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

E

edgeIsLayouted(ReactionGlyph, SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if the incoming edge is layouted, i.e. if it has a curve.

either - org.sbml.jsbml.ext.multi.BindingStatus

element - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

ELEMENT_XML_PREFIX - Static variable in class org.sbml.jsbml.JSBML

Key used to store the XML prefix of an element when needed.

ElementOrderValidationFunction<T extends SBase> - Class in org.sbml.jsbml.validator.offline.constraints.helper

Class used to validate the order of the XML elements.

ElementOrderValidationFunction(String[]) - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.ElementOrderValidationFunction

ellipse - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Ellipse - Class in org.sbml.jsbml.ext.render

Encodes an ellipse.

Ellipse() - Constructor for class org.sbml.jsbml.ext.render.Ellipse

Creates a new Ellipse instance.

Ellipse(int, int) - Constructor for class org.sbml.jsbml.ext.render.Ellipse

Creates a new Ellipse instance.

Ellipse(Ellipse) - Constructor for class org.sbml.jsbml.ext.render.Ellipse

Creates a new Ellipse instance, copied from the given ellipse.

EllipseConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Ellipse class.

EllipseConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.EllipseConstraints

email - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

EMPTY_SET - Static variable in class org.sbml.jsbml.math.compiler.HTMLFormula

HTML code for the empty set symbol “∅”.

EMPTY_SET - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula

HTML code for the empty set symbol “∅”.

EmptyListElement - org.sbml.jsbml.SBMLException.Code

A given listOf___, if present, cannot be empty

EmptyListInKineticLaw - org.sbml.jsbml.SBMLException.Code

The list of parameters component, if present, cannot be empty

EmptyListInReaction - org.sbml.jsbml.SBMLException.Code

Reaction components, if present, cannot be empty

EmptyListOfUnits - org.sbml.jsbml.SBMLException.Code

Empty list of units not permitted

enable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParser

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParser

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Enable tracing.

enable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Enable tracing.

enableCheckCategories(SBMLValidator.CHECK_CATEGORY[], boolean) - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Calls ValidationContext.enableCheckCategory(CHECK_CATEGORY, boolean) for every SBMLValidator.CHECK_CATEGORY in the array.

enableCheckCategory(SBMLValidator.CHECK_CATEGORY, boolean) - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Enables or disables the selected category.

enablePackage(String) - Method in class org.sbml.jsbml.AbstractSBase

Enables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String) - Method in class org.sbml.jsbml.ASTNode

Enables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String) - Method in interface org.sbml.jsbml.SBase

Enables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String) - Method in class org.sbml.jsbml.SBMLDocument

Enables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String, boolean) - Method in class org.sbml.jsbml.AbstractSBase

Enables or disables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String, boolean) - Method in class org.sbml.jsbml.ASTNode

Enables or disables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String, boolean) - Method in interface org.sbml.jsbml.SBase

Enables or disables the given SBML Level 3 package on this SBMLDocument.

enablePackage(String, boolean) - Method in class org.sbml.jsbml.SBMLDocument

Enables or disables the given SBML Level 3 package on this SBMLDocument.

enableRotationMapping - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

This previously (before 2020/03) held the outdated value "enable-rotation-mapping"

encodeArrayDoubleToString(Double[]) - Static method in class org.sbml.jsbml.ext.render.XMLTools

encodeArrayShortToString(Short[]) - Static method in class org.sbml.jsbml.ext.render.XMLTools

encodeColorToString(Color) - Static method in class org.sbml.jsbml.ext.render.XMLTools

encodeForHTML(String) - Static method in class org.sbml.jsbml.util.StringTools

encoding - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

encoding - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

end - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

END - org.sbml.jsbml.ext.render.HTextAnchor

endColumn - Variable in class org.sbml.jsbml.math.parser.Token

The column number of the last character of this Token.

endColumn - Variable in class org.sbml.jsbml.text.parser.Token

The column number of the last character of this Token.

endHead - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

endLine - Variable in class org.sbml.jsbml.math.parser.Token

The line number of the last character of this Token.

endLine - Variable in class org.sbml.jsbml.text.parser.Token

The line number of the last character of this Token.

EOF - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

End of File.

EOF - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

End of File.

EOF - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

End of File.

EOF - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

End of File.

EOF - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

End of File.

EOF - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

End of File.

EOF - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

End of File.

EOF - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

End of File.

EOF - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

End of File.

EOL - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

EOL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

RegularExpression Id.

eq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Creates a new ASTNode of type RELATIONAL_EQ.

