- id - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- id - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- 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
-
- IdenticalUnitDefinitionFilter(UnitDefinition) - Constructor for class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter
-
- IdentifierException - Exception in org.sbml.jsbml
-
This exception is thrown when trying to set or add an identifier to an
instance of
NamedSBase
but if the given identifier is already
registered in the containing
Model
.
- IdentifierException(NamedSBase, String) - Constructor for exception org.sbml.jsbml.IdentifierException
-
- IdentifierException(SBase, String) - Constructor for exception org.sbml.jsbml.IdentifierException
-
- identifyingParent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- idList - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- IdManager - Interface in org.sbml.jsbml.util
-
Manages an id namespace.
- 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 - 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
- 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.
- 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
-
- index - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
-
- 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 - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
-
- index - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- INDEX_EXCEEDS_SIZE - Static variable in class org.sbml.jsbml.JSBML
-
- IndexArrayDimCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints
-
This 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
-
Constructs a new IndexArrayDimCheck 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
-
- indexOf(TreeNode, TreeNode) - Static method in class org.sbml.jsbml.AbstractTreeNode
-
Searches the given child in the list of sub-nodes of the parent element.
- indexOf(Object) - Method in class org.sbml.jsbml.ListOf
-
- IndexValidator - Class in org.sbml.jsbml.ext.arrays.validator
-
This 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
-
- init() - Method in class org.sbml.jsbml.ext.comp.ModelDefinition
-
- initDefaults() - Method in class org.sbml.jsbml.Compartment
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Compartment
-
Initializes the default values using the current Level/Version configuration.
- initDefaults() - Method in class org.sbml.jsbml.Event
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Event
-
Initializes the default values of this
Event
.
- initDefaults() - Method in class org.sbml.jsbml.ExplicitRule
-
- initDefaults() - Method in class org.sbml.jsbml.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 using the namespace.
- 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.DistribInput
-
Initializes the default values using the namespace.
- initDefaults() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
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.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.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.DenotedSpeciesTypeComponentIndex
-
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.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.SpeciesFeatureChange
-
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.SpeciesType
-
Initializes the default values.
- 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.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.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.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.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.SpatialPoints
-
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(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() - Method in class org.sbml.jsbml.Parameter
-
Initializes the default values using the current Level/Version configuration.
- initDefaults() - Method in class org.sbml.jsbml.Reaction
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Reaction
-
Initializes the default variables of this Reaction.
- initDefaults() - Method in class org.sbml.jsbml.Species
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Species
-
Initializes the default values of this Species.
- initDefaults() - Method in class org.sbml.jsbml.SpeciesReference
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.SpeciesReference
-
Initializes the default values of this SpeciesReference.
- initDefaults() - Method in class org.sbml.jsbml.Trigger
-
- initDefaults() - Method in class org.sbml.jsbml.Unit
-
Initializes the default values using the current Level/Version configuration.
- initDefaults(int, int) - Method in class org.sbml.jsbml.Unit
-
Initializes the attributes of this Unit (except for 'kind') to their
defaults values.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Unit
-
- initialAmount - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- InitialAssignment - Class in org.sbml.jsbml
-
Represents the initialAssignment XML element of a SBML file.
- InitialAssignment() - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment instance.
- InitialAssignment(InitialAssignment) - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment instance from a given InitialAssignment.
- InitialAssignment(int, int) - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment from level and version.
- InitialAssignment(Variable) - Constructor for class org.sbml.jsbml.InitialAssignment
-
Creates an InitialAssignment instance from a
Variable
.
- InitialAssignment(Variable, ASTNode, int, int) - Constructor for class org.sbml.jsbml.InitialAssignment
-
- 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
-
Helper method to initialize newly created lists.
- Input - Class in org.sbml.jsbml.ext.qual
-
- Input() - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- Input(String) - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- Input(String, QualitativeSpecies, InputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- Input(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- Input(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- Input(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- Input(Input) - Constructor for class org.sbml.jsbml.ext.qual.Input
-
- 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
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- insertChild(int, XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
-
Inserts a node as the
n
th child of this
XMLNode
.
