Method in interface org.sbml.jsbml.SBase
-
Returns true if the id is not null.
- isSetInitialAmount() - Method in class org.sbml.jsbml.Species
-
- isSetInitialConcentration() - Method in class org.sbml.jsbml.Species
-
- isSetInitialValue() - Method in class org.sbml.jsbml.Trigger
-
- isSetInteger() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
Returns True iff value has been set
- isSetKey() - Method in class org.sbml.jsbml.util.Pair
-
- isSetKind() - Method in class org.sbml.jsbml.Unit
-
Predicate to test whether the 'kind' attribute of this
Unit has been set.
- isSetKineticLaw() - Method in class org.sbml.jsbml.Reaction
-
- isSetL() - Method in class org.sbml.jsbml.util.ValuePair
-
- isSetLeftChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
Return true iff left child has been set
- isSetLeftChild() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- isSetLeftChild() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- isSetLengthUnits() - Method in class org.sbml.jsbml.Model
-
Returns true if the lengthUnitsID of this Model is not null
.
- isSetLengthUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns true if the UnitDefinition which has the lengthUnitsID of
this
Model as id is not null.
- isSetLevel() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetLevel() - Method in interface org.sbml.jsbml.SBase
-
Returns true if the level is set.
- isSetLevelAndVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetLevelAndVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns
true if both, Level and Version are set for this
SBase.
- isSetList() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns true iff listOfNodes has been set
- isSetListOfCompartments() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfCompartments of this Model is not
null and not
empty.
- isSetListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
- isSetListOfConstraints() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfConstraints of this Model is not
null and not
empty.
- isSetListOfCreators() - Method in class org.sbml.jsbml.History
-
- isSetListOfCVTerms() - Method in class org.sbml.jsbml.Annotation
-
Checks if the list of
CVTerm is not empty.
- isSetListOfErrors() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns true if the list of errors is defined and contain at least
one error.
- isSetListOfEventAssignments() - Method in class org.sbml.jsbml.Event
-
Returns true, if listOfEventAssignments contains at least one element.
- isSetListOfEvents() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfEvents of this Model is not null
and not empty.
- isSetListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfFunctionDefinitions of this Model is not
null and
not empty.
- isSetListOfInitialAssignments() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfInitialAssignments of this Model is not
null and
not empty.
- isSetListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
-
Returns true, if the list of local parameters is set and not empty..
- isSetListOfModification() - Method in class org.sbml.jsbml.History
-
- isSetListOfModifiers() - Method in class org.sbml.jsbml.Reaction
-
- isSetListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- isSetListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- isSetListOfParameters() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfParameters of this Model is not
null and not
empty.
- isSetListOfProducts() - Method in class org.sbml.jsbml.Reaction
-
- isSetListOfReactants() - Method in class org.sbml.jsbml.Reaction
-
- isSetListOfReactions() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfReactions of this Model is not
null and not
empty.
- isSetListOfRules() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfRules of this Model is not null
and not empty.
- isSetListOfSpecies() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfSpecies of this Model is not null
and not empty.
- isSetListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
-
- isSetListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
Returns true if the listOfUnitDefinitions of this Model is not
null and not
empty.
- isSetListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
Returns true if the listOfUnits is not null and not empty.
- isSetMantissa() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Returns true iff mantissa has been set
- isSetMath() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- isSetMath() - Method in interface org.sbml.jsbml.MathContainer
-
- isSetMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff mathMLClass has been set
- isSetMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetMessage() - Method in class org.sbml.jsbml.Constraint
-
Returns
true if the message of this
Constraint is not
null.
- isSetMetaId() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetMetaId() - Method in interface org.sbml.jsbml.SBase
-
Returns true or false depending on whether this object's
'metaid' attribute has been set.
- isSetModel() - Method in class org.sbml.jsbml.SBMLDocument
-
- isSetModelHistory() - Method in class org.sbml.jsbml.Model
-
- isSetModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- isSetModifiedDate() - Method in class org.sbml.jsbml.History
-
Predicate returning true or false depending on whether this
History's modifiedDate has been set.
- isSetMultiplier - Variable in class org.sbml.jsbml.Unit
-
- isSetMultiplier() - Method in class org.sbml.jsbml.Unit
-
- isSetName() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetName() - Method in class org.sbml.jsbml.ASTNode
-
- isSetName() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Deprecated.
- isSetName() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetName() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
Returns True iff name has been set
- isSetName() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetName() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns True iff name has been set
- isSetName() - Method in interface org.sbml.jsbml.NamedSBase
-
Returns true if the name is not null.
- isSetName() - Method in interface org.sbml.jsbml.SBase
-
Returns true if the name is not null.
- isSetName() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- isSetNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- isSetNewValue() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isSetNonRDFannotation() - Method in class org.sbml.jsbml.Annotation
-
Checks if the non RDF part of the Annotation is initialized.
- isSetNotes() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetNotes() - Method in interface org.sbml.jsbml.SBase
-
Returns true or false depending on whether this object's
'notes' sub-element exists and has content.
- isSetNumber() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns True iff base has been set
- isSetNumberType - Variable in class org.sbml.jsbml.ASTNode
-
Tells if the type attribute of the cn element was set and we need to
write it back or if it is set to the default (REAL).
- isSetNumberType() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if the number type is set.
- isSetNumberType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isSetNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Returns true iff numerator has been set
- isSetOffset - Variable in class org.sbml.jsbml.Unit
-
- isSetOffset() - Method in class org.sbml.jsbml.Unit
-
- isSetOldValue() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isSetOrganisation() - Method in class org.sbml.jsbml.Creator
-
Returns
true or false depending on whether this
Creator's organisation has been set.
- isSetOrganization() - Method in class org.sbml.jsbml.Creator
-
Returns
true or false depending on whether this
Creator's organisation has been set.
- isSetOtherAnnotationThanRDF() - Method in class org.sbml.jsbml.Annotation
-
- isSetOtherAttributes() - Method in class org.sbml.jsbml.Creator
-
- isSetOutside() - Method in class org.sbml.jsbml.Compartment
-
Returns true if the outsideID of this compartment is not
null.
- isSetOutsideInstance() - Method in class org.sbml.jsbml.Compartment
-
Returns true if the compartment instance which matches the
outsideID of
this compartment is not null.
- isSetPackageRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns true.
- isSetPackageVErsion() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- isSetPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- isSetPackageVersion() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin
-
Returns true if a package version is set, false otherwise.
- isSetPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns true if a package version is set, false otherwise.
- isSetPackageVErsion() - Method in interface org.sbml.jsbml.SBase
-
Returns true if the package version is not equals to '-1'.
- isSetParent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- isSetParent() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetParent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- isSetParentSBMLObject() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetParentSBMLObject() - Method in class org.sbml.jsbml.ASTNode
-
Checks if a parent SBML object, i.e., a
MathContainer, is set as a
parent SBML object for this
ASTNode.
