I-Index (JSBML 1.6.1-SNAPSHOT API Specification)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

I

IBoundingBox - Interface in org.sbml.jsbml.ext.layout: Defines classes that are inside a BoundingBox, which specifies the position and the size of the object.
ICurve - Interface in org.sbml.jsbml.ext.layout
id - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
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.
identicalAttribute - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
IdenticalUnitDefinitionFilter - Class in org.sbml.jsbml.util.filters: This Filter only accepts instances of UnitDefinition that satisfy the method UnitDefinition.areIdentical(UnitDefinition, UnitDefinition).
IdenticalUnitDefinitionFilter(UnitDefinition) - Constructor for class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter: Initializes this Filter with a UnitDefinition to be used in the IdenticalUnitDefinitionFilter.accepts(Object) method for comparison.
IDENTIFIER_CONSISTENCY - org.sbml.jsbml.SBMLException.Category: Category of errors that can occur while validating symbol identifiers in a model.
IDENTIFIER_CONSISTENCY - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY: Correctness and consistency of identifiers used for model entities.
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(SBase, String, String, String) - Constructor for exception org.sbml.jsbml.IdentifierException: Creates a new IdentifierException instance.
identifyingParent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
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: Creates a new instance of IdFilter.
IdFilter(String) - Constructor for class org.sbml.jsbml.util.filters.IdFilter: Creates a new instance of IdFilter.
idList - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
IdManager - Interface in org.sbml.jsbml.util: Manages an id namespace.
IdNotValidAttribute - org.sbml.jsbml.SBMLException.Code: Attribute id on species references not supported in SBML Level 1
idRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
idRef - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
idRef - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
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.
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.
image - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
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.
Image - Class in org.sbml.jsbml.ext.render
Image() - Constructor for class org.sbml.jsbml.ext.render.Image: Creates an Image instance
Image(String) - Constructor for class org.sbml.jsbml.ext.render.Image: Creates a Image instance with an id.
Image(Image) - Constructor for class org.sbml.jsbml.ext.render.Image: Clone constructor
ImageConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the Image class.
ImageConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ImageConstraints
imageData - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
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: The String representing the actual implementation of this class, values can be ASTNode.IMPLEMENTATION_HISTORIC or ASTNode.IMPLEMENTATION_ASTNODE2.
implies - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
implies(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
implies(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
implies(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
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(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
inclusive - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
InconsistentArgUnits - org.sbml.jsbml.SBMLException.Code: Units of arguments to function call do not match function's definition
IncorrectCompartmentSpatialDimensions - org.sbml.jsbml.SBMLException.Code: in SBML Level 1, only three-dimensional compartments are permitted
IncorrectOrderInConstraint - org.sbml.jsbml.SBMLException.Code: Incorrect order of elements in constraint definition
IncorrectOrderInEvent - org.sbml.jsbml.SBMLException.Code: Incorrect ordering of components in event definition
IncorrectOrderInKineticLaw - org.sbml.jsbml.SBMLException.Code: Incorrect ordering of components in kinetic law definition
IncorrectOrderInModel - org.sbml.jsbml.SBMLException.Code: Incorrect ordering of components in model definition
IncorrectOrderInReaction - org.sbml.jsbml.SBMLException.Code: Incorrect ordering of components in reaction definition
index - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
index - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
Index - Class in org.sbml.jsbml.ext.arrays: The Index is used to referenced an arrayed element specified in an attribute.
Index() - Constructor for class org.sbml.jsbml.ext.arrays.Index: Creates an Index instance
Index(int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Index: Creates a Index instance with a level and version.
Index(Index) - Constructor for class org.sbml.jsbml.ext.arrays.Index: Clone constructor
INDEX_EXCEEDS_SIZE - Static variable in class org.sbml.jsbml.JSBML
IndexArrayDimCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints: Checks if the Index objects of a given SBase have valid array dimension.
IndexArrayDimCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.IndexArrayDimCheck: Creates a new IndexArrayDimCheck instance with a model and sbase
IndexAttributesCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints: This checks that a given Index object references a valid referenced attribute and that it doesn't go out of bounds.
IndexAttributesCheck(Model, Index) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.IndexAttributesCheck
IndexConstraints - Class in org.sbml.jsbml.validator.offline.constraints
IndexConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.IndexConstraints
indexOf(Object) - Method in class org.sbml.jsbml.ListOf
indexOf(String) - Method in class org.sbml.jsbml.xml.XMLNode: Searches for the first among the immediate children of this XMLNode whose name is the given one, and returns the index with which that child could be accessed e.g. via XMLNode.getChildAt(int)
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(XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode: Searches for first occurrence of the given XMLNode among the immediate children of this XMLNode and returns the index with which that child could be accessed e.g.
IndexValidator - Class in org.sbml.jsbml.ext.arrays.validator: Validates a given Index object in the context of a given model and makes sure that the Index object is in accordance with the arrays package specification.
IndexValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.IndexValidator
info(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
INFO - org.sbml.jsbml.SBMLError.SEVERITY
INFO - org.sbml.jsbml.SBMLException.Type
Inhibition<T> - Interface in org.sbml.jsbml.ext.render.director: interface all the different graphical representations for inhibition arcs have to implement
INHIBITOR - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
init() - Method in class org.sbml.jsbml.ext.comp.ModelDefinition
InitAssignCompartmenMismatch - org.sbml.jsbml.SBMLException.Code: Mismatched units in initial assignment to compartment
InitAssignmentAndRuleForSameId - org.sbml.jsbml.SBMLException.Code: Cannot set a value with both initial assignments and assignment rules simultaneously
InitAssignParameterMismatch - org.sbml.jsbml.SBMLException.Code: Mismatched units in initial assignment to parameter
InitAssignSpeciesMismatch - org.sbml.jsbml.SBMLException.Code: Mismatched units in initial assignment to species
initDefaults() - Method in class org.sbml.jsbml.Compartment: Initializes the default values using the current Level/Version configuration.
initDefaults() - Method in class org.sbml.jsbml.Event: Initializes the default values using the current Level/Version configuration.
initDefaults() - Method in class org.sbml.jsbml.ExplicitRule
initDefaults() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.arrays.Dimension: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.arrays.Index: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.Deletion: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.Port: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Initializes the default values.
initDefaults() - Method in class org.sbml.jsbml.ext.comp.Submodel: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin: Initializes custom Class attributes
initDefaults() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin
initDefaults() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin: Initializes custom Class attributes
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Initializes the default values.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
initDefaults() - Method in class org.sbml.jsbml.ext.groups.ListOfMembers
initDefaults() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.

Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.Point: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.layout.TextGlyph: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType: Initializes the default values.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.qual.Input
initDefaults() - Method in class org.sbml.jsbml.ext.qual.Output
initDefaults() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
initDefaults() - Method in class org.sbml.jsbml.ext.qual.Transition
initDefaults() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.ColorDefinition: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.DefaultValues: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
initDefaults() - Method in class org.sbml.jsbml.ext.render.GradientBase: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.GradientStop: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D
initDefaults() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
initDefaults() - Method in class org.sbml.jsbml.ext.render.Image
initDefaults() - Method in class org.sbml.jsbml.ext.render.LinearGradient
initDefaults() - Method in class org.sbml.jsbml.ext.render.LineEnding
initDefaults() - Method in class org.sbml.jsbml.ext.render.ListOfGlobalRenderInformation: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.ListOfLocalRenderInformation: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
initDefaults() - Method in class org.sbml.jsbml.ext.render.Polygon
initDefaults() - Method in class org.sbml.jsbml.ext.render.RadialGradient
initDefaults() - Method in class org.sbml.jsbml.ext.render.Rectangle
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderCurve
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderGroup
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin
initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderPoint: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.Style: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.Text: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.Transformation: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.render.Transformation2D
initDefaults() - Method in class org.sbml.jsbml.ext.req.ChangedMath: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.

Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.PolygonObject: Deprecated.

Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.KineticLaw
initDefaults() - Method in class org.sbml.jsbml.Model: Initializes the default values using the current Level/Version configuration.
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() - Method in class org.sbml.jsbml.Species: Initializes the default values using the current Level/Version configuration.
initDefaults() - Method in class org.sbml.jsbml.SpeciesReference: Initializes the default values using the current Level/Version configuration.
initDefaults() - Method in class org.sbml.jsbml.Trigger: Sets the properties Trigger.initialValue and Trigger.persistent to null, i.e., undefined.
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.Compartment: 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(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) - Method in class org.sbml.jsbml.Reaction: Initializes the default variables of this Reaction.
initDefaults(int, int) - Method in class org.sbml.jsbml.Species: Initializes the default values of this Species.
initDefaults(int, int) - Method in class org.sbml.jsbml.SpeciesReference: Initializes the default values of this SpeciesReference.