- InSpeciesTypeBond - Class in org.sbml.jsbml.ext.multi
-
- InSpeciesTypeBond() - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond
-
Creates an InSpeciesTypeBond instance
- InSpeciesTypeBond(String) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond
-
Creates a InSpeciesTypeBond instance with an id.
- InSpeciesTypeBond(int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond
-
Creates a InSpeciesTypeBond instance with a level and version.
- 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
- instance - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
-
- 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 - Class in org.sbml.jsbml.ext.spatial
-
- InteriorPoint() - Constructor for class org.sbml.jsbml.ext.spatial.InteriorPoint
-
- InteriorPoint(InteriorPoint) - Constructor for class org.sbml.jsbml.ext.spatial.InteriorPoint
-
- InteriorPoint(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.InteriorPoint
-
- interiorPoint - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- interpolation - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- InterpolationKind - Enum in org.sbml.jsbml.ext.spatial
-
This enum type was created following the specifications defined in Spatial Package v0.90.
- IntraSpeciesReaction - Class in org.sbml.jsbml.ext.multi
-
- IntraSpeciesReaction() - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction
-
Creates an IntraSpeciesReaction instance
- IntraSpeciesReaction(String) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction
-
Creates a IntraSpeciesReaction instance with an id.
- IntraSpeciesReaction(int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction
-
Creates a IntraSpeciesReaction instance with a level and version.
- 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_ATTRIBUTE_VALUE - Static variable in class org.sbml.jsbml.JSBML
-
- INVALID_OBJECT - Static variable in class org.sbml.jsbml.JSBML
-
- INVALID_XML_OPERATION - Static variable in class org.sbml.jsbml.JSBML
-
- 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.
- isAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Image
-
- isAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsolutePosition(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
-
- isAbsoluteR() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Image
-
- isAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Image
-
- isAbsoluteX() - Method in interface org.sbml.jsbml.ext.render.Point3D
-
- isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.RenderPoint
-
- isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Text
-
- isAbsoluteX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isAbsoluteX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Image
-
- isAbsoluteY() - Method in interface org.sbml.jsbml.ext.render.Point3D
-
- isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.RenderPoint
-
- isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Text
-
- isAbsoluteY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isAbsoluteY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Image
-
- isAbsoluteZ() - Method in interface org.sbml.jsbml.ext.render.Point3D
-
- isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint
-
- isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Text
-
- isAbsoluteZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isAbsoluteZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isActive() - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition
-
- isActive - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- 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.
- 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.
- 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
-
- isBoundaryConditionMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
-
- isBuiltIn(String, int) - Static method in class org.sbml.jsbml.Unit
-
- isBuiltIn(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
- isBuiltIn() - Method in class org.sbml.jsbml.UnitDefinition
-
- isCallableSBase() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isCallableSBase() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isCandela() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind candela
- isCatalyst(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isCatalyticActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isCelsius() - Method in class org.sbml.jsbml.Unit
-
- isChildOf(int, int) - Static method in class org.sbml.jsbml.SBO
-
Checks whether the given sboTerm is a member of the SBO subgraph rooted
at parent.
- 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.SpeciesType
-
- 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
-
- 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
-
- isDimensionless() - Method in class org.sbml.jsbml.Unit
-
- isDiscreteFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the term is-a discrete framework, false
otherwise
- isDissociation(int) - Static method in class org.sbml.jsbml.SBO
-
- isDrug(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isElement() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns
true
or
false
depending on whether
this
XMLToken
is an XML element.
- isEmpty() - Method in class org.sbml.jsbml.Annotation
-
- isEmpty() - Method in class org.sbml.jsbml.History
-
Checks whether at least one attribute has been set for this
History
.
- isEmpty() - Method in class org.sbml.jsbml.ListOf
-
- isEmpty() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns
true
or
false
depending on whether
this
XMLAttributes
set is empty.
- isEmpty() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Returns
true
or
false
depending on whether this
XMLNamespaces
list is empty.
- isEmpty() - Method in class org.sbml.jsbml.xml.XMLTriple
-
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.