- isSetParentSBMLObject() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetParentSBMLObject() - Method in interface org.sbml.jsbml.math.ASTNode2
-
- isSetParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetParentSBMLObject() - Method in interface org.sbml.jsbml.SBase
-
Check whether this
SBase has been linked to a parent within the
hierarchical SBML data structure.
- isSetPersistent() - Method in class org.sbml.jsbml.Trigger
-
- isSetPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isSetPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetPlugin(String) - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if an
ASTNodePlugin is defined
for the given package.
- isSetPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true if an
SBasePlugin is defined
for the given package.
- isSetPrefix() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- isSetPriority() - Method in class org.sbml.jsbml.Event
-
- isSetProgramName() - Method in class org.sbml.jsbml.SBMLWriter
-
Check if a program name has been defined for this
SBMLWriter.
- isSetProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter
-
Check if a program version has been defined for this
SBMLWriter.
- isSetQualifier() - Method in class org.sbml.jsbml.CVTerm
-
- isSetQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- isSetRDFannotation() - Method in class org.sbml.jsbml.Annotation
-
Checks if the RDF part of the Annotation is initialized.
- isSetReal() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns true iff a value has been set
- isSetRefId() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Return true iff refId is set
- isSetRefId() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Return true iff refId is set
- isSetReversible - Variable in class org.sbml.jsbml.Reaction
-
Checks whether the
Reaction.reversible attribute has been set by using a default or
by changing its value.
- isSetReversible() - Method in class org.sbml.jsbml.Reaction
-
- isSetRightChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
Return true iff right child has been set
- isSetRightChild() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- isSetRightChild() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- isSetSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetSBOTerm() - Method in interface org.sbml.jsbml.SBase
-
Returns true if the SBOTerm is set.
- isSetScale - Variable in class org.sbml.jsbml.Unit
-
- isSetScale() - Method in class org.sbml.jsbml.Unit
-
- isSetSize() - Method in class org.sbml.jsbml.Compartment
-
Returns true if the size of this compartment has been set by a
user.
- isSetSource() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isSetSpatialDimensions - Variable in class org.sbml.jsbml.Compartment
-
Helper variable to check if spatial dimensions has been set by the user.
- isSetSpatialDimensions() - Method in class org.sbml.jsbml.Compartment
-
Returns true if the spatialDimensions of this compartment has been
set by a user.
- isSetSpatialSizeUnits() - Method in class org.sbml.jsbml.Species
-
- isSetSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- isSetSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- isSetSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- isSetSpeciesType() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- isSetSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- isSetStoichiometry - Variable in class org.sbml.jsbml.SpeciesReference
-
- isSetStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
-
- isSetStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference
-
- isSetStyle() - Method in class org.sbml.jsbml.ASTNode
-
- isSetStyle() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetStyle() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff style has been set
- isSetStyle() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetSubstanceUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetSubstanceUnits() - Method in class org.sbml.jsbml.Model
-
Returns true if the substanceUnitsID of this Model is not
null.
- isSetSubstanceUnits() - Method in class org.sbml.jsbml.Species
-
- isSetSubstanceUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns true if the UnitDefinition which has the substanceUnitsID
of this
Model as id is not null.
- isSetSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- isSetSymbol() - Method in class org.sbml.jsbml.InitialAssignment
-
- isSetTimeUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- isSetTimeUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetTimeUnits() - Method in class org.sbml.jsbml.Model
-
Returns
true if the timeUnitsID of this
Model is not
null.
- isSetTimeUnitsInstance() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- isSetTimeUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetTimeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns true if the UnitsDefinition which has the timeUnistID of
this Model
as id is not null.
- isSetTrigger() - Method in class org.sbml.jsbml.Event
-
- isSetType() - Method in class org.sbml.jsbml.CVTerm
-
- isSetType() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetType() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff type has been set
- isSetType() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetTypeQualifier() - Method in class org.sbml.jsbml.CVTerm
-
- isSetUnit() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isSetUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isSetUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- isSetUnits() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if a unit is defined on this node.
- isSetUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- isSetUnits() - Method in class org.sbml.jsbml.ExplicitRule
-
- isSetUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetUnits() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns True iff units has been set
- isSetUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- isSetUnitsInstance() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- isSetUnitsInstance() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- isSetUnitsInstance() - Method in class org.sbml.jsbml.ExplicitRule
-
- isSetUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- isSetUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- isSetUserObjects() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- isSetUserObjects() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetUserObjects() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Checks whether any user-defined key-value pairs have been attached
to this object.
- isSetUseValuesFromTriggerTime - Variable in class org.sbml.jsbml.Event
-
- isSetUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
-
- isSetV() - Method in class org.sbml.jsbml.util.ValuePair
-
- isSetValue() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
Returns true iff value has been set
- isSetValue() - Method in interface org.sbml.jsbml.Quantity
-
Returns
true if the value of this
Quantity is set.
- isSetValue - Variable in class org.sbml.jsbml.QuantityWithUnit
-
a boolean to help knowing is the value as been set by the user or is the
default one.
- isSetValue() - Method in class org.sbml.jsbml.QuantityWithUnit
-
- isSetValue() - Method in class org.sbml.jsbml.SpeciesReference
-
- isSetValue() - Method in class org.sbml.jsbml.util.Pair
-
- isSetVariable() - Method in interface org.sbml.jsbml.Assignment
-
Returns
true if the variableID of this
Assignment is not
null.
- isSetVariable() - Method in class org.sbml.jsbml.EventAssignment
-
- isSetVariable() - Method in class org.sbml.jsbml.ExplicitRule
-
- isSetVariable() - Method in class org.sbml.jsbml.InitialAssignment
-
- isSetVariable() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns true iff this
ASTNumber node
represents a variable.
- isSetVariableInstance() - Method in interface org.sbml.jsbml.Assignment
-
Returns
true if the
Variable instance which has the variableID of
this
Assignment as id is not
null.
- isSetVariableInstance() - Method in class org.sbml.jsbml.EventAssignment
-
- isSetVariableInstance() - Method in class org.sbml.jsbml.ExplicitRule
-
- isSetVariableInstance() - Method in class org.sbml.jsbml.InitialAssignment
-
- isSetVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns true if the version is not null.
- isSetVolume() - Method in class org.sbml.jsbml.Compartment
-
- isSetVolumeUnits() - Method in class org.sbml.jsbml.Model
-
Returns true if the volumeUnitsID of this Model is not null
.
- isSetVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns true if the UnitDefinition which has the volumeUnitsID of
this
Model as id is not null.
- isSiemens() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind siemens
- isSievert() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind sievert
- isSimpleMolecule(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isSmallLetter(char) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A small letter is a ASCII symbol between 'a' and 'z'.
- isSpeciesConcentration() - Method in class org.sbml.jsbml.AlgebraicRule
-
- isSpeciesConcentration() - Method in class org.sbml.jsbml.ExplicitRule
-
- isSpeciesConcentration() - Method in class org.sbml.jsbml.Rule
-
(SBML Level 1 only) Predicate returning
true or
false depending on
whether this
Rule is an SpeciesConcentrationRule.