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.Compartment
initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Parameter
initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Reaction
initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Species: Initializes the default values of this Species.
initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.SpeciesReference
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(int, int) - Constructor for class org.sbml.jsbml.InitialAssignment: Creates an InitialAssignment from level and version.
InitialAssignment(InitialAssignment) - Constructor for class org.sbml.jsbml.InitialAssignment: Creates an InitialAssignment instance from a given InitialAssignment.
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: Creates an InitialAssignment from a Variable, ASTNode, level and version.
InitialAssignmentConstraints - Class in org.sbml.jsbml.validator.offline.constraints
InitialAssignmentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints
InitialAssignNotValidComponent - org.sbml.jsbml.SBMLException.Code: Initial assignments are not supported in this Level+Version of SBML
initializeAnnotationParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLReader: Initializes the packageParser HashMap of this class.
initialLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
initialValue - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
initListOf(SBase, ListOf<T>, ListOf.Type) - Static method in class org.sbml.jsbml.ListOf: Initializes newly created lists.
Input - Class in org.sbml.jsbml.ext.qual: Each Input refers to a QualitativeSpecies that participates in the corresponding Transition.
Input() - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance.
Input(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance.
Input(String) - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance.
Input(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance.
Input(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance.
Input(String, QualitativeSpecies, InputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance.
Input(Input) - Constructor for class org.sbml.jsbml.ext.qual.Input: Creates a new Input instance cloned from the given Input.
InputConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the Input class.
InputConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InputConstraints
InputTransitionEffect - Enum in org.sbml.jsbml.ext.qual: The transitionInputEffect is an enumeration of values used to indicate the effect of an Input Transition within the system.
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: Inserts the given ASTNode2 at point n in the list of children of this ASTNode2.
insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction: Inserts the given ASTNode2 at point n in the list of children of this ASTNode2.
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.
InSpeciesTypeBond - Class in org.sbml.jsbml.ext.multi: Defines a bond existing within a MultiSpeciesType.
InSpeciesTypeBond() - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Creates an InSpeciesTypeBond instance
InSpeciesTypeBond(int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Creates a InSpeciesTypeBond instance with a level and version.
InSpeciesTypeBond(String) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Creates a InSpeciesTypeBond instance with an id.
InSpeciesTypeBond(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Creates a InSpeciesTypeBond instance with an id, level, and version.
InSpeciesTypeBond(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Creates a InSpeciesTypeBond instance with an id, name, level, and version.
InSpeciesTypeBond(InSpeciesTypeBond) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Clone constructor
InSpeciesTypeBondConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Constraints declaration for the MultiCompartmentPlugin class.
InSpeciesTypeBondConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints
instance - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
INTEGER - org.sbml.jsbml.ASTNode.Type
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.
interiorPoint - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
InteriorPoint - Class in org.sbml.jsbml.ext.spatial
InteriorPoint() - Constructor for class org.sbml.jsbml.ext.spatial.InteriorPoint
InteriorPoint(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.InteriorPoint
InteriorPoint(InteriorPoint) - Constructor for class org.sbml.jsbml.ext.spatial.InteriorPoint
InteriorPointConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the InteriorPoint class.
InteriorPointConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InteriorPointConstraints
INTERNAL - org.sbml.jsbml.SBMLException.Category: This category of errors are basically a catch for something completely unexpected so as to avoid just crashing.
INTERNAL - org.sbml.jsbml.SBMLException.Type
INTERNAL_CONSISTENCY - org.sbml.jsbml.SBMLException.Category: Category of errors that can occur while validating libSBML's internal representation of SBML constructs.
internaliseExternalModelDefinitions(SBMLDocument) - Static method in class org.sbml.jsbml.ext.comp.util.CompFlatteningConverter: Collects any ExternalModelDefinitions that might be contained in the given SBMLDocument and transfers them into local ModelDefinitions (recursively, if the external models themselves include external models; in that case, renaming may occur).
InterpolationKind - Enum in org.sbml.jsbml.ext.spatial: This enum type was created following the specifications defined in Spatial Package v0.90.
interpolationType - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
interquartileRange - org.sbml.jsbml.ext.distrib.UncertParameter.Type: The interquartile range is the range between the 1st and 3rd quartiles.
intersection - org.sbml.jsbml.ext.spatial.SetOperation
intraSpeciesReaction - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
IntraSpeciesReaction - Class in org.sbml.jsbml.ext.multi
IntraSpeciesReaction() - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Creates an IntraSpeciesReaction instance
IntraSpeciesReaction(int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Creates a IntraSpeciesReaction instance with a level and version.
IntraSpeciesReaction(String) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Creates a IntraSpeciesReaction instance with an id.
IntraSpeciesReaction(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Creates a IntraSpeciesReaction instance with an id, level, and version.
IntraSpeciesReaction(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Creates a IntraSpeciesReaction instance with an id, name, level, and version.
IntraSpeciesReaction(IntraSpeciesReaction) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction: Clone constructor
intToString(int) - Static method in class org.sbml.jsbml.SBO: Returns the integer as a correctly formatted SBO string.
INVALID - org.sbml.jsbml.Unit.Kind: Marker used to indicate an invalid or not yet set unit.
INVALID_ATTRIBUTE_VALUE - Static variable in class org.sbml.jsbml.JSBML
INVALID_OBJECT - Static variable in class org.sbml.jsbml.JSBML
INVALID_XML - Static variable in class org.sbml.jsbml.JSBML: Key used to store any invalid XML encountered while reading an SBML file (in particular used for invalid attributes, for validation purpose.
INVALID_XML_OPERATION - Static variable in class org.sbml.jsbml.JSBML
Invalid1DCompartmentUnits - org.sbml.jsbml.SBMLException.Code: Invalid value of units for a one-dimensional compartment
Invalid2DCompartmentUnits - org.sbml.jsbml.SBMLException.Code: Invalid value of units for a two-dimensional compartment
Invalid3DCompartmentUnits - org.sbml.jsbml.SBMLException.Code: Invalid value of units for a three-dimensional compartment
InvalidApplyCiInLambda - org.sbml.jsbml.SBMLException.Code: Invalid forward reference in <apply><ci>...</ci></apply> value
InvalidAreaRedefinition - org.sbml.jsbml.SBMLException.Code: Invalid redefinition of area
InvalidAssignRuleVariable - org.sbml.jsbml.SBMLException.Code: Invalid variable reference in assignment rule
InvalidAttributeValidationFunction<T extends TreeNodeWithChangeSupport> - Class in org.sbml.jsbml.validator.offline.constraints.helper: Class used to check if any invalid XML attributes where found.
InvalidAttributeValidationFunction(String) - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.InvalidAttributeValidationFunction: Creates a new InvalidAttributeValidationFunction instance.