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

eq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Equal.

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

eq(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates a new ASTRelationalOperatorNode of type RELATIONAL_EQ.

eq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Equal.

eq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

eq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

eq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

eq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

eq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

eqBegin - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler

Surrounded by new line symbols.

eqBegin - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler

Surrounded by new line symbols.

eqEnd - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler

End equation; cf. eqBegin.

eqEnd - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler

End equation; cf. eqBegin.

EQUAL - org.sbml.jsbml.ext.fbc.FluxBound.Operation

Deprecated.

equal

equals(Object) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit

equals(Object) - Method in class org.sbml.jsbml.AbstractSBase

equals(Object) - Method in class org.sbml.jsbml.AbstractTreeNode

equals(Object) - Method in class org.sbml.jsbml.Annotation

equals(Object) - Method in class org.sbml.jsbml.ASTNode

equals(Object) - Method in class org.sbml.jsbml.Compartment

equals(Object) - Method in class org.sbml.jsbml.Creator

equals(Object) - Method in class org.sbml.jsbml.CVTerm

equals(Object) - Method in class org.sbml.jsbml.Event

equals(Object) - Method in class org.sbml.jsbml.EventAssignment

equals(Object) - Method in class org.sbml.jsbml.ExplicitRule

equals(Object) - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.arrays.Dimension

equals(Object) - Method in class org.sbml.jsbml.ext.arrays.Index

equals(Object) - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

equals(Object) - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

equals(Object) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

equals(Object) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

equals(Object) - Method in class org.sbml.jsbml.ext.comp.Submodel

equals(Object) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

equals(Object) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynElement

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

equals(Object) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

equals(Object) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective

equals(Object) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct

equals(Object) - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef

equals(Object) - Method in class org.sbml.jsbml.ext.fbc.Objective

equals(Object) - Method in class org.sbml.jsbml.ext.groups.Group

equals(Object) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

Deprecated.

equals(Object) - Method in class org.sbml.jsbml.ext.groups.Member

equals(Object) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Deprecated.

equals(Object) - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

equals(Object) - Method in class org.sbml.jsbml.ext.layout.BoundingBox

equals(Object) - Method in class org.sbml.jsbml.ext.layout.CubicBezier

equals(Object) - Method in class org.sbml.jsbml.ext.layout.Curve

equals(Object) - Method in class org.sbml.jsbml.ext.layout.CurveSegment

equals(Object) - Method in class org.sbml.jsbml.ext.layout.Dimensions

equals(Object) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

equals(Object) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject

equals(Object) - Method in class org.sbml.jsbml.ext.layout.Layout

equals(Object) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.layout.LineSegment

equals(Object) - Method in class org.sbml.jsbml.ext.layout.Point

equals(Object) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

equals(Object) - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph

equals(Object) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

equals(Object) - Method in class org.sbml.jsbml.ext.layout.TextGlyph

equals(Object) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

equals(Object) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

equals(Object) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

equals(Object) - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

equals(Object) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

equals(Object) - Method in class org.sbml.jsbml.ext.qual.Input

equals(Object) - Method in class org.sbml.jsbml.ext.qual.Output

equals(Object) - Method in class org.sbml.jsbml.ext.qual.QualConstants

equals(Object) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

equals(Object) - Method in class org.sbml.jsbml.ext.qual.Transition

equals(Object) - Method in class org.sbml.jsbml.ext.render.ColorDefinition

equals(Object) - Method in class org.sbml.jsbml.ext.render.Ellipse

equals(Object) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.GradientBase

equals(Object) - Method in class org.sbml.jsbml.ext.render.GradientStop

equals(Object) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

equals(Object) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

equals(Object) - Method in class org.sbml.jsbml.ext.render.Image

equals(Object) - Method in class org.sbml.jsbml.ext.render.LinearGradient

equals(Object) - Method in class org.sbml.jsbml.ext.render.LineEnding

equals(Object) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.LocalStyle

equals(Object) - Method in class org.sbml.jsbml.ext.render.Polygon

equals(Object) - Method in class org.sbml.jsbml.ext.render.RadialGradient

equals(Object) - Method in class org.sbml.jsbml.ext.render.Rectangle

equals(Object) - Method in class org.sbml.jsbml.ext.render.RelAbsVector

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderCurve

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderGroup

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderPoint

equals(Object) - Method in class org.sbml.jsbml.ext.render.Style

equals(Object) - Method in class org.sbml.jsbml.ext.render.Text

equals(Object) - Method in class org.sbml.jsbml.ext.render.Transformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.Transformation2D

equals(Object) - Method in interface org.sbml.jsbml.ext.SBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.Boundary

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference

Deprecated.