- isSpeciesReference(Model, String) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- isSpecificActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isSqrt() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents a square root function, false
otherwise.
- isStart() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
this
XMLToken is an XML start element.
- isStartElement - Variable in class org.sbml.jsbml.xml.XMLToken
-
- isStateTransition(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isSteadyStateExpression(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isSteradian() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind steradian
- isStimulator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isStrict() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isStrict() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Specifies strictness.
- isStrict() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isString() - Method in class org.sbml.jsbml.ASTNode
-
- isString() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isString() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- issuedWarnings - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Remember already issued warnings to avoid having multiple lines, saying
the same thing (Warning: Skipping detailed parsing of name space 'XYZ'.
- isSum() - Method in class org.sbml.jsbml.ASTNode
-
Checks if this
ASTNode represents a sum.
- isSum() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isSum() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isSystem() - Method in exception org.sbml.jsbml.SBMLError
-
Returns
true is the
SBMLError category is of type
system
- isSystem() - Method in exception org.sbml.jsbml.SBMLException
-
- isTesla() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind tesla
- isText - Variable in class org.sbml.jsbml.xml.XMLToken
-
- isText() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true or
false depending on whether
this
XMLToken is an XML text element.
- isTranscription(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTranscriptionalActivation(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTranscriptionalInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTransitionOmitted(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTranslation(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTranslationalActivation(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTranslationalInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTransport(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTrigger(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isTruncated(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isUMinus() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node is a unary minus operator, false otherwise.
- isUMinus() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isUMinus() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isUnary() - Method in class org.sbml.jsbml.ASTNode
-
Checks whether the number of child nodes is exactly one.
- isUnary() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isUnary() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isUnitKind(Unit.Kind, int, int) - Static method in class org.sbml.jsbml.Unit
-
- isUnitKind(String, int, int) - Static method in class org.sbml.jsbml.Unit
-
Predicate to test whether a given string is the name of a valid base unit
in SBML (such as 'gram' or 'mole').
- isUnitKind() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests whether this
UnitDefinition contains
exactly one
Unit that itself represents a
Unit.Kind, i.e.,
multiplier = 1, exponent = 1, scale = 1.
- isUnitsDefined - Variable in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- isUnitsDefined() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- isUnitsDefined - Variable in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- isUnitsDefined() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- isUnknown() - Method in class org.sbml.jsbml.ASTNode
-
- isUnknownMolecule(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isUnknownTransition(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isUserObjectRecursiveDataType() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- isUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
-
- isValidChemicalFormula(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
- isValidCreatedDate(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidCreator(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidEmailAddress(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Definition of valid e-mail address Strings.
- isValidId(String, int, int) - Static method in class org.sbml.jsbml.AbstractNamedSBase
-
- isValidId(String, int, int) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Checks whether the given idCandidate is a valid identifier according to
the SBML specifications.
- isValidLevelAndVersionCombination(int, int) - Static method in class org.sbml.jsbml.AbstractSBase
-
Returns true if the level and version combination is a valid one,
false otherwise.
- isValidMetaId(String) - Static method in class org.sbml.jsbml.AbstractSBase
-
- isValidMetaId(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Checks if the given identifier candidate satisfies the requirements for a
valid meta identifier (see SBML L2V4 p.
- isValidRDF(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidRDFDescription(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidRDFHistory(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidRDFURIs(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidSBMLRDF(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Returns true if the SBML RDF block is recognized as valid or partially valid.
- isValidUnit(Model, String) - Static method in class org.sbml.jsbml.Unit
-
Returns
true if the
unit is a valid unit kind name or an
identifier of an existing
UnitDefinition.
- isValidUnitKindString(String, int, int) - Static method in enum org.sbml.jsbml.Unit.Kind
-
- isValidVariable(Variable, int) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- isValidVCard(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Returns
SBMLRDFAnnotationParser.NODE_COLOR.GREEN if at least one of these three nodes is present: vCard:N, vCard:EMAIL or vCard:ORG,
meaning that we consider that the VCard is at least partially defined.
- isVariable() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true if this node represents a
Variable.
- isVariantOfArea() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfArea() - Method in class org.sbml.jsbml.UnitDefinition
-
Returns true if this UnitDefinition is a variant of Area
- isVariantOfDimensionless() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if a given unit definition is a variant
of the predefined unit identifier 'dimensionless'.
- isVariantOfLength() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfLength() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if a given unit definition is a variant
of the predefined unit identifier 'length'.
- isVariantOfSubstance() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfSubstance() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if a given unit definition is a variant
of the predefined unit identifier 'substance'.
- isVariantOfSubstancePerArea() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if a given unit definition is a variant
of the predefined unit identifier 'substance per area'.
- isVariantOfSubstancePerLength() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if this UnitDefinition is a variant of substance per
length.
- isVariantOfSubstancePerTime() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if this UnitDefinition is a variant of substance per
time.
- isVariantOfSubstancePerVolume() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if this UnitDefinition is a variant of substance per volume.
- isVariantOfTime() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfTime() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if a given unit definition is a variant
of the predefined unit identifier 'time'.
- isVariantOfVolume() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfVolume() - Method in class org.sbml.jsbml.UnitDefinition
-
Tests if a given unit definition is a variant
of the predefined unit identifier 'volume'.
- isVector() - Method in class org.sbml.jsbml.ASTNode
-
Checks if this
ASTNode represents a vector.
- isVolt() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind volt
- isWarning() - Method in exception org.sbml.jsbml.SBMLError
-
- isWarning() - Method in exception org.sbml.jsbml.SBMLException
-
- isWatt() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind watt
- isWeber() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind weber
- isXML() - Method in exception org.sbml.jsbml.SBMLError
-
Returns
true is the
SBMLError category is of type
xml
- isXML() - Method in exception org.sbml.jsbml.SBMLException
-
- isXmlId(String) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
A XML ID (defined in the XML Schema 1.0) starts with a letter, '-' or ':'
which can be followed by a unlimited amout of NameChars.
- isZero() - Method in class org.sbml.jsbml.ASTNode
-
Returns true if this node represents the number zero (either as integer
or as real value).
- iterator() - Method in class org.sbml.jsbml.ListOf
-
- l - Variable in class org.sbml.jsbml.util.Pair
-
Left value.
- label(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- label(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- lambda(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- lambda(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- lambda(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- lambda(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- lambda(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- lambda(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- lambdaBody(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Creates the body of a lambda function, i.e., the argument list and the
actual mathematical operation, all comma separated and surrounded in
brackets.
- lambdaBody(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Creates the body of a lambda function, i.e., the argument list and the
actual mathematical operation, all comma separated and surrounded in
brackets.
- lang - Variable in class org.sbml.jsbml.util.Message
-
- lastElementCreated - Variable in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
The last top Element that has been created in the previous step.