InvalidCiInLambda - org.sbml.jsbml.SBMLException.Code: Unknown <ci> reference in <lambda>
InvalidCompartmentSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for compartment
InvalidCompartmentTypeRef - org.sbml.jsbml.SBMLException.Code: Invalid compartmentType reference
InvalidCompartmentTypeSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for compartment type
InvalidConstraintContent - org.sbml.jsbml.SBMLException.Code: Invalid content for constraint message
InvalidConstraintSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for constraint
InvalidDelaySBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for event delay
InvalidEventAssignmentSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for event assignment
InvalidEventAssignmentVariable - org.sbml.jsbml.SBMLException.Code: Invalid value for variable in event assignment
InvalidEventSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for event
InvalidFunctionDefReturnType - org.sbml.jsbml.SBMLException.Code: Function return type must be either numerical or boolean
InvalidFunctionDefSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for function definition
InvalidIdSyntax - org.sbml.jsbml.SBMLException.Code: Invalid identifier syntax
InvalidInitAssignSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for initial assignment
InvalidInitAssignSymbol - org.sbml.jsbml.SBMLException.Code: Invalid symbol reference in initial assignment
InvalidKineticLawSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for kinetic law
InvalidL1CompartmentUnits - org.sbml.jsbml.SBMLException.Code: Invalid units for a compartment in SBML Level 1
InvalidLengthRedefinition - org.sbml.jsbml.SBMLException.Code: Invalid redefinition of length
InvalidMathElement - org.sbml.jsbml.SBMLException.Code: Invalid MathML
InvalidMetaidSyntax - org.sbml.jsbml.SBMLException.Code: Invalid metaid value syntax
InvalidModelSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for model
InvalidModifiersList - org.sbml.jsbml.SBMLException.Code: Invalid element in list of modifiers
InvalidNamespaceOnSBML - org.sbml.jsbml.SBMLException.Code: Invalid XML namespace for SBML container
InvalidNoArgsPassedToFunctionDef - org.sbml.jsbml.SBMLException.Code: Incorrect number of arguments to function
InvalidNotesContent - org.sbml.jsbml.SBMLException.Code: Invalid notes content
InvalidParameterSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for parameter
InvalidParameterUnits - org.sbml.jsbml.SBMLException.Code: Invalid value for units in parameter definition
InvalidRateRuleVariable - org.sbml.jsbml.SBMLException.Code: Invalid variable reference in rate rule
InvalidReactantsProductsList - org.sbml.jsbml.SBMLException.Code: Invalid element in list of reactants or products
InvalidReactionSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for reaction
InvalidRuleOrdering - org.sbml.jsbml.SBMLException.Code: Invalid ordering of rules
InvalidRuleSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for rule
InvalidSBMLLevelVersion - org.sbml.jsbml.SBMLException.Code: Invalid SBML Level and Version
InvalidSBOTermSyntax - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value syntax
InvalidSpeciesCompartmentRef - org.sbml.jsbml.SBMLException.Code: Invalid compartment reference
InvalidSpeciesReference - org.sbml.jsbml.SBMLException.Code: Invalid species value in species reference
InvalidSpeciesReferenceSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for species reference
InvalidSpeciesSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for species
InvalidSpeciesSusbstanceUnits - org.sbml.jsbml.SBMLException.Code: Invalid value of units
InvalidSpeciesTypeRef - org.sbml.jsbml.SBMLException.Code: Invalid speciesType reference
InvalidSpeciesTypeSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for species type
InvalidSubstanceRedefinition - org.sbml.jsbml.SBMLException.Code: Invalid redefinition of substance
InvalidTimeRedefinition - org.sbml.jsbml.SBMLException.Code: Invalid redefinition of time
InvalidTriggerSBOTerm - org.sbml.jsbml.SBMLException.Code: Invalid sboTerm value for event trigger
InvalidUnitDefId - org.sbml.jsbml.SBMLException.Code: Invalid id value for unit definition
InvalidUnitIdSyntax - org.sbml.jsbml.SBMLException.Code: Invalid unit identifier syntax
InvalidUnitKind - org.sbml.jsbml.SBMLException.Code: Invalid value of kind in unit definition
InvalidVolumeRedefinition - org.sbml.jsbml.SBMLException.Code: Invalid redefinition of volume
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.
isAbsolutePosition(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
isActive - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
isActive() - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition
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.
isApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin
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.
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() - Method in class org.sbml.jsbml.UnitDefinition: Deprecated.
use UnitDefinition.isPredefined()
isBuiltIn(String, int) - Static method in class org.sbml.jsbml.Unit: Deprecated.
use Unit.isPredefined(String, int)
isBuiltIn(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition: Deprecated.
use UnitDefinition.isPredefined()
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: Deprecated.
Unit.Kind.CELSIUS should no longer be used.
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.
isCompartmentMandatory() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
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.
isCubicBezier() - Method in class org.sbml.jsbml.ext.layout.CurveSegment
isDebugMode() - Static method in class org.sbml.jsbml.ListOf: If this method returns true, the AbstractSBase.toString() method of this ListOf displays the whole content of the list.
isDefaultTerm() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm: Returns true if it is a defaultTerm.
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: Predicate for testing whether this Unit is of the Unit.Kind Unit.Kind.DIMENSIONLESS.
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: Deprecated.
libSBML internal
isEmptySet(int) - Static method in class org.sbml.jsbml.SBO: Returns true if the given term identifier comes from the stated branch of SBO.
isEnabledCategory(SBMLValidator.CHECK_CATEGORY) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Returns true if the given SBMLValidator.CHECK_CATEGORY is enabled in this ValidationContext.
isEnableRotationMapping() - Method in class org.sbml.jsbml.ext.render.LineEnding
isEnd() - Method in class org.sbml.jsbml.xml.XMLToken: Returns true or false depending on whether this XMLToken is an XML end element.
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() - 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: Returns true is the SBMLError severity is of type SBMLError.SEVERITY.ERROR
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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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.
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: Returns true is the SBMLError severity is of type SBMLError.SEVERITY.FATAL
isFatal() - Method in exception org.sbml.jsbml.SBMLException
isFilterForSpecies() - Method in class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter
isFilterForSpecies() - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
isFontStyleItalic() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Returns the value of fontStyleItalic
isFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.Text
isFontWeightBold() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Returns the value of fontWeightBold
isFontWeightBold() - Method in class org.sbml.jsbml.ext.render.Text
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.
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.ext.arrays.Dimension
isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.Deletion
isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition
isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.Port
isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.Submodel
isIdMandatory() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
isIdMandatory() - Method in class org.sbml.jsbml.ext.dyn.DynElement
isIdMandatory() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.Objective
isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.Group
isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.Member
isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.
isIdMandatory() - Method in class org.sbml.jsbml.ext.layout.BoundingBox
isIdMandatory() - Method in class org.sbml.jsbml.ext.layout.Curve
isIdMandatory() - Method in class org.sbml.jsbml.ext.layout.Dimensions
isIdMandatory() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject
isIdMandatory() - Method in class org.sbml.jsbml.ext.layout.Layout
isIdMandatory() - Method in class org.sbml.jsbml.ext.layout.Point
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex
isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance
isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.Input
isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.Output
isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
isIdMandatory() - Method in class org.sbml.jsbml.ext.render.ColorDefinition
isIdMandatory() - Method in class org.sbml.jsbml.ext.render.GradientBase
isIdMandatory() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isIdMandatory() - Method in class org.sbml.jsbml.ext.render.Style
isIdMandatory() - Method in class org.sbml.jsbml.ext.req.ChangedMath
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: Deprecated.
use SBMLDocument.isIgnoredPackage(String)
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: Returns true is the SBMLError severity is of type SBMLError.SEVERITY.INFO
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.
isInitialLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
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 - 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'.
isInteraction(int) - Static method in class org.sbml.jsbml.SBO: Function for checking the SBO term is from correct part of SBO.
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.util.SBMLtools
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.
isLineSegment() - Method in class org.sbml.jsbml.ext.layout.CurveSegment
isListOfColorDefinitionsEmpty() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isListOfCompartmentsEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfCompartments is !
isListOfCompartmentTypesEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfCompartmentTypes is !
isListOfConstraintsEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfConstraints is !
isListOfCurveSegmentsEmpty() - Method in class org.sbml.jsbml.ext.render.Polygon
isListOfCurveSegmentsEmpty() - Method in class org.sbml.jsbml.ext.render.RenderCurve
isListOfElementsEmpty() - Method in class org.sbml.jsbml.ext.render.Polygon
isListOfElementsEmpty() - Method in class org.sbml.jsbml.ext.render.RenderCurve
isListOfElementsEmpty() - Method in class org.sbml.jsbml.ext.render.RenderGroup
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 !
isListOfFunctionDefinitionsEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfFunctionDefinitions is !
isListOfFunctionTermsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
isListOfGlobalRenderInformationEmpty() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin
isListOfGradientDefinitionsEmpty() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isListOfGradientStopsEmpty() - Method in class org.sbml.jsbml.ext.render.GradientBase
isListOfInitialAssignmentsEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfInitialAssignments is !
isListOfInputsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
isListOfLineEndingsEmpty() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isListOfLocalParametersEmpty() - Method in class org.sbml.jsbml.KineticLaw: Returns true, if the list of local parameters is not null.
isListOfLocalRenderInformationEmpty() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
isListOfLocalStylesEmpty() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
isListOfModifiersEmpty() - Method in class org.sbml.jsbml.Reaction: Returns true if the listOfModifiers of this Reaction is empty.
isListOfOutputsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
isListOfParametersEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfParameters is !
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 !
isListOfRulesEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfRules is !
isListOfSpeciesEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfSpecies is !
isListOfSpeciesTypesEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfSpeciesTypes is !
isListOfStylesEmpty() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
isListOfUnitDefinitionEmpty() - Method in class org.sbml.jsbml.Model: Checks if the listOfUnitDefinitions is !
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.
isLocal - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
isLocal() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
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 - 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'.
isMaterialEntity(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'.
isMathematicalExpression(int) - Static method in class org.sbml.jsbml.SBO: Function for checking the SBO term is from correct part of SBO.
isMaxLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
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 - 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'.
isModellingFramework(int) - Static method in class org.sbml.jsbml.SBO: Function for checking the SBO term is from correct part of SBO.
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.
isModifier(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector: Check if a species reference glyph can be interpreted as an activator, inhibitor, or generic modifier.
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, '
isNamespacesEmpty() - Method in class org.sbml.jsbml.xml.XMLToken: Returns true or false depending on whether the XMLNamespaces of this XMLToken is empty.