- 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
-
- 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() - Method in class org.sbml.jsbml.LocalParameter
-
In SBML prior to Level 3 it was possible to explicitly state that a local
parameter represents a constant
Quantity
.
- isExplicitlySetConstant - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isExtendedByOtherPackages() - Method in class org.sbml.jsbml.AbstractSBase
-
- isExtendedByOtherPackages() - Method in 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
-
- isFatal() - Method in exception org.sbml.jsbml.SBMLError
-
- 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.
- 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.DistribInput
-
- 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.ListOfMemberConstraint
-
Deprecated.
- 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.PossibleSpeciesFeatureValue
-
- isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange
-
- isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- 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.RenderGroup
-
- 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
-
This method can be used to query 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 class org.sbml.jsbml.SimpleSpeciesReference
-
- isIdMandatory() - Method in class org.sbml.jsbml.SpeciesType
-
Deprecated.
- isIdMandatory() - Method in class org.sbml.jsbml.UnitDefinition
-
- isIgnoredPackage(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns true
if the given package extension is one of an ignored
packages, otherwise returns false
.
- isIgnoredPkg(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isInfinity() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node represents the special IEEE 754 value infinity,
false
otherwise.
- isInfinity() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns
true
if this
ASTCnRealNode
represents the special IEEE 754 value infinity,
false
otherwise.
- isInfo() - Method in exception org.sbml.jsbml.SBMLError
-
- isInfo() - Method in exception org.sbml.jsbml.SBMLException
-
- isInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- 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(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
-
This method checks, if this UnitDefinition only contains Invalid as
Unit.Kind
.
- 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
-
- isLineSegment() - Method in class org.sbml.jsbml.ext.layout.CurveSegment
-
- isListOfFunctionTermsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
-
- isListOfInputsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
-
- isListOfOutputsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition
-
- 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
-
- isLog10() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node represents a log10() function, false
otherwise.
- isLogical() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node is a MathML logical operator (i.e., and, or,
not, xor).
- isLogicalFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isLumen() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind lumen
- isLux() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind lux
- isMaterialEntity(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- 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(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.
- 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 delay or time.
- isNamespacesEmpty() - Method in class org.sbml.jsbml.xml.XMLToken
-
- isNaN() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true
if this node is a type Real and represents the special IEEE
754 value 'not a number'
Double.NaN
,
false
otherwise.
- isNegInfinity() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true
if this node represents the special IEEE 754 value 'negative
infinity'
Double.NEGATIVE_INFINITY
,
false
otherwise.
- isNegInfinity() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- isNewton() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind newton
- isNode() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Checks whether the value encapsulated in this
ASTNodeValue
is an
instance of
Node
.
- isNode() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
Checks whether the value encapsulated in this
ASTNodeValue
is an
instance of
Node
.
- isNonCompetetiveInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isNonEssentialActivator(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isNumber() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node contains a number, false
otherwise.
- isNumber() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isNumber() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ISO_8601_DATE_FORMAT - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
-
ISO 8601 [W3CDTF] date format for GMT
- isObsolete() - Method in class org.sbml.jsbml.ontology.Term
-
Checks whether or not this
Term
is obsolete.
- isObsolete(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking whether the SBO term is obsolete.
- 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).
- 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 interface org.sbml.jsbml.SBase
-
Returns
true
if the given SBML Level 3 package is enabled within
the containing
SBMLDocument
.
- isPackageEnabled(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns
true
if the given SBML Level 3 package is enabled within
the
SBMLDocument
.
- isPackageEnabledOrDisabled(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isPackageURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isPackageURIEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true
if the given SBML Level 3 package is enabled within
the containing
SBMLDocument
.
- isParameter() - Method in class org.sbml.jsbml.AlgebraicRule
-
- isParameter() - Method in class org.sbml.jsbml.ExplicitRule
-
- isParameter() - Method in class org.sbml.jsbml.Rule
-
(SBML Level 1 only) Predicate returning true or false depending on
whether this Rule is an ParameterRule.