- lastElementWasApply - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- lastIndexOf(Object) - Method in class org.sbml.jsbml.ListOf
-
- LaTeXCompiler - Class in org.sbml.jsbml.math.compiler
-
Converts
ASTNode2Value objects into a LaTeX
String to be
included into scientific writings or to be displayed in a GUI.
- LaTeXCompiler() - Constructor for class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- LaTeXCompiler(boolean) - Constructor for class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- LaTeXCompiler - Class in org.sbml.jsbml.util.compilers
-
Converts
ASTNodeValue objects into a LaTeX
String to be
included into scientific writings or to be displayed in a GUI.
- LaTeXCompiler() - Constructor for class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- LaTeXCompiler(boolean) - Constructor for class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- LAYOUT_10100 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010100:
- LAYOUT_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010101:
To conform to Version 1 of the Layout 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/layout/version1' Reference: L3V1
Layout V1 Section 3.1
- LAYOUT_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010102:
Wherever they appear in an SBML document, elements and attributes from the
Layout package must be declared either implicitly or explicitly to be in the XML
namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1' Reference:
L3V1 Layout V1 Section 3.1
- LAYOUT_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010301:
(Extends validation rule #10301 in the SBML Level 3 Version 1 Core
specification.) Within a <model> object the values of the attributes id and
layout:id on every instance of the following classes of objects must be unique
across the set of all id and layout: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 <boundingBox>, <compartmentGlyph>,
<generalGlyph>, <graphicalObject>, <layout>, <speciesGlyph>,
<speciesReferenceGlyph>, <reactionGlyph>, <referenceGlyph> and <textGlyph>
objects defined by the Layout package.
- LAYOUT_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010302:
The value of the 'layout:id' attribute must conform to the SBML data type SId
Reference: L3V1 Layout V1 Section 3.3
- LAYOUT_10401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010401:
The attribute 'xsi:type' must be present on all <lineSegment> and <cubicBezier>
objects.
- LAYOUT_10402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6010402:
The value of the 'xsi:type' attribute must be either 'LineSegment' or
'CubicBezier' appropriate to the object where it is located.
- LAYOUT_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020101:
In all SBML documents using the Layout package, the SBML object must include a
value for the attribute 'layout:required'.
- LAYOUT_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020102:
The value of attribute 'layout:required' on the SBML object must be of the data
type Boolean.
- LAYOUT_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020103:
The value of attribute 'layout:required' on the SBML object must be set to
'false'.
- LAYOUT_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020201:
There may be at most one instance of <listOfLayouts> element within a <model>
object using Layout.
- LAYOUT_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020202:
The <listOfLayouts> within a <model> object is optional, but if present, this
object must not be empty.
- LAYOUT_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020203:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfLayouts> container object may only contain <layout> objects.
- LAYOUT_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020204:
A <listOfLayouts> object may have the optional attributes 'metaid' and 'sboTerm'
defined by SBML Level 3 Core.
- LAYOUT_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020301:
A <layout> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- LAYOUT_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020302:
A <layout> object may have the optional SBML Level 3 Core attributes 'metaid'
and 'sboTerm'.
- LAYOUT_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020303:
There may be at most one instance of each of the following kinds of objects
within a <layout> object: <listOfCompartmentGlyphs>, <listOfSpeciesGlyphs>,
<listOfReactionGlyphs>, <listOfTextGlyphs>, <listOfAdditionalGraphicalObjects>.
- LAYOUT_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020304:
The various ListOf subobjects within a <layout> object are optional, but if
present, these container object must not be empty.
- LAYOUT_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020305:
A <layout> object must have the required attribute 'layout:id' and may have the
optional attribute 'layout:name'.
- LAYOUT_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020306:
The attribute 'layout:name' of a <layout> must be of the data type 'string'.
- LAYOUT_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020307:
A <listOfCompartmentGlyphs> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020308:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfCompartmentGlyphs> container object may only contain
<compartmentGlyph> objects.
- LAYOUT_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020309:
A <listOfSpeciesGlyphs> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020310:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfSpeciesGlyphs> container object may only contain
<compartmentGlyph> objects.
- LAYOUT_20311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020311:
A <listOfReactionGlyphs> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20312 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020312:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfReactionGlyphs> container object may only contain
<compartmentGlyph> objects.
- LAYOUT_20313 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020313:
A <listOfAdditionalGraphicalObjectGlyphs> object may have the optional
attributes 'metaid' and 'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20314 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020314:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfAdditionalGraphicalObjectGlyphs> container object may only
contain <compartmentGlyph> objects.
- LAYOUT_20315 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020315:
A <layout> object must contain exactly one <dimensions> object.
- LAYOUT_20316 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020316:
A <listOfTextGlyphs> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20317 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020317:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfTextGlyphs> container object may only contain
<compartmentGlyph> objects.
- LAYOUT_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020401:
A <graphicalObject> object may have the optional SBML Level 3 Core subobjects
for notes and annotations.
- LAYOUT_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020402:
A <graphicalObject> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020403:
There may be at most one instance of a <boundingBox> object on a
<graphicalObject>.
- LAYOUT_20404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020404:
A <graphicalObject> object must have the required attribute 'layout:id' and may
have the optional attribute 'layout:metaidRef'.
- LAYOUT_20405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020405:
The attribute 'layout:metaidRef' of a <graphicalObject> must be of the data type
'IDREF'.
- LAYOUT_20406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020406:
The value of a 'layout:metaidRef' attribute of a <graphicalObject> must be of
the 'metaid' of an existing element in the <model>.
- LAYOUT_20407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020407:
A <graphicalObject> must contain exactly one <boundingBox> object.
- LAYOUT_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020501:
A <compartmentGlyph> object may have the optional SBML Level 3 Core subobjects
for notes and annotations.
- LAYOUT_20502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020502:
A <compartmentGlyph> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_20503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020503:
There may be at most one instance of a <boundingBox> object on a
<compartmentGlyph>.
- LAYOUT_20504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020504:
A <compartmentGlyph> object must have the required attribute 'layout:id' and may
have the optional attributes 'layout:metaidRef' or 'layout:compartment'.
- LAYOUT_20505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020505:
The attribute 'layout:metaidRef' of a <compartmentGlyph> must be of the data
type 'IDREF'.
- LAYOUT_20506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020506:
The value of a 'layout:metaidRef' attribute of a <compartmentGlyph> must be of
the 'metaid' of an existing element in the <model>.
- LAYOUT_20507 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020507:
The attribute 'layout:compartment' of a <compartmentGlyph> must be the data type
'SIdRef'.
- LAYOUT_20508 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020508:
The value of the 'layout:compartment' attribute of a <compartmentGlyph> must be
of the 'id' of an existing <compartment> in the <model>.
- LAYOUT_20509 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020509:
If both attributes 'layout:compartment' and 'layout:metaidRef' are specified on
a <compartmentGlyph> they have to reference the same <compartment> in the
<model>.
- LAYOUT_20510 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020510:
The attribute 'layout:order' of a <compartmentGlyph> must be the data type
'double'.
- LAYOUT_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020601:
A <speciesGlyph> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020602:
A <speciesGlyph> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_20603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020603:
There may be at most one instance of a <boundingBox> object on a <speciesGlyph>.