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 - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints: Checks if the SBO of the SBase is obsolete.
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.
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).
isotropic - org.sbml.jsbml.ext.spatial.DiffusionKind: Isotropic
isOutputLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.Output
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: Returns true if the given SBML Level 3 package is enabled within the SBMLDocument, false if the package was disabled using the method SBMLDocument.disablePackage(String) or null if this package was neither enabled or disabled on this 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 - 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'.
isParticipantRole(int) - Static method in class org.sbml.jsbml.SBO: Function for checking the SBO term is from correct part of SBO.
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: Deprecated.
use SBase.isPackageEnabled(String)
isPkgURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase: Deprecated.
isPkgURIEnabled(String) - Method in interface org.sbml.jsbml.SBase: Deprecated.
use SBase.isPackageEnabled(String)
isPredefined() - Method in class org.sbml.jsbml.UnitDefinition: Tests if this unit definition is a predefined unit.
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(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.Unit: Tests whether the given UnitDefinition belongs to the predefined SBML units.
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').
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.
isProduct(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector: Check if a species reference glyph is a product.
isProductReady() - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder
isProductReady() - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder: method to check if the builder has produced a complete product
isProtein(int) - Static method in class org.sbml.jsbml.SBO: Returns true if the given term identifier comes from the stated branch of SBO.
isQualitativeSpeciesMandatory() - Method in class org.sbml.jsbml.ext.qual.Input
isQualitativeSpeciesMandatory() - Method in class org.sbml.jsbml.ext.qual.Output
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'.
isQuantitativeParameter(int) - Static method in class org.sbml.jsbml.SBO: Function for checking the SBO term is from correct part of SBO.
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 - 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'.
isRateLaw(int) - Static method in class org.sbml.jsbml.SBO: Function for checking the SBO term is from correct part of SBO.
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.
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 !
isRenderCubicBezier() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment: Returns true if the type is equals to RenderCurveSegment.Type.RENDER_CUBIC_BEZIER.
isRenderPoint() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment: Returns true if the type is equals to RenderCurveSegment.Type.RENDER_POINT.
isRequired() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.CompParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.DistribParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.DynParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.GroupsParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.MultiParser
isRequired() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser: Returns the value of the required attribute for this package.
isRequired() - Method in class org.sbml.jsbml.xml.parsers.QualParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.RenderParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
isRequired() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser
isResultLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm: Returns false, resultLevel is not mandatory.
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: Opposite of TreeNodeWithChangeSupport.isSetParent().
isSBMLNamespaceNeeded(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
isSBMLNamespaceNeeded(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
isSecond() - Method in class org.sbml.jsbml.Unit: Predicate for testing whether this Unit is of the kind second
isSelfLogging() - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractValidationFunction: Returns true is this ValidationFunction is logging itself the SBMLError(s) to the ValidationContext.
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.
isSetAbsoluteValue() - Method in class org.sbml.jsbml.ext.render.RelAbsVector
isSetActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
isSetActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Returns whether activeObjective is set
isSetAddGraphicalObjects() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetAddWhiskers() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector: Returns whether addWhiskers is set
isSetAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
isSetAnnotation() - Method in class org.sbml.jsbml.Annotation: Checks if the Annotation is initialized.
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.
isSetApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin: Returns whether applyToAll is set
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.
isSetArrayData() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Returns whether SpatialPoints.arrayData is set.
isSetArrayDataLength() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Returns whether arrayDataLength is set.
isSetArrayDimension() - Method in class org.sbml.jsbml.ext.arrays.Dimension: Returns whether arrayDimension is set
isSetArrayDimension() - Method in class org.sbml.jsbml.ext.arrays.Index: Returns whether arrayDimension is set
isSetAssociatedSpecies() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Returns whether GeneProduct.associatedSpecies is set.
isSetAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Returns whether GeneProductAssociation.association is set.
isSetAttributes() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
isSetBackgroundColor() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isSetBasePoint1() - Method in class org.sbml.jsbml.ext.layout.CubicBezier
isSetBasePoint2() - Method in class org.sbml.jsbml.ext.layout.CubicBezier
isSetBindingSite1() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Returns whether InSpeciesTypeBond.bindingSite1 is set.
isSetBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Returns whether InSpeciesTypeBond.bindingSite2 is set.
isSetBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite: Returns whether OutwardBindingSite.bindingStatus is set.
isSetBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm: Returns true if the CVTerm.Qualifier is set and is of type CVTerm.Type.BIOLOGICAL_QUALIFIER
isSetBoundaryCondition() - Method in class org.sbml.jsbml.Species
isSetBoundaryDomainType() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition: Returns whether boundaryDomainType is set
isSetBoundaryMaximum() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Returns whether boundaryMaximum is set
isSetBoundaryMinimum() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Returns whether boundaryMinimum is set
isSetBoundingBox() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject
isSetBoundingBox() - Method in interface org.sbml.jsbml.ext.layout.IBoundingBox: Returns true is the BoundingBox is set.
isSetBoundingBox() - Method in class org.sbml.jsbml.ext.render.LineEnding
isSetCBOTerm() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin: Returns whether CBO is set
isSetChangedBy() - Method in class org.sbml.jsbml.ext.req.ChangedMath: Returns whether changedBy is set
isSetCharacters() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
isSetCharge() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Returns whether FBCSpeciesPlugin.charge is set.
isSetCharge() - Method in class org.sbml.jsbml.Species
isSetChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Returns whether FBCSpeciesPlugin.chemicalFormula is set.
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
isSetCloneMarker() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker
isSetCloneMarker() - Method in interface org.sbml.jsbml.ext.render.director.SBGNNodeWithCloneMarker
isSetCoefficient() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns whether coefficient is set
isSetCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
isSetCompartment() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
isSetCompartment() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference: Returns whether CompartmentReference.compartment is set.
isSetCompartment() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
isSetCompartment() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
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.ext.layout.CompartmentGlyph
isSetCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
isSetCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
isSetCompartmentInstance() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
isSetCompartmentInstance() - Method in class org.sbml.jsbml.Reaction
isSetCompartmentInstance() - Method in class org.sbml.jsbml.Species
isSetCompartmentMapping() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin: Returns whether compartmentMapping is set
isSetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin: Returns whether MultiSimpleSpeciesReferencePlugin.compartmentReference is set.
isSetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Returns whether SpeciesTypeInstance.compartmentReference is set.
isSetCompartmentType() - Method in class org.sbml.jsbml.Compartment: Returns true if the compartmentID of this compartment is not null.
isSetCompartmentType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Returns whether MultiCompartmentPlugin.compartmentType is set.
isSetCompartmentTypeInstance() - Method in class org.sbml.jsbml.Compartment: Deprecated.
isSetComplementA() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Returns whether complementA is set
isSetComplementB() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Returns whether complementB is set
isSetComponent() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite: Returns whether OutwardBindingSite.component is set.
isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Returns whether SpeciesFeature.component is set.
isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Returns whether SpeciesTypeComponentIndex.component is set.
isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Returns whether SubListOfSpeciesFeature.component is set.
isSetComponents() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent: Returns whether components is set
isSetComponentsLength() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent: Returns whether componentsLength is set
isSetCompression() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Returns whether compression is set.
isSetCompression() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether compression is set
isSetCompression() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Returns whether compression is set.
isSetConstant() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
isSetConstant() - Method in class org.sbml.jsbml.SpeciesReference
isSetConstant() - Method in class org.sbml.jsbml.Symbol
isSetConstant() - Method in interface org.sbml.jsbml.Variable
isSetConstantMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
isSetConversionFactor() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: Returns whether conversionFactor is set
isSetConversionFactor() - Method in class org.sbml.jsbml.Model: Returns true if the Model.conversionFactorID of this Model is not null.
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
isSetCoord1() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Returns whether coord1 is set
isSetCoord2() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Returns whether coord2 is set
isSetCoord3() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Returns whether coord3 is set
isSetCoordinate() - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient: Returns whether coordinate is set
isSetCoordinate() - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
isSetCoordinateBoundary() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition: Returns whether coordinateBoundary is set
isSetCoordinateReference1() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Returns whether coordinateReference1 is set
isSetCoordinateReference2() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Returns whether coordinateReference2 is set
isSetCoordinateSystem() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns whether coordinateSystem is set
isSetCreatedDate() - Method in class org.sbml.jsbml.History: Predicate returning true or false depending on whether this History's createdDate has been set.
isSetCSGNode() - Method in class org.sbml.jsbml.ext.spatial.CSGObject: Returns whether csgNode is set
isSetCSGNode() - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation: Returns whether csgNode is set
isSetCsgObjectRef() - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive: Returns whether csgObjectRef is set
isSetCurve() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Returns true if the Curve element is not null.
isSetCurve() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
isSetCurve() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
isSetCurve() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
isSetCx() - Method in class org.sbml.jsbml.ext.render.Ellipse
isSetCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetCy() - Method in class org.sbml.jsbml.ext.render.Ellipse
isSetCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetCz() - Method in class org.sbml.jsbml.ext.render.Ellipse
isSetCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetData() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether data is set
isSetDataType() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Returns whether dataType is set.
isSetDataType() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether dataType is set
isSetDataType() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Returns whether dataType is set.
isSetDefaultValues() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Returns whether ListOfRenderInformation.defaultValues is set.
isSetDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
isSetDefinitionURL() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Returns whether UncertParameter.definitionURL is set.