- isPartialInhibitor(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isParticipant(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isParticipantRole(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isPascal() - Method in class org.sbml.jsbml.Unit
-
Predicate for testing whether this Unit is of the kind pascal
- isPersistent() - Method in class org.sbml.jsbml.Trigger
-
- isPhenotype(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isPhysicalCompartment(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isPhysicalParticipant(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isPiecewise() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node is the MathML <piecewise> construct,
false
otherwise.
- isPkgEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- isPkgEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
- isPkgURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- isPkgURIEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
- isPredefined(String, int) - Static method in class org.sbml.jsbml.Unit
-
Predicate to test whether a given string is the name of a predefined SBML
unit.
- isPredefined(UnitDefinition) - Static method in class org.sbml.jsbml.Unit
-
Tests whether the given
UnitDefinition
belongs to the predefined
SBML units.
- isPredefined(String, int) - Static method in class org.sbml.jsbml.UnitDefinition
-
- isPredefined(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
Test if the given unit is a predefined unit.
- isPredefined() - Method in class org.sbml.jsbml.UnitDefinition
-
This method tests if this unit definition is a predefined unit.
- isPredefinedUnitsID(String) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
Checks whether or not a given identifier for a
Unit.Kind
or
UnitDefinition
equals a predefined unit identifier for this type.
- isPrefixNotationInLogicalOperations() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- isPrintNameIfAvailable() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- isPrintNameIfAvailable() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- isProcess(int) - Static method in class org.sbml.jsbml.SBO
-
- isProduct(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking the SBO term is from correct part of SBO.
- isProtein(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isQualitativeSpeciesMandatory() - Method in class org.sbml.jsbml.ext.qual.Input
-
- isQualitativeSpeciesMandatory() - Method in class org.sbml.jsbml.ext.qual.Output
-
- 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(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 !
- 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
-
Return 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
-
- isSBMLNamespaceNeeded(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- isSBMLNamespaceNeeded(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- 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
- isSetAbout() - Method in class org.sbml.jsbml.Annotation
-
Checks whether the 'about' element has been initialized.
- isSetAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isSetAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isSetAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isSetAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Image
-
- isSetAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteR() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- isSetAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isSetAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Ellipse
-
- isSetAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Image
-
- isSetAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Image
-
- isSetAbsoluteX() - Method in interface org.sbml.jsbml.ext.render.Point3D
-
- isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.RenderPoint
-
- isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Text
-
- isSetAbsoluteX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isSetAbsoluteX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Image
-
- isSetAbsoluteY() - Method in interface org.sbml.jsbml.ext.render.Point3D
-
- isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.RenderPoint
-
- isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Text
-
- isSetAbsoluteY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isSetAbsoluteY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Image
-
- isSetAbsoluteZ() - Method in interface org.sbml.jsbml.ext.render.Point3D
-
- isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint
-
- isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Text
-
- isSetAbsoluteZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- isSetAbsoluteZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- 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
-
- isSetAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetAnnotation() - Method in class org.sbml.jsbml.Annotation
-
- isSetAnnotation() - Method in interface org.sbml.jsbml.SBase
-
Returns true
or false
depending on whether this object's
'annotation' sub-elements exists and have some content.
- 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
-
- 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
-
- isSetAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- 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
-
- isSetBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond
-
- isSetBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite
-
- isSetBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- 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 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
-
- isSetCharge() - Method in class org.sbml.jsbml.Species
-
- isSetChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
-
- 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
-
- 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
-
- isSetCompartment() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- 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.SpeciesType
-
- 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
-
- isSetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance
-
- 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
-
- 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
-
- isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex
-
- 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
-
- 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
-
- 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.
- isSetDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
Returns True iff definitionURL has been set
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetDelay() - Method in class org.sbml.jsbml.Event
-
- 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
-
- isSetDiffusionKind() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
-
Returns whether diffusionKind is set
- 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
- isSetDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin
-
Returns whether drawFromDistribution 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
-
- 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
-
- 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
-
- isSetGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
-
- 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
-
- 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.AbstractNamedSBase
-
- isSetId() - Method in class org.sbml.jsbml.ASTNode
-
- isSetId() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- isSetId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint
-
Deprecated.