- LAYOUT_20604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020604:
A <speciesGlyph> object must have the required attribute 'layout:id' and may
have the optional attributes 'layout:metaidRef' or 'layout:species'.
- LAYOUT_20605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020605:
The attribute 'layout:metaidRef' of a <speciesGlyph> must be of the data type
'IDREF'.
- LAYOUT_20606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020606:
The value of a 'layout:metaidRef' attribute of a <speciesGlyph> must be of the
'metaid' of an existing element in the <model>.
- LAYOUT_20607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020607:
The attribute 'layout:species' of a <speciesGlyph> must be the data type
'SIdRef'.
- LAYOUT_20608 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020608:
The value of the 'layout:species' attribute of a <speciesGlyph> must be of the
'id' of an existing <species> in the <model>.
- LAYOUT_20609 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020609:
If both attributes 'layout:species' and 'layout:metaidRef' are specified on a
<speciesGlyph> they have to reference the same <species> in the <model>.
- LAYOUT_20701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020701:
A <reactionGlyph> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_20702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020702:
A <reactionGlyph> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_20703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020703:
There may be at most one instance of each of the following kinds of objects
within a <reactionGlyph> object: <boundingBox>, and <curve> and there must be
one instance of the <listOfSpeciesReferenceGlyphs>.
- LAYOUT_20704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020704:
A <reactionGlyph> object must have the required attribute 'layout:id' and may
have the optional attributes 'layout:metaidRef' or 'layout:reaction'.
- LAYOUT_20705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020705:
The attribute 'layout:metaidRef' of a <reactionGlyph> must be of the data type
'IDREF'.
- LAYOUT_20706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020706:
The value of a 'layout:metaidRef' attribute of a <reactionGlyph> must be of the
'metaid' of an existing element in the <model>.
- LAYOUT_20707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020707:
The attribute 'layout:reaction' of a <reactionGlyph> must be the data type
'SIdRef'.
- LAYOUT_20708 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020708:
The value of the 'layout:reaction' attribute of a <reactionGlyph> must be of the
'id' of an existing <reaction> in the <model>.
- LAYOUT_20709 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020709:
If both attributes 'layout:reaction' and 'layout:metaidRef' are specified on a
<reactionGlyph> they have to reference the same <reaction> in the <model>.
- LAYOUT_20710 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020710:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfSpeciesReferenceGlyphs> container object may only contain
<speciesReferenceGlyph> objects.
- LAYOUT_20711 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020711:
A <listOfSpeciesReferenceGlyphs> object may have the optional attributes
'metaid' and 'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20712 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020712:
A <listOfSpeciesReferenceGlyphs> container object must not be empty.
- LAYOUT_20801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020801:
A <generalGlyph> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_20802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020802:
A <generalGlyph> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_20803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020803:
There may be at most one instance of each of the following kinds of objects
within a <generalGlyph> object: <boundingBox>, <curve>, <listOfReferenceGlyphs>
and <listOfSubGlyphs>.
- LAYOUT_20804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020804:
A <generalGlyph> object must have the required attribute 'layout:id' and may
have the optional attributes 'layout:metaidRef' or 'layout:reference'.
- LAYOUT_20805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020805:
The attribute 'layout:metaidRef' of a <generalGlyph> must be of the data type
'IDREF'.
- LAYOUT_20806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020806:
The value of a 'layout:metaidRef' attribute of a <generalGlyph> must be of the
'metaid' of an existing element in the <model>.
- LAYOUT_20807 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020807:
The attribute 'layout:reference' of a <generalGlyph> must be the data type
'SIdRef'.
- LAYOUT_20808 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020808:
The value of the 'layout:reference' attribute of a <generalGlyph> must be of the
'id' of an existing element in the <model>.
- LAYOUT_20809 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020809:
If both attributes 'layout:reference' and 'layout:metaidRef' are specified on a
<generalGlyph> they have to reference the same element in the <model>.
- LAYOUT_20810 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020810:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfReferenceGlyphs> container object may only contain
<referenceGlyph> objects.
- LAYOUT_20811 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020811:
A <listOfReferenceGlyphs> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20812 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020812:
- LAYOUT_20813 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020813:
A <listOfSubGlyphs> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_20901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020901:
A <textGlyph> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_20902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020902:
A <textGlyph> object may have the optional SBML Level 3 Core attributes 'metaid'
and 'sboTerm'.
- LAYOUT_20903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020903:
A <textGlyph> must contain exactly one <boundingBox> object.
- LAYOUT_20904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020904:
A <textGlyph> object must have the required attribute 'layout:id' and may have
the optional attributes 'layout:metaidRef', 'layout:graphicalObject',
'layout:text' and 'layout:originOfText'.
- LAYOUT_20905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020905:
The attribute 'layout:metaidRef' of a <textGlyph> must be of the data type
'IDREF'.
- LAYOUT_20906 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020906:
The value of a 'layout:metaidRef' attribute of a <textGlyph> must be of the
'metaid' of an existing element in the <model>.
- LAYOUT_20907 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020907:
The attribute 'layout:originOfText' of a <textGlyph> must be the data type
'SIdRef'.
- LAYOUT_20908 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020908:
The value of the 'layout:originOfText' attribute of a <textGlyph> must be of the
'id' of an existing element in the <model>.
- LAYOUT_20909 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020909:
If both attributes 'layout:originOfText' and 'layout:metaidRef' are specified on
a <textGlyph> they have to reference the same element in the <model>.
- LAYOUT_20910 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020910:
The attribute 'layout:graphicalObject' of a <textGlyph> must be the data type
'SIdRef'.
- LAYOUT_20911 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020911:
The value of the 'layout:graphicalObject' attribute of a <textGlyph> must be of
the 'id' of an existing <graphicalObject> (or derived) element in the <layout>.
- LAYOUT_20912 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6020912:
The attribute 'layout:text' of a <textGlyph> must be the data type 'string'.
- LAYOUT_21001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021001:
A <speciesReferenceGlyph> object may have the optional SBML Level 3 Core
subobjects for notes and annotations.
- LAYOUT_21002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021002:
A <speciesReferenceGlyph> object may have the optional SBML Level 3 Core
attributes 'metaid' and 'sboTerm'.
- LAYOUT_21003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021003:
A <speciesReferenceGlyph> may have at most one instance of a <boundingBox> and
<curve> object.
- LAYOUT_21004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021004:
A <speciesReferenceGlyph> object must have the required attribute 'layout:id'
and may have the optional attributes 'layout:metaidRef',
'layout:speciesReference' and 'layout:role'.
- LAYOUT_21005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021005:
The attribute 'layout:metaidRef' of a <speciesReferenceGlyph> must be of the
data type 'IDREF'.
- LAYOUT_21006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021006:
The value of a 'layout:metaidRef' attribute of a <speciesReferenceGlyph> must be
of the 'metaid' of an existing element in the <model>.