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
isSetDeletion() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: Returns whether deletion is set
isSetDenominator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode: Returns true iff denominator has been set
isSetDenominator() - Method in class org.sbml.jsbml.SpeciesReference
isSetDepth() - Method in class org.sbml.jsbml.ext.layout.Dimensions
isSetDimensions() - Method in class org.sbml.jsbml.ext.layout.BoundingBox
isSetDimensions() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetDistinctAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.

Returns whether distinctAttribute is set
isSetDomain1() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains: Returns whether domain1 is set
isSetDomain2() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains: Returns whether domain2 is set
isSetDomainType() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Returns whether domainType is set
isSetDomainType() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping: Returns whether domainType is set
isSetDomainType() - Method in class org.sbml.jsbml.ext.spatial.CSGObject: Returns whether domainType is set
isSetDomainType() - Method in class org.sbml.jsbml.ext.spatial.Domain: Returns whether domainType is set
isSetDomainType() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Returns whether domain is set
isSetDomainType() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Returns whether domainType is set
isSetElementName() - Method in class org.sbml.jsbml.ext.layout.Point
isSetElementName() - Method in class org.sbml.jsbml.ext.spatial.Boundary: Returns whether Boundary.elementName is set.
isSetEmail() - Method in class org.sbml.jsbml.Creator: Returns true or false depending on whether this Creator's email has been set.
isSetEnableRotationMapping() - Method in class org.sbml.jsbml.ext.render.LineEnding
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
isSetEnd() - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Returns true if the End Point is set.
isSetEnd() - Method in class org.sbml.jsbml.ext.layout.LineSegment
isSetEndHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve: Returns true if endHead is set.
isSetEndHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetExponent() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode: Returns True iff exponent has been set
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.
isSetExtentConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel: Returns whether extentConversionFactor is 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() - Method in class org.sbml.jsbml.Reaction
isSetFill() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
isSetFillRule() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
isSetFontFamily() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isSetFontFamily() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetFontFamily() - Method in class org.sbml.jsbml.ext.render.Text
isSetFontSize() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isSetFontSize() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetFontSize() - Method in class org.sbml.jsbml.ext.render.Text
isSetFontStyleItalic() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isSetFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Returns whether fontStyleItalic is set
isSetFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.Text
isSetFontWeightBold() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isSetFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetFontWeightBold() - Method in class org.sbml.jsbml.ext.render.Text
isSetForwardTransformation() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation: Returns whether forwardTransformation is set
isSetFunctionType() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Returns whether functionType is set
isSetFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Returns whether GeneProductRef.geneProduct is set.
isSetGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns whether FBCReactionPlugin.geneProductAssociation is set.
isSetGeneProductInstance() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Returns whether the gene product id is set and this id is a valid GeneProduct id in this model.
isSetGeometry() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin: Returns whether geometry is set
isSetGeometryDefinition() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping: Returns whether geometryDefinition is set
isSetGivenName() - Method in class org.sbml.jsbml.Creator: Returns true or false depending on whether this Creator's givenName has been set.
isSetGlyph() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
isSetGraphicalObject() - Method in class org.sbml.jsbml.ext.layout.TextGlyph
isSetGraphicalObjectInstance() - Method in class org.sbml.jsbml.ext.layout.TextGlyph: Method to test if an instance of a GraphicalObject with the id given by TextGlyph.getGraphicalObject() can be found in the Model.
isSetGroup() - Method in class org.sbml.jsbml.ext.render.LineEnding
isSetGroup() - Method in class org.sbml.jsbml.ext.render.Style
isSetHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
isSetHeight() - Method in class org.sbml.jsbml.ext.layout.Dimensions
isSetHeight() - Method in class org.sbml.jsbml.ext.render.Image
isSetHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle
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.
isSetHref() - Method in class org.sbml.jsbml.ext.render.Image
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.
isSetIdenticalAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.

Returns whether identicalAttribute is set
isSetIDList() - Method in class org.sbml.jsbml.ext.render.LocalStyle
isSetIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Returns whether idRef is set
isSetIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement: Returns whether idRef is set
isSetIdRef() - Method in class org.sbml.jsbml.ext.groups.Member: Returns whether idRef is set
isSetidToValue() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler: Returns true, if idToValue contains at least one element.
isSetIdToVector() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
isSetIndentifyingParent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Returns whether SpeciesTypeComponentIndex.identifyingParent is set.
isSetInitialAmount() - Method in class org.sbml.jsbml.Species
isSetInitialConcentration() - Method in class org.sbml.jsbml.Species
isSetInitialLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
isSetInitialValue() - Method in class org.sbml.jsbml.Trigger
isSetInteger() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode: Returns True iff value has been set
isSetInterpolation() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether interpolation type is set
isSetInterpolationType() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether interpolation type is set
isSetIsActive() - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition: Returns whether isActive is set
isSetIsLocal() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin: Returns whether isLocal is set
isSetIsType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Returns whether MultiCompartmentPlugin.isType is set.
isSetKey() - Method in class org.sbml.jsbml.util.Pair
isSetKind() - Method in class org.sbml.jsbml.ext.groups.Group
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
isSetLabel() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Returns whether GeneProduct.label is set
isSetLayout() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm
isSetLayout() - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm
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.
isSetListOfAdditionalGraphicalObjects() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetListOfAdjacentDomains() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns true, if listOfAdjacentDomains contains at least one element.
isSetListOfAnalyticVolumes() - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry: Returns true, if listOfAnalyticVolumes contains at least one element.
isSetListOfAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Returns true if LogicalOperator.listOfAssociations contains at least one element.
isSetListOfChangedMaths() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin: Returns true, if listOfChangedMaths contains at least one element.
isSetListOfColorDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isSetListOfCompartmentGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetListOfCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Returns true if MultiCompartmentPlugin.listOfCompartmentReferences contains at least one element.
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: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
isSetListOfConstraints() - Method in class org.sbml.jsbml.Model: Returns true if the listOfConstraints of this Model is not null and not empty.
isSetListOfCoordinateComponents() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns true, if listOfCoordinateComponents contains at least one element.
isSetListOfCreators() - Method in class org.sbml.jsbml.History
isSetListOfCSGNodes() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Returns true, if listOfCSGNodes contains at least one element.
isSetListOfCSGObjects() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry: Returns true, if listOfCSGObjects contains at least one element.
isSetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.layout.Curve
isSetListOfCurveSegments() - Method in interface org.sbml.jsbml.ext.layout.ICurve
isSetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon: Returns true if Polygon.listOfCurveSegments contains at least one element.
isSetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve: Returns true if RenderCurve.listOfCurveSegments contains at least one element.
isSetListOfCVTerms() - Method in class org.sbml.jsbml.Annotation: Checks if the list of CVTerm is not empty.
isSetListOfDeletions() - Method in class org.sbml.jsbml.ext.comp.Submodel: Returns true, if listOfDeletions contains at least one element.
isSetListOfDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Returns true, if listOfDimensions contains at least one element.
isSetListOfDomains() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns true, if listOfDomains contains at least one element.
isSetListOfDomainTypes() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns true, if listOfDomainTypes contains at least one element.
isSetListOfDynElements() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin: Returns whether listOfDynElements is set
isSetListOfElements() - Method in class org.sbml.jsbml.ext.render.Polygon: To check, whether Polygon.listOfElements is non-null, but empty, use Polygon.isListOfElementsEmpty()
isSetListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderCurve
isSetListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup: Returns true, if listOfElements contains at least one element.