- isSetId() - Method in class org.sbml.jsbml.ext.render.RenderGroup
-
- isSetId() - Method in class org.sbml.jsbml.FunctionDefinition
-
- 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
-
- 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
-
- isSetIndex() - Method in class org.sbml.jsbml.ext.distrib.DistribInput
-
Returns whether index 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 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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.
- isSetListOfDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
Returns true
, if listOfDistribInputs 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
-
- 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
-
- 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.SpeciesType
-
- 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
-
- 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
-
- 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
-
- 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
-
- isSetListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- isSetListOfParameters() - Method in class org.sbml.jsbml.Model
-
Returns true
if the listOfParameters of this Model is not null
and not
empty.
- 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
-
- 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
-
- 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.
- isSetListOfSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- isSetListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- isSetListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- isSetListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- isSetListOfSpeciesGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
-
- isSetListOfSpeciesReferencesGlyphs() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
-
- isSetListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- isSetListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
- isSetListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- 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.
- 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.
- 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
-
- isSetLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
-
- 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 interface org.sbml.jsbml.MathContainer
-
- isSetMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff mathMLClass has been set
- isSetMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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.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
- isSetMetaidRef() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject
-
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
-
- isSetModelHistory() - Method in class org.sbml.jsbml.Model
-
- isSetModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- 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.AbstractNamedSBase
-
- isSetName() - Method in class org.sbml.jsbml.ASTNode
-
- isSetName() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- isSetName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint
-
Deprecated.
- isSetName() - Method in class org.sbml.jsbml.ext.render.RenderGroup
-
- isSetName() - Method in class org.sbml.jsbml.FunctionDefinition
-
- 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
-
- 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() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if the number type is set.
- isSetNumberType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- isSetNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Returns true
iff numerator has been set
- isSetNumericValue() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
-
- 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
- isSetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- isSetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- 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
-
- 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.AbstractSBase
-
- isSetPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- isSetPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- 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
-
- isSetParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetParentSBMLObject() - Method in interface org.sbml.jsbml.SBase
-
Check whether this
SBase
has been linked to a parent within the
hierarchical SBML data structure.
- isSetPersistent() - Method in class org.sbml.jsbml.Trigger
-
- isSetPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isSetPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetPlugin(String) - Method in 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
-
- 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
-
- isSetProductSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange
-
- 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
-
- isSetQualifierType() - Method in class org.sbml.jsbml.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
-
- 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
-
- isSetReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- isSetReactantSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange
-
- 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.
- 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
-
- isSetReferencedAttribute() - Method in class org.sbml.jsbml.ext.arrays.Index
-
Returns whether referencedAttribute is set
- 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
- isSetRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
- 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
-
- 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
- isSetRotateAxisX() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation
-
Returns whether rotateAxisX is set
- isSetRotateAxisY() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation
-
Returns whether rotateAxisY is set
- isSetRotateAxisZ() - 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
-
- isSetSamplesLength() - Method in class org.sbml.jsbml.ext.spatial.SampledField
-
- 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 class org.sbml.jsbml.ext.spatial.AnalyticVolume
-
- isSetSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase
-
Returns whether spatialId is set
- 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
-
- isSetSpatialRef() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- isSetSpatialRef() - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference
-
- 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
-
- 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
-
- isSetSpeciesReference() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- isSetSpeciesReferenceRole() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
-
- isSetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- isSetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance
-
- isSetSpeciesType() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- isSetSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex
-
- isSetSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- isSetSpId() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- 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
-
- 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
-
- 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
-
- 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.Transformation2D
-
- 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
-
- 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.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.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
-
- isSetUncertainty() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- isSetUncertML() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
Returns whether uncertML is set
- isSetUncertML() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
-
- isSetUnit() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isSetUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- 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 Parameter
s.
In this case this AssignmentRule
represents the SBML
element ParameterRule.
- 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 Parameter
s.
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
-
- 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
-
- 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.fbc.FluxBound
-
Deprecated.
Only defined in FBC version 1.
- isSetValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue
-
- 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
-
- 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
-
- 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
-
- 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.AbstractRenderPlugin
-
- isSetVersionMinor() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
- isSetViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath
-
Returns whether viableWithoutChange is set
- isSetVolume() - Method in class org.sbml.jsbml.Compartment
-
- isSetVolumeUnits() - Method in class org.sbml.jsbml.Model
-
Returns true
if the volumeUnitsID of this Model is not null
.
- isSetVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
Returns true
if the UnitDefinition which has the volumeUnitsID of this
Model as id is not null
.
- 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.
- 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.
- 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, Index) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
-
This method is used to determine whether a
MathContainer
object is
statically computable.
- isStaticallyComputable(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
-
This method is used to determine whether a
MathContainer
object is statically computable.
- isStaticallyComputable(Model, MathContainer, String...) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
-
This method is used to determine whether a
MathContainer
object is statically computable given
a list of ids that can appear in the math.
- isStaticallyComputable(Model, ASTNode, String...) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
-
This method is used to determine 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
-
- isStrict() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isStrict() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Specifies strictness.
- isStrict() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isString() - Method in class org.sbml.jsbml.ASTNode
-
- isString() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isString() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- 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() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
- isType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- isUMinus() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node is a unary minus operator, false
otherwise.
- isUMinus() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isUMinus() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isUnary() - Method in class org.sbml.jsbml.ASTNode
-
Checks whether the number of child nodes is exactly one.
- isUnary() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- isUnary() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isUnitKind(Unit.Kind, int, int) - Static method in class org.sbml.jsbml.Unit
-
- isUnitKind(String, int, int) - Static method in class org.sbml.jsbml.Unit
-
Predicate to test whether a given string is the name of a valid base unit
in SBML (such as 'gram' or 'mole').
- isUnitKind() - Method in class org.sbml.jsbml.UnitDefinition
-
Convenient method to test whether this
UnitDefinition
contains
exactly one
Unit
that itself represents a
Unit.Kind
, i.e.,
multiplier = 1, exponent = 1, scale = 1.
- 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
-
- isUnknownMolecule(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isUnknownTransition(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isUserObjectRecursiveDataType() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- isUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
-
- isValidChemicalFormula(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
- isValidEmailAddress(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Definition of valid e-mail address
String
s.
- isValidId(String, int, int) - Static method in class org.sbml.jsbml.AbstractNamedSBase
-
- isValidId(String, int, int) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Checks whether the given idCandidate is a valid identifier according to
the SBML specifications.
- isValidLevelAndVersionCombination(int, int) - Static method in class org.sbml.jsbml.AbstractSBase
-
Returns true
if the level and version combination is a valid one, false
otherwise.
- isValidMetaId(String) - Static method in class org.sbml.jsbml.AbstractSBase
-
- isValidMetaId(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Checks if the given identifier candidate satisfies the requirements for a
valid meta identifier (see SBML L2V4 p. 12 for details).
- 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
-
- isVariable() - Method in class org.sbml.jsbml.ASTNode
-
Returns
true
if this node represents a
Variable
.
- isVariantOfArea() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfArea() - Method in class org.sbml.jsbml.UnitDefinition
-
- isVariantOfLength() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfLength() - Method in class org.sbml.jsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a variant
of the predefined unit identifier 'length'.
- isVariantOfSubstance() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfSubstance() - Method in class org.sbml.jsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a variant
of the predefined unit identifier 'substance'.
- isVariantOfSubstancePerArea() - Method in class org.sbml.jsbml.UnitDefinition
-
- isVariantOfSubstancePerLength() - Method in class org.sbml.jsbml.UnitDefinition
-
- isVariantOfSubstancePerTime() - Method in class org.sbml.jsbml.UnitDefinition
-
- isVariantOfSubstancePerVolume() - Method in class org.sbml.jsbml.UnitDefinition
-
- isVariantOfTime() - Method in class org.sbml.jsbml.Unit
-
- isVariantOfTime() - Method in class org.sbml.jsbml.UnitDefinition
-
Convenience function for testing 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
-
Convenience function for testing 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
-
- 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
-
- isZero() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node represents the number zero (either as integer
or as real value).
- iterator() - Method in class org.sbml.jsbml.ListOf
-