- LAYOUT_21007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021007:
The attribute 'layout:speciesReference' of a <speciesReferenceGlyph> must be the
data type 'SIdRef'.
- LAYOUT_21008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021008:
The value of the 'layout:speciesReference' attribute of a
<speciesReferenceGlyph> must be of the 'id' of an existing <speciesReference> in
the <model>.
- LAYOUT_21009 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021009:
If both attributes 'layout:speciesReference' and 'layout:metaidRef' are
specified on a <speciesReferenceGlyph> they have to reference the same
<speciesReference> in the <model>.
- LAYOUT_21010 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021010:
The attribute 'layout:speciesGlyph' of a <speciesReferenceGlyph> must be the
data type 'SIdRef'.
- LAYOUT_21011 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021011:
The value of the 'layout:speciesGlyph' attribute of a <speciesReferenceGlyph>
must be of the 'id' of an existing <speciesGlyph> element in the <layout>.
- LAYOUT_21012 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021012:
The attribute 'layout:role' of a <speciesReferenceGlyph> must be of data type
'SpeciesReferenceRole', i.e.
- LAYOUT_21101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021101:
A <referenceGlyph> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_21102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021102:
A <referenceGlyph> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_21103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021103:
There may be at most one instance of a <boundingBox> and <curve> object on a
<referenceGlyph>.
- LAYOUT_21104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021104:
A <referenceGlyph> object must have the required attributes 'layout:id' and
'layout:glyph' and may have the optional attributes 'layout:metaidRef',
'layout:reference' and 'layout:role'.
- LAYOUT_21105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021105:
The attribute 'layout:metaidRef' of a <referenceGlyph> must be of the data type
'IDREF'.
- LAYOUT_21106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021106:
The value of a 'layout:metaidRef' attribute of a <referenceGlyph> must be of the
'metaid' of an existing element in the <model>.
- LAYOUT_21107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021107:
The attribute 'layout:reference' of a <referenceGlyph> must be the data type
'SIdRef'.
- LAYOUT_21108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021108:
The value of the 'layout:reference' attribute of a <referenceGlyph> must be of
the 'id' of an existing element in the <model>.
- LAYOUT_21109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021109:
If both attributes 'layout:reference' and 'layout:metaidRef' are specified on a
<referenceGlyph> they have to reference the same element in the <model>.
- LAYOUT_21110 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021110:
The attribute 'layout:glyph' of a <referenceGlyph> must be the data type
'SIdRef'.
- LAYOUT_21111 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021111:
The value of the 'layout:glyph' attribute of a <referenceGlyph> must be of the
'id' of an existing <graphicalObject> (or derived) element in the <layout>.
- LAYOUT_21112 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021112:
The attribute 'layout:role' of a <referenceGlyph> must be the data type
'string'.
- LAYOUT_21201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021201:
A <point> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- LAYOUT_21202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021202:
A <point> object may have the optional SBML Level 3 Core attributes 'metaid' and
'sboTerm'.
- LAYOUT_21203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021203:
A <point> object must have the required attributes 'layout:x' and 'layout:y' and
may have the optional attributes 'layout:id', and 'layout:z'.
- LAYOUT_21204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021204:
The attributes 'layout:x', 'layout:y' and 'layout:z' of a <point> element must
be of the data type 'double'.
- LAYOUT_21301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021301:
A <boundingBox> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_21302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021302:
A <boundingBox> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_21303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021303:
There must be exactly one instance of a <point> and a <dimensions> object on a
<boundingBox>.
- LAYOUT_21304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021304:
A <boundingBox> object may have the optional attributes 'layout:id'.
- LAYOUT_21305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021305:
If the 'layout:z' attribute on a <point> element of a <boundingBox> is not
specified, the attribute 'layout:depth' must not be specified.
- LAYOUT_21401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021401:
A <curve> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- LAYOUT_21402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021402:
A <curve> object may have the optional SBML Level 3 Core attributes 'metaid' and
'sboTerm'.
- LAYOUT_21403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021403:
There must be exactly one instance of a <listOfCurveSegments> object on a
<curve>.
- LAYOUT_21404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021404:
No attributes from the Layout namespace are permitted on a <curve>.
- LAYOUT_21405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021405:
A <listOfCurveSegments> object may have the optional attributes 'metaid' and
'sboTerm' defined by SBML Level 3 Core.
- LAYOUT_21406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021406:
Apart from the general notes and annotation subobjects permitted on all SBML
objects, a <listOfCurveSegments> container object may only contain
<referenceGlyph> objects.
- LAYOUT_21407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021407:
A <listOfCurveSegments> container object may not be empty.
- LAYOUT_21501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021501:
A <lineSegment> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_21502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021502:
A <lineSegment> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_21503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021503:
A <lineSegment> must specify two <point> elements 'start' and 'end'.
- LAYOUT_21504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021504:
No attributes from the Layout namespace are permitted on a <lineSegment>.
- LAYOUT_21601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021601:
A <cubicBezier> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_21602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021602:
A <cubicBezier> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_21603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021603:
A <cubicBezier> must specify four <point> elements 'start' 'basePoint1',
'basePoint2' and 'end'.
- LAYOUT_21604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021604:
No attributes from the Layout namespace are permitted on a <cubicBezier>.
- LAYOUT_21701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021701:
A <dimensions> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- LAYOUT_21702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021702:
A <dimensions> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- LAYOUT_21703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021703:
A <dimensions> object must have the required attributes 'layout:width' and
'layout:height' and may have the optional attributes 'layout:id', and
'layout:depth'.
- LAYOUT_21704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 6021704:
The attributes 'layout:width', 'layout:height' and 'layout:depth' of a
<dimensions> element must be of the data type 'double'.
- leadingZeros(int, int) - Static method in class org.sbml.jsbml.util.StringTools
-
This method creates a String representation of the given number and
inserts as many zero characters as the prefix of this String as
needed
to result in a String of the given length.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LEFT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- leftBrace - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Left parenthesis.
- leftBrace - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Left parenthesis.
- leftQuotationMark - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
An opening quotation mark.
- leftQuotationMark - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
An opening quotation mark.
- LENGTH - Static variable in class org.sbml.jsbml.UnitDefinition
-
Identifier of the (for SBML Level 2) predefined
UnitDefinition
length.
- length(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns the predefined unit for length.
- lengthUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- lengthUnitsID - Variable in class org.sbml.jsbml.Model
-
Represents the 'lengthUnits' XML attribute of a model element.
- leq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode representing less or equal for
the two given left and right child.
- leq(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- leq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Less equal.
- leq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- leq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- leq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- leq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- leq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- leq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Less equal.
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- LETTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LETTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- level - Variable in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- level - Variable in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
SBML level field
- level - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- level - Variable in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
The SBML level to be used in this class.
- level - Variable in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
SBML level field
- level - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- level - Variable in class org.sbml.jsbml.validator.offline.ValidationContext
-
- LEVEL_MISMATCH - Static variable in class org.sbml.jsbml.JSBML
-
- LEVEL_MISMATCH_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError
-
Message to display in cases that two objects do not have identical level
attributes.