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.
isSetListOfExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: Returns true, if listOfExternalModelDefinitions contains at least one element.
isSetListOfFluxBounds() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
isSetListOfFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective
isSetListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model: Returns true if the listOfFunctionDefinitions of this Model is not null and not empty.
isSetListOfFunctionTerms() - Method in class org.sbml.jsbml.ext.qual.Transition
isSetListOfGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns true if FBCModelPlugin.listOfGeneProducts contains at least one element.
isSetListOfGeometryDefinitions() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns true, if listOfGeometryDefinitions contains at least one element.
isSetListOfGeometryDefinitions() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Returns true, if listOfGeometryDefinitions contains at least one element.
isSetListOfGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin
isSetListOfGradientDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isSetListOfGradientStops() - Method in class org.sbml.jsbml.ext.render.GradientBase
isSetListOfGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
isSetListOfIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Returns true, if listOfIndices contains at least one element.
isSetListOfInitialAssignments() - Method in class org.sbml.jsbml.Model: Returns true if the listOfInitialAssignments of this Model is not null and not empty.
isSetListOfInputs() - Method in class org.sbml.jsbml.ext.qual.Transition
isSetListOfInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType: Returns true if MultiSpeciesType.listOfInSpeciesTypeBonds contains at least one element.
isSetListOfInteriorPoints() - Method in class org.sbml.jsbml.ext.spatial.Domain: Returns true, if listOfInteriorPoints contains at least one element.
isSetListOfLayouts() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
isSetListOfLineEndings() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
isSetListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw: Returns true, if the list of local parameters is set and not empty..
isSetListOfLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
isSetListOfLocalStyles() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
isSetListOfMembers() - Method in class org.sbml.jsbml.ext.groups.Group: Returns true if Group.listOfMembers is not null.
isSetListOfModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: Returns true, if listOfModelDefinitions contains at least one element.
isSetListOfModification() - Method in class org.sbml.jsbml.History
isSetListOfModifiers() - Method in class org.sbml.jsbml.Reaction
isSetListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm: Returns true if CVTerm.listOfNestedCVTerms contains at least one element.
isSetListOfObjectives() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns true if listOfObjectives is not null.
isSetListOfOrdinalMappings() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Returns true, if listOfOrdinalMappings contains at least one element.
isSetListOfOutputs() - Method in class org.sbml.jsbml.ext.qual.Transition
isSetListOfOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Returns true if MultiSpeciesPlugin.listOfOutwardBindingSites is not null.
isSetListOfParameters() - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
use KineticLaw.isSetListOfLocalParameters()
isSetListOfParameters() - Method in class org.sbml.jsbml.Model: Returns true if the listOfParameters of this Model is not null and not empty.
isSetListOfParametricObjects() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry: Returns true, if listOfParametricObjects contains at least one element.
isSetListOfPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Returns true, if listOfPorts contains at least one element.
isSetListOfPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Returns true if SpeciesFeatureType.listOfPossibleSpeciesFeatureValues contains at least one element.
isSetListOfProducts() - Method in class org.sbml.jsbml.Reaction
isSetListOfQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Returns true if the listOfQualitativeSpecies is set.
isSetListOfReactants() - Method in class org.sbml.jsbml.Reaction
isSetListOfReactionGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetListOfReactions() - Method in class org.sbml.jsbml.Model: Returns true if the listOfReactions of this Model is not null and not empty.
isSetListOfReferenceGlyphs() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Returns true if the GeneralGlyph.listOfReferenceGlyphs element is not null.
isSetListOfReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Returns true, if listOfReplacedElements contains at least one element, otherwise false
isSetListOfRules() - Method in class org.sbml.jsbml.Model: Returns true if the listOfRules of this Model is not null and not empty.
isSetListOfSampledFields() - Method in class org.sbml.jsbml.ext.spatial.Geometry: Returns true, if listOfSampledFields contains at least one element.
isSetListOfSampledVolumes() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Returns true, if listOfSampledVolumes contains at least one element.
isSetListOfSpatialComponents() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin: Returns whether listOfSpatialComponents is set
isSetListOfSpecies() - Method in class org.sbml.jsbml.Model: Returns true if the listOfSpecies of this Model is not null and not empty.
isSetListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Returns true if MultiSpeciesPlugin.listOfSpeciesFeatures is not null.
isSetListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType: Returns true if MultiSpeciesType.listOfSpeciesFeatureTypes contains at least one element.
isSetListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Returns true if SpeciesFeature.listOfSpeciesFeatureValues contains at least one element.
isSetListOfSpeciesGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetListOfSpeciesReferenceGlyphs() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Returns true is the list of SpeciesReferenceGlyph is set.
isSetListOfSpeciesReferencesGlyphs() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Deprecated.
use ReactionGlyph.isSetListOfSpeciesReferenceGlyphs()
isSetListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType: Returns true if MultiSpeciesType.listOfSpeciesTypeComponentIndexes contains at least one element.
isSetListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin: Returns true if MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts contains at least one element.
isSetListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType: Returns true if MultiSpeciesType.listOfSpeciesTypeInstances contains at least one element.
isSetListOfSpeciesTypes() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Returns true if the listOfSpeciesType is set.
isSetListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
isSetListOfStyles() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
isSetListOfSubGlyphs() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Returns true, if listOfSubGlyphs contains at least one element.
isSetListOfSubListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Returns true if MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures contains at least one element.
isSetListOfSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Returns true, if listOfSubmodels contains at least one element.
isSetListOfTextGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
isSetListOfTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: Returns true if the listOfTransitions is set.
isSetListOfUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin: Returns true if DistribSBasePlugin.listOfUncertainties contains at least one element.
isSetListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty: Returns true if Uncertainty.listOfUncertParameters contains at least one element.
isSetListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Returns true if UncertParameter.listOfUncertParameters contains at least one element.
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.
isSetLocationURI() - Method in class org.sbml.jsbml.SBMLDocument: Returns true if the location URI of this SBMLDocument is not null.
isSetLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns whether FBCReactionPlugin.lowerFluxBound is set.
isSetLowerFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
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 class org.sbml.jsbml.ext.distrib.UncertParameter
isSetMath() - Method in interface org.sbml.jsbml.MathContainer: Checks if an ASTNode has been set for this 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
isSetMaxLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
isSetMaxValue() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Returns whether maxValue is set
isSetMd5() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Returns whether md5 is set
isSetMembersShareType() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.

Returns whether membersShareType is set
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.
isSetMetaidRef() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Returns whether metaidRef is set
isSetMetaIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Returns whether metaIdRef is set
isSetMetaIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement: Returns whether metaIdRef is set
isSetMetaIdRef() - Method in class org.sbml.jsbml.ext.groups.Member: Returns whether metaIdRef is set
isSetMinValue() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Returns whether minValue is set
isSetModel() - Method in class org.sbml.jsbml.SBMLDocument: Returns true if the Model of this SBMLDocument is not null.
isSetModelHistory() - Method in class org.sbml.jsbml.Model: Deprecated.
use SBase.isSetHistory()
isSetModelQualifierType() - Method in class org.sbml.jsbml.CVTerm: Returns true if the CVTerm.Qualifier is set and is of type CVTerm.Type.MODEL_QUALIFIER
isSetModelRef() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Returns whether modelRef is set
isSetModelRef() - Method in class org.sbml.jsbml.ext.comp.Submodel: Returns whether modelRef is set
isSetModifiedDate() - Method in class org.sbml.jsbml.History: Predicate returning true or false depending on whether this History's modifiedDate has been set.
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.ext.qual.QualConstants: Returns true is the new value is set.
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.
isSetNumberType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
isSetNumberType() - Method in class org.sbml.jsbml.ASTNode: Returns true if the number type is set.
isSetNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode: Returns true iff numerator has been set
isSetNumericValue() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue: Returns whether PossibleSpeciesFeatureValue.numericValue is set.
isSetNumSamples1() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether numSamples1 is set
isSetNumSamples2() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether numSamples2 is set
isSetNumSamples3() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether numSamples3 is set
isSetObjectRole() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin: Returns whether RenderGraphicalObjectPlugin.objectRole is set.
isSetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Returns whether SpeciesFeature.occur is set.
isSetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Returns whether SpeciesFeatureType.occur is set.
isSetOffset() - Method in class org.sbml.jsbml.ext.render.GradientStop
isSetOffset() - Method in class org.sbml.jsbml.Unit: Deprecated.
the offset attribute should no longer be used.
isSetOldValue() - Method in class org.sbml.jsbml.ext.qual.QualConstants: Returns true is the old value is set.
isSetOldValue() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
isSetOperation() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetOperationType() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Returns whether operationType is set
isSetOrder() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph: Returns whether order is set
isSetOrdinal() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Returns whether ordinal is set
isSetOrdinal() - Method in class org.sbml.jsbml.ext.spatial.CSGObject: Returns whether ordinal is set
isSetOrdinal() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping: Returns whether ordinal is set
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.
isSetOriginOfText() - Method in class org.sbml.jsbml.ext.layout.TextGlyph
isSetOtherAnnotationThanRDF() - Method in class org.sbml.jsbml.Annotation: Deprecated.
please use Annotation.isSetNonRDFannotation()
isSetOtherAttributes() - Method in class org.sbml.jsbml.Creator: Deprecated.
those other attributes are not saved when writing the model
isSetOutputLevel() - Method in class org.sbml.jsbml.ext.qual.Output
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.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 class org.sbml.jsbml.AbstractSBase
isSetPackageVErsion() - Method in interface org.sbml.jsbml.SBase: Returns true if the package version is not equals to '-1'.
isSetParamType() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
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: Checks if a parent SBML object, i.e., a MathContainer, is set as a parent SBML object for this 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: Deprecated.
use SBMLDocument.isSetPackageRequired(String)
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.
isSetPointIndex() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Returns whether ParametricObject.pointIndex is set.
isSetPointIndex() - Method in class org.sbml.jsbml.ext.spatial.PolygonObject: Deprecated.