- levelMismatchMessage(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
-
Creates an error message if the level fields of both elements are not
identical, or an empty String otherwise.
- LevelVersionError - Exception in org.sbml.jsbml
-
An
SBMLError that indicates that associated instances of
SBase cannot be combined within the same model due to their
differently set Level or Version attribute.
- LevelVersionError(SBase) - Constructor for exception org.sbml.jsbml.LevelVersionError
-
- LevelVersionError(int, int) - Constructor for exception org.sbml.jsbml.LevelVersionError
-
- LevelVersionError(String, int, int) - Constructor for exception org.sbml.jsbml.LevelVersionError
-
- LevelVersionError(SBase, SBase) - Constructor for exception org.sbml.jsbml.LevelVersionError
-
- LevelVersionError(SBasePlugin, SBase) - Constructor for exception org.sbml.jsbml.LevelVersionError
-
- LEXICAL_ERROR - Static variable in error org.sbml.jsbml.math.parser.TokenMgrError
-
Lexical error occurred.
- LEXICAL_ERROR - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
-
Lexical error occurred.
- LexicalError(boolean, int, int, int, String, char) - Static method in error org.sbml.jsbml.math.parser.TokenMgrError
-
Returns a detailed message for the Error when it is thrown by the
token manager to indicate a lexical error.
- LexicalError(boolean, int, int, int, String, char) - Static method in error org.sbml.jsbml.text.parser.TokenMgrError
-
Returns a detailed message for the Error when it is thrown by the
token manager to indicate a lexical error.
- lexStateNames - Static variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Lexer state names.
- lexStateNames - Static variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Lexer state names.
- LibSBMLFormulaCompiler - Class in org.sbml.jsbml.math.compiler
-
- LibSBMLFormulaCompiler() - Constructor for class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- LibSBMLFormulaCompiler - Class in org.sbml.jsbml.util.compilers
-
This class creates C-like infix formula
Strings that represent the
content of
ASTNodes and try to reproduce the output generated by the LibSBML historical parser (compatible with SBML L1 infix).
- LibSBMLFormulaCompiler() - Constructor for class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- line - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- line - Variable in exception org.sbml.jsbml.SBMLError
-
- line - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- line - Variable in class org.sbml.jsbml.xml.XMLToken
-
- lineBreak - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
This is a LaTeX line break.
- lineBreak - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
This is a LaTeX line break.
- listener - Variable in class org.sbml.jsbml.validator.offline.ValidationContext
-
- listIterator() - Method in class org.sbml.jsbml.ListOf
-
- listIterator(int) - Method in class org.sbml.jsbml.ListOf
-
- ListOf<T extends SBase> - Class in org.sbml.jsbml
-
This list implementation is a Java
List that extends
AbstractSBase.
- ListOf() - Constructor for class org.sbml.jsbml.ListOf
-
Creates a ListOf instance.
- ListOf(int, int) - Constructor for class org.sbml.jsbml.ListOf
-
Creates a
ListOf instance from a level and version.
- ListOf(ListOf<? extends SBase>) - Constructor for class org.sbml.jsbml.ListOf
-
Creates a ListOf instance from a given ListOf.
- ListOf(String) - Constructor for class org.sbml.jsbml.ListOf
-
Creates a new
ListOf instance with the given id.
- ListOf(String, int, int) - Constructor for class org.sbml.jsbml.ListOf
-
Creates a new
ListOf instance.
- ListOf(String, String, int, int) - Constructor for class org.sbml.jsbml.ListOf
-
Creates a new
ListOf instance.
- listOf - Variable in class org.sbml.jsbml.ListOf
-
list containing all the SBase elements of this object.
- ListOf.Type - Enum in org.sbml.jsbml
-
This enum lists all the possible names of the listXXX components.
- listOfCompartments - Variable in class org.sbml.jsbml.Model
-
Represents the listOfCompartments subnode of a model element.
- listOfCompartmentTypes - Variable in class org.sbml.jsbml.Model
-
- listOfConstraints - Variable in class org.sbml.jsbml.Model
-
Represents the listOfConstraints subnode of a model element.
- listOfCreators - Variable in class org.sbml.jsbml.History
-
- listOfCVTerms - Variable in class org.sbml.jsbml.Annotation
-
contains all the CVTerm of the RDF annotation
- listOfErrors - Variable in class org.sbml.jsbml.SBMLDocument
-
Memorizes all
SBMLError when parsing the file containing this
document.
- listOfEventAssignments - Variable in class org.sbml.jsbml.Event
-
Represents the listOfEventAssignments sub-element of an event element.
- listOfEvents - Variable in class org.sbml.jsbml.Model
-
Represents the listOfEvents subnode of a model element.
- listOfFunctionDefinitions - Variable in class org.sbml.jsbml.Model
-
Represents the listOfFunctionDefinitions subnode of a model element.
- listOfInitialAssignments - Variable in class org.sbml.jsbml.Model
-
Represents the listOfInitialAssignments subnode of a model element.
- listOfListeners - Variable in class org.sbml.jsbml.AbstractTreeNode
-
List of listeners for this component
- listOfLocalParameters - Variable in class org.sbml.jsbml.KineticLaw
-
Represents the listOfLocalParameters or listOfParameters sub-element of a
kineticLaw element.
- listOfModification - Variable in class org.sbml.jsbml.History
-
Contains all the modified date instances of this
History.
- listOfModifiers - Variable in class org.sbml.jsbml.Reaction
-
Represents the 'listOfModifiers' XML subNode of a reaction element.
- listOfNestedCVTerms - Variable in class org.sbml.jsbml.CVTerm
-
- listOfNodes - Variable in class org.sbml.jsbml.ASTNode
-
Child nodes.
- listOfNodes - Variable in class org.sbml.jsbml.math.ASTFunction
-
Child nodes.
- listOfParameters - Variable in class org.sbml.jsbml.Model
-
Represents the listOfParameters subnode of a model element.
- listOfPredefinedUnitDefinitions - Variable in class org.sbml.jsbml.Model
-
Represents the list of predefined UnitDefinitions for a given SBML level
and version.
- listOfProducts - Variable in class org.sbml.jsbml.Reaction
-
Represents the 'listOfProducts' XML subNode of a reaction element.
- listOfReactants - Variable in class org.sbml.jsbml.Reaction
-
Represents the 'listOfReactants' XML subNode of a reaction element.
- listOfReactions - Variable in class org.sbml.jsbml.Model
-
Represents the listOfReactions subnode of a model element.
- listOfRules - Variable in class org.sbml.jsbml.Model
-
Represents the listOfRules subnode of a model element.
- listOfSpecies - Variable in class org.sbml.jsbml.Model
-
Represents the listOfSpecies subnode of a model element.
- listOfSpeciesTypes - Variable in class org.sbml.jsbml.Model
-
- listOfUnitDefinitions - Variable in class org.sbml.jsbml.Model
-
Represents the listOfUnitDefinitions sub-node of a model element.