Returns whether pointIndex is set
isSetPointIndexLength() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Returns whether pointIndexLength is set.
isSetPolygonType() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Returns whether polygonType is set
isSetPortRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Returns whether portRef is set
isSetPosition() - Method in class org.sbml.jsbml.ext.layout.BoundingBox
isSetPrefix() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
isSetPrimitiveType() - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive: Returns whether primitiveType is set
isSetPriority() - Method in class org.sbml.jsbml.Event
isSetProductComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Returns whether SpeciesTypeComponentMapInProduct.productComponent is set.
isSetProgramName() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
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.ext.render.RenderInformationBase
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: Returns true if the CVTerm.Qualifier of this CVTerm is set and is different from CVTerm.Qualifier.BQM_UNKNOWN and CVTerm.Qualifier.BQB_UNKNOWN.
isSetQualifierType() - Method in class org.sbml.jsbml.CVTerm: Checks whether or not the CVTerm.Type has been set for this CVTerm.
isSetQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Input
isSetQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Output
isSetR() - Method in class org.sbml.jsbml.ext.render.RadialGradient
isSetRatio() - Method in class org.sbml.jsbml.ext.render.Ellipse
isSetRatio() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetRDFannotation() - Method in class org.sbml.jsbml.Annotation: Checks if the RDF part of the Annotation is initialized.
isSetReactant() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Returns whether SpeciesTypeComponentMapInProduct.reactant is set.
isSetReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Returns whether SpeciesTypeComponentMapInProduct.reactantComponent is set.
isSetReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns whether reaction is set
isSetReaction() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
isSetReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns whether reaction is set and is a valid Reaction in the model.
isSetReactionInstance() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
isSetReal() - Method in class org.sbml.jsbml.math.ASTCnRealNode: Returns true iff a value has been set
isSetReference() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph: Returns true if the reference attribute is not null and not empty.
isSetReferencedAttribute() - Method in class org.sbml.jsbml.ext.arrays.Index: Returns whether referencedAttribute is set
isSetReferenceInstance() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
isSetReferenceRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
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
isSetRelation() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Returns whether SubListOfSpeciesFeature.relation is set.
isSetRelativeValue() - Method in class org.sbml.jsbml.ext.render.RelAbsVector
isSetRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Deprecated.
This goes beyond/is besides the render-package's specification and will be removed in a future release. Use the LocalRenderInformation-related methods of RenderLayoutPlugin, and the GlobalRenderInformation-related methods of RenderListOfLayoutsPlugin instead.
isSetReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Returns whether replacedBy is set
isSetRepresentationType() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin: Returns whether MultiASTNodePlugin.representationType is set.
isSetResultLevel() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm: Returns true if resultLevel is set.
isSetReverseTransformation() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation: Returns whether reverseTransformation is set
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
isSetRole() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
isSetRoleList() - Method in class org.sbml.jsbml.ext.render.Style
isSetRotateAngleInRadians() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Returns whether rotateAngleInRadians is set
isSetRotateX() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Returns whether rotateAxisX is set
isSetRotateY() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Returns whether rotateAxisY is set
isSetRotateZ() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Returns whether rotateAxisZ is set
isSetRx() - Method in class org.sbml.jsbml.ext.render.Ellipse
isSetRx() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetRy() - Method in class org.sbml.jsbml.ext.render.Ellipse
isSetRy() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetSampledField() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Returns whether sampledField is set
isSetSampledValue() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Returns whether sampledValue is set
isSetSamples() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether SampledField.samples is set.
isSetSamplesLength() - Method in class org.sbml.jsbml.ext.spatial.SampledField: Returns whether SampledField.samplesLength is set.
isSetSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Returns whether sBaseRef is set
isSetSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
isSetSBOTerm() - Method in interface org.sbml.jsbml.SBase: Returns true if the SBOTerm is set.
isSetScale() - Method in class org.sbml.jsbml.Unit
isSetScaleX() - Method in class org.sbml.jsbml.ext.spatial.CSGScale: Returns whether scaleX is set
isSetScaleY() - Method in class org.sbml.jsbml.ext.spatial.CSGScale: Returns whether scaleY is set
isSetScaleZ() - Method in class org.sbml.jsbml.ext.spatial.CSGScale: Returns whether scaleZ is set
isSetSign() - Method in class org.sbml.jsbml.ext.qual.Input
isSetSize() - Method in class org.sbml.jsbml.Compartment: Returns true if the size of this compartment has been set by a user.
isSetSize() - Method in class org.sbml.jsbml.ext.arrays.Dimension: Returns whether size is set
isSetSource() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Returns whether source is set
isSetSource() - Method in class org.sbml.jsbml.ext.qual.QualConstants: Returns true is the source is set.
isSetSource() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
isSetSpatial() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
isSetSpatialDimensions() - Method in class org.sbml.jsbml.Compartment: Returns true if the spatialDimensions of this compartment has been set by a user.
isSetSpatialDimensions() - Method in class org.sbml.jsbml.ext.spatial.DomainType: Returns whether spatialDimension is set
isSetSpatialId() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
isSetSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase: Deprecated.
use SBase.isSetId()
isSetSpatialIndex() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent: Returns whether spatialIndex is set
isSetSpatialPoints() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry: Returns whether ParametricGeometry.spatialPoints is set.
isSetSpatialRef() - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Returns true is the spatial reference is set.
isSetSpatialSizeUnits() - Method in class org.sbml.jsbml.Species: Deprecated.
Only valid for SBML Level 2 Versions 1 and 2.
isSetSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species: Deprecated.
Only valid for SBML Level 2 Versions 1 and 2.
isSetSpecies() - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph
isSetSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference
isSetSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Returns whether SpeciesFeature.speciesFeatureType is set.
isSetSpeciesGlyph() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
isSetSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference
isSetSpeciesReference() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
isSetSpeciesReference() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin: Returns whether MultiASTNodePlugin.speciesReference is set.
isSetSpeciesReference() - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Returns whether ParameterType.variable is set.
isSetSpeciesReferenceInstance() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
isSetSpeciesReferenceRole() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
isSetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Returns whether MultiSpeciesPlugin.speciesType is set.
isSetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Returns whether SpeciesTypeInstance.speciesType is set.
isSetSpeciesType() - Method in class org.sbml.jsbml.Species: Deprecated.
isSetSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species: Deprecated.
isSetSpId() - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Returns true is the spatial reference is set.
isSetSpreadMethod() - Method in class org.sbml.jsbml.ext.render.GradientBase
isSetStart() - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Returns true if the Start Point is set.
isSetStart() - Method in class org.sbml.jsbml.ext.layout.LineSegment
isSetStartHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve: Returns true if startHead is set
isSetStartHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
isSetStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference: Deprecated.
since SBML L3V1
isSetStopColor() - Method in class org.sbml.jsbml.ext.render.GradientStop
isSetStrict() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns whether FBCModelPlugin.strict is set.
isSetStroke() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D
isSetStrokeDashArray() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D
isSetStrokeWidth() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D
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
isSetSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy: Returns whether submodelRef is set
isSetSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: Returns whether submodelRef is set
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
isSetText() - Method in class org.sbml.jsbml.ext.layout.TextGlyph
isSetText() - Method in class org.sbml.jsbml.ext.render.Text: Checks whether the text-field has been set.
isSetTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isSetTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text
isSetThresholdLevel() - Method in class org.sbml.jsbml.ext.qual.Input
isSetTimeConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel: Returns whether timeConversionFactor is set
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.
isSetTransform() - Method in class org.sbml.jsbml.ext.render.Transformation
isSetTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Input
isSetTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Output
isSetTranslateX() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation: Returns whether translateX is set
isSetTranslateY() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation: Returns whether translateY is set
isSetTranslateZ() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation: Returns whether translateZ is set
isSetTrigger() - Method in class org.sbml.jsbml.Event
isSetType() - Method in class org.sbml.jsbml.CVTerm: Returns true if the CVTerm.Type of this CVTerm is set and is different from CVTerm.Type.UNKNOWN_QUALIFIER.
isSetType() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Returns whether UncertParameter.type is set.
isSetType() - Method in class org.sbml.jsbml.ext.fbc.Objective: Returns whether type is set
isSetType() - Method in class org.sbml.jsbml.ext.layout.CurveSegment
isSetType() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment: Returns true if the type is set.
isSetType() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition: Returns whether type is set
isSetType() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Returns whether type is set
isSetType() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Returns whether diffusionKind is set
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
isSetTypeList() - Method in class org.sbml.jsbml.ext.render.Style
isSetTypeQualifier() - Method in class org.sbml.jsbml.CVTerm: Deprecated.
use CVTerm.isSetQualifier()
isSetUnit() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value: Test if this value can be evaluated to a UnitDefinition
isSetUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue: Test if this value can be evaluated to a UnitDefinition
isSetUnitRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Returns whether unitRef is set
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: Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
isSetUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Returns whether UncertParameter.units is set.
isSetUnits() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Returns whether unit is set
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: Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
isSetUnitsInstance() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
isSetUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
isSetUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit: Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.
isSetUnitSize() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping: Returns whether unitSize is set
isSetUpperFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns whether FBCReactionPlugin.upperFluxBound is set.
isSetUpperFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
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() - Method in class org.sbml.jsbml.Event
isSetV() - Method in class org.sbml.jsbml.util.ValuePair
isSetValue() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Returns whether UncertParameter.value is set.
isSetValue() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Returns whether SpeciesFeatureValue.value is set.
isSetValue() - Method in class org.sbml.jsbml.ext.render.ColorDefinition
isSetValue() - Method in class org.sbml.jsbml.ext.spatial.Boundary: Returns whether value is set
isSetValue() - Method in interface org.sbml.jsbml.Quantity: Returns true if the value of this Quantity is set.
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
isSetValueLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Returns whether UncertSpan.valueLower is set.
isSetValueUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Returns whether UncertSpan.valueUpper is set.
isSetVar() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Returns whether UncertParameter.var is set.
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.ext.dyn.SpatialComponent: Returns whether variable is set
isSetVariable() - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Returns whether ParameterType.variable is set.
isSetVariable() - Method in class org.sbml.jsbml.InitialAssignment
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
isSetVarLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Returns whether UncertSpan.varLower is set.
isSetVarUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Returns whether UncertSpan.varUpper is set.
isSetVersion() - Method in class org.sbml.jsbml.AbstractSBase
isSetVersion() - Method in interface org.sbml.jsbml.SBase: Returns true if the version is not null.
isSetVersionMajor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Returns true if versionMajor is set.
isSetVersionMinor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Returns true if versionMinor is set.
isSetViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath: Returns whether viableWithoutChange is set
isSetVolume() - Method in class org.sbml.jsbml.Compartment: Deprecated.
The volume attribute is only defined in SBML Level 1. Please use Compartment.isSetSize()
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.
isSetVTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle
isSetVTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup
isSetVTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text
isSetWidth() - Method in class org.sbml.jsbml.ext.layout.Dimensions
isSetWidth() - Method in class org.sbml.jsbml.ext.render.Image
isSetWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetX() - Method in class org.sbml.jsbml.ext.layout.Point: Returns true if the x coordinate is set.
isSetX() - Method in class org.sbml.jsbml.ext.render.Image
isSetX() - Method in interface org.sbml.jsbml.ext.render.Point3D
isSetX() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetX() - Method in class org.sbml.jsbml.ext.render.RenderPoint
isSetX() - Method in class org.sbml.jsbml.ext.render.Text
isSetX1() - Method in class org.sbml.jsbml.ext.render.LinearGradient
isSetX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
isSetX2() - Method in class org.sbml.jsbml.ext.render.LinearGradient
isSetX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
isSetY() - Method in class org.sbml.jsbml.ext.layout.Point: Returns true if the y coordinate is set.
isSetY() - Method in class org.sbml.jsbml.ext.render.Image
isSetY() - Method in interface org.sbml.jsbml.ext.render.Point3D
isSetY() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetY() - Method in class org.sbml.jsbml.ext.render.RenderPoint
isSetY() - Method in class org.sbml.jsbml.ext.render.Text
isSetY1() - Method in class org.sbml.jsbml.ext.render.LinearGradient
isSetY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
isSetY2() - Method in class org.sbml.jsbml.ext.render.LinearGradient
isSetY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
isSetZ() - Method in class org.sbml.jsbml.ext.layout.Point: Returns true if the z coordinate is set.
isSetZ() - Method in class org.sbml.jsbml.ext.render.Image
isSetZ() - Method in interface org.sbml.jsbml.ext.render.Point3D
isSetZ() - Method in class org.sbml.jsbml.ext.render.Rectangle
isSetZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint
isSetZ() - Method in class org.sbml.jsbml.ext.render.Text
isSetZ1() - Method in class org.sbml.jsbml.ext.render.LinearGradient
isSetZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
isSetZ2() - Method in class org.sbml.jsbml.ext.render.LinearGradient
isSetZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
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
isSignMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
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'.
isSpatial - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
isSpatial() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
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.
isStateTransition(int) - Static method in class org.sbml.jsbml.SBO: Returns true if the given term identifier comes from the stated branch of SBO.
isStaticallyComputable(Model, ASTNode, String...) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath: Determines whether a MathContainer object is statically computable given a list of ids that can appear in the math.
isStaticallyComputable(Model, Index) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath: Determines whether a MathContainer object is statically computable.
isStaticallyComputable(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath: Determines whether a MathContainer object is statically computable.
isStaticallyComputable(Model, MathContainer, String...) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath: Determines whether a MathContainer object is statically computable given a list of ids that can appear in the math.
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.ext.fbc.FBCModelPlugin: Returns the value of FBCModelPlugin.strict.
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: Returns true if this node is a name or refers to a FunctionDefinition.
isString() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
isString() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
isSubstrate(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector: Check if a species reference glyph is a substrate.
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() - Method in class org.sbml.jsbml.xml.XMLToken: Returns true or false depending on whether this XMLToken is an XML text element.
isThresholdLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.Input
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.
isTransitionEffectMandatory() - Method in class org.sbml.jsbml.ext.qual.Input
isTransitionEffectMandatory() - Method in class org.sbml.jsbml.ext.qual.Output
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.
isType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
isType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Returns the value of MultiCompartmentPlugin.isType, return false if isType is not defined.
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() - 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.
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(Unit.Kind, int, int) - Static method in class org.sbml.jsbml.Unit
isUnitsDefined() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
isUnitsDefined() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
isUnknown() - Method in class org.sbml.jsbml.ASTNode: Returns true if this node has an ASTNode.Type.UNKNOWN type.
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: Checks whether or not the user's object has been set (see TreeNodeAdapter.isSetUserObject()) and if so if it belongs to those elements returned by the method TreeNodeAdapter.getChildAt(int).
isUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
isValidChemicalFormula(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
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: Deprecated.
use SyntaxChecker.isValidId(String, int, int)
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: Deprecated.
use SyntaxChecker.isValidMetaId(String)
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. 12 for details).
isValidMetaId(String, int, int) - Static method in class org.sbml.jsbml.validator.SyntaxChecker: Checks if the given identifier candidate satisfies the requirements for a valid meta identifier (for any version and level).
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: This method is equivalent to converting the String to a Unit.Kind and then calling its Unit.Kind.isDefinedIn(int, int) method.
isValidVariable(Variable, int) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
isVariable() - Method in class org.sbml.jsbml.ASTNode: Returns true if this node represents a Variable.
isVariantOfArea() - Method in class org.sbml.jsbml.Unit: Returns true if this Unit is a variant of area, meaning of Unit.Kind.METRE with an exponent of 2.
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: Tests if this Unit is a variant of 'substance'.
isVariantOfSubstance() - Method in class org.sbml.jsbml.UnitDefinition: Tests if this UnitDefinition is a variant of 'substance'.
isVariantOfSubstance(boolean) - Method in class org.sbml.jsbml.Unit: Tests if this Unit is a variant of '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.
isVectorBalanced(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
isVectorOperation(ASTNode) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
isViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath: Returns the value of viableWithoutChange
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: Returns true is the SBMLError severity is of type SBMLError.SEVERITY.WARNING
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).
ITEM - org.sbml.jsbml.Unit.Kind: A pseudo-unit representing a single 'thing'.
iterator() - Method in class org.sbml.jsbml.ListOf


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