- listOfUnits - Variable in class org.sbml.jsbml.UnitDefinition
-
Represents the 'listOfUnit' XML sub-element of a UnitDefinition.
- listOfUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- ListOfWithName<T extends SBase> - Class in org.sbml.jsbml.util
-
- ListOfWithName(String) - Constructor for class org.sbml.jsbml.util.ListOfWithName
-
Deprecated.
- ListOfWithName(int, int, String) - Constructor for class org.sbml.jsbml.util.ListOfWithName
-
Deprecated.
- ListOfWithName(ListOfWithName<? extends SBase>) - Constructor for class org.sbml.jsbml.util.ListOfWithName
-
Deprecated.
- listType - Variable in class org.sbml.jsbml.ListOf
-
name of the list at it appears in the SBMLFile.
- ln(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Natural logarithm.
- ln(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- ln(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- ln(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- ln(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- ln(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- ln(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Natural logarithm.
- ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- ln(double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the ln of n
- loadBundle(String, Locale) - Static method in class org.sbml.jsbml.util.ResourceManager
-
This loads a ResourceBundle from the file system for the given
Locale.
- loadClasses(String, Map<String, Class<? extends T>>) - Static method in class org.sbml.jsbml.JSBML
-
Loads Properties from a configuration file with the given path
assuming that all values represent class names.
- loadConstraints(Class<?>) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Loads the constraints to validate a Object from the class.
- loadConstraints(Class<?>, int, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Sets the level and version and loads the constraints.
- loadConstraints(Class<?>, int, int, SBMLValidator.CHECK_CATEGORY[]) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
- loadConstraintsForAttribute(Class<?>, String) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
Validates a single attribute.
- loaded - Static variable in class org.sbml.jsbml.util.ResourceManager
-
Locale-dependent memory for already loaded ResourceBundle
instances.
- LocalParameter - Class in org.sbml.jsbml
-
A local parameter can only be used to specify a constant within a
KineticLaw.
- LocalParameter() - Constructor for class org.sbml.jsbml.LocalParameter
-
- LocalParameter(int, int) - Constructor for class org.sbml.jsbml.LocalParameter
-
- LocalParameter(LocalParameter) - Constructor for class org.sbml.jsbml.LocalParameter
-
- LocalParameter(Parameter) - Constructor for class org.sbml.jsbml.LocalParameter
-
Creates a new local parameter that will have the same properties than the
given global parameter.
- LocalParameter(String) - Constructor for class org.sbml.jsbml.LocalParameter
-
- LocalParameter(String, int, int) - Constructor for class org.sbml.jsbml.LocalParameter
-
- LocalParameter(String, String, int, int) - Constructor for class org.sbml.jsbml.LocalParameter
-
- LocalParameterConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- LocalParameterConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints
-
- log(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode representing a logarithm to base 10 of the given value.
- log(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode that represents the logarithm function with
the given base and value.
- log(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Creates an
ASTLogarithmNode representing a logarithm to base 10 of the given value.
- log(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Creates an
ASTLogarithmNode that represents the logarithm function with
the given base and value.
- log(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Logarithm of the given value to base 10.
- log(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Logarithm of the given value to the given base.
- log(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- log(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- log(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- log(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- log(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- log(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- log(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- log(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- log(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- log(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- LOG - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- LOG - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- log(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Logarithm of the given value to base 10.
- log(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Logarithm of the given value to the given base.
- log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- log(double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the log of n to the base 10
- log(double, double) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the logarithm of a number x to a giving base b.
- log - Variable in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- log(Priority, String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
-
- logFailure(int) - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- logger - Static variable in class org.sbml.jsbml.AbstractMathContainer
-
A logger for user-messages.
- logger - Static variable in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.AbstractSBase
-
A logger for this class.
- logger - Static variable in class org.sbml.jsbml.AbstractTreeNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.ASTNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.Compartment
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.Creator
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- logger - Static variable in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- logger - Static variable in exception org.sbml.jsbml.IdentifierException
-
- logger - Static variable in class org.sbml.jsbml.KineticLaw
-
A logger for this class.
- logger - Static variable in class org.sbml.jsbml.ListOf
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.AbstractASTNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTBoolean
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCiFunctionNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCiNumberNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCnExponentialNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCnIntegerNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCnNumberNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCnRationalNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCnRealNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTConstantNumber
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTDivideNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTFunction
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTHyperbolicNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTLogarithmNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTMinusNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTPlusNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTPowerNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTRootNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTTimesNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTTrigonometricNode
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
A Logger for this class.
- logger - Variable in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- logger - Static variable in class org.sbml.jsbml.Model
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.SBMLDocument
-
logger used to print messages
- logger - Static variable in class org.sbml.jsbml.Species
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.Unit
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.UnitDefinition
-
The logger for this class.
- logger - Static variable in class org.sbml.jsbml.util.CobraUtil
-
- logger - Static variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedElementValidationFunction
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ElementOrderValidationFunction
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.validator.offline.constraints.ValidationConstraint
-
- logger - Static variable in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.validator.offline.ValidationContext
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.xml.parsers.ParserManager
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
Log4j logger
- logger - Static variable in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Logger to be able to send informative, debug, warning or error messages.
- logger - Static variable in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
-
- logger - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.stax.SBMLReader
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.stax.SBMLWriter
-
A Logger for this class.
- logger - Static variable in class org.sbml.jsbml.xml.stax.XMLLogger
-
logger
- LoggingValidationContext - Class in org.sbml.jsbml.validator.offline
-
- LoggingValidationContext(int, int) - Constructor for class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- LoggingValidationContext(int, int, AnyConstraint<Object>, Set<SBMLValidator.CHECK_CATEGORY>) - Constructor for class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- logicalOperation(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- logicalOperation(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- logicalOperation(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- logicalOperation(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- logicalOperationFunction(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- longtableHead(String, String, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Creates a head for a longtable in LaTeX.
- longtableHead(String, String, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Creates a head for a longtable in LaTeX.
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.math.parser.FormulaParser.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.math.parser.FormulaParserASTNode2.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.math.parser.FormulaParserLL3.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.text.parser.CobraFormulaParser.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.text.parser.FormulaParser.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.text.parser.FormulaParserASTNode2.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.text.parser.FormulaParserLL3.LookaheadSuccess
-
- LookaheadSuccess() - Constructor for error org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2.LookaheadSuccess
-
- LOOP_DETECTED - Static variable in error org.sbml.jsbml.math.parser.TokenMgrError
-
Detected (and bailed out of) an infinite loop in the token manager.
- LOOP_DETECTED - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
-
Detected (and bailed out of) an infinite loop in the token manager.
- lt(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode that performs a less than comparison between
two
ASTNodes.
- lt(String, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates an
ASTNode that performs a less than comparison between a
variable and another
ASTNode.
- lt(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- lt(String, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- lt(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Less than.
- lt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- lt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- lt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- lt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- lt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- lt(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Less than.
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- lv - Variable in class org.sbml.jsbml.AbstractSBase
-
Level and version of the SBML component.