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGNode

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGScale

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.Domain

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.DomainType

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.Geometry

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.PolygonObject

Deprecated.

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SampledField

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference

equals(Object) - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

equals(Object) - Method in class org.sbml.jsbml.History

equals(Object) - Method in class org.sbml.jsbml.InitialAssignment

equals(Object) - Method in class org.sbml.jsbml.KineticLaw

equals(Object) - Method in class org.sbml.jsbml.ListOf

equals(Object) - Method in class org.sbml.jsbml.LocalParameter

equals(Object) - Method in class org.sbml.jsbml.math.AbstractASTNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCiNumberNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCnNumberNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCnRealNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

equals(Object) - Method in class org.sbml.jsbml.math.ASTFunction

equals(Object) - Method in class org.sbml.jsbml.Model

equals(Object) - Method in class org.sbml.jsbml.ontology.Term

equals(Object) - Method in class org.sbml.jsbml.ontology.Triple

equals(Object) - Method in class org.sbml.jsbml.QuantityWithUnit

equals(Object) - Method in class org.sbml.jsbml.Reaction

equals(Object) - Method in interface org.sbml.jsbml.SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

equals(Object) - Method in class org.sbml.jsbml.SBMLDocument

equals(Object) - Method in class org.sbml.jsbml.SBMLReader

equals(Object) - Method in class org.sbml.jsbml.SBMLWriter

equals(Object) - Method in class org.sbml.jsbml.SimpleSpeciesReference

equals(Object) - Method in class org.sbml.jsbml.Species

equals(Object) - Method in class org.sbml.jsbml.SpeciesReference

equals(Object) - Method in class org.sbml.jsbml.Symbol

equals(Object) - Method in class org.sbml.jsbml.Trigger

equals(Object) - Method in class org.sbml.jsbml.Unit

equals(Object) - Method in class org.sbml.jsbml.util.Pair

equals(Object) - Method in class org.sbml.jsbml.util.TreeNodeAdapter

equals(Object) - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent

equals(Object) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode

equals(Object) - Method in class org.sbml.jsbml.validator.offline.constraints.ValidationConstraint

Returns true if the two ValidationConstraint objects have the same error code.

equals(Object) - Method in class org.sbml.jsbml.xml.XMLAttributes

Equality comparison method for XMLAttributes.

equals(Object) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Equality comparison method for XMLNamespaces.

equals(Object) - Method in class org.sbml.jsbml.xml.XMLToken

equals(Object) - Method in class org.sbml.jsbml.xml.XMLTriple

Equality comparison method for XMLTriple.

error(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger

ERROR - org.sbml.jsbml.SBMLError.SEVERITY

ERROR - org.sbml.jsbml.SBMLException.Type

euclideanDistance(Point, Point) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

Calculates the Eucledian distance between two points a and b.

evaluateBounds(Map<String, Double>, ASTNode, double) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if the math does not evaluate to a negative number or to a value greater or equal to a given size value.

evaluateIndexBounds(Model, Index) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if the index math does not go out of bounds.

evaluateIndexBounds(Model, SBase, int, ASTNode, Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.

evaluateIndexBounds(Model, SBase, String, ASTNode, int) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.

evaluateSelectorBounds(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if the arguments of a selector function does not go out of bounds.

EVENODD - org.sbml.jsbml.ext.render.GraphicalPrimitive2D.FillRule

Event - Class in org.sbml.jsbml

Represents the event XML element of a SBML file.

Event() - Constructor for class org.sbml.jsbml.Event

Creates an Event instance.

Event(int, int) - Constructor for class org.sbml.jsbml.Event

Creates an Event from a level and version.

Event(String) - Constructor for class org.sbml.jsbml.Event

Event(String, int, int) - Constructor for class org.sbml.jsbml.Event

Creates an Event instance from an id, level and version.

Event(String, String, int, int) - Constructor for class org.sbml.jsbml.Event

Creates an Event instance from an id, name, level and version.

Event(Event) - Constructor for class org.sbml.jsbml.Event

Creates an Event instance from a given event.

EVENT_ELEMENTS_ORDER - Static variable in class org.sbml.jsbml.validator.offline.constraints.EventConstraints

EventAndAssignmentRuleForId - org.sbml.jsbml.SBMLException.Code

variable value used in both event assignments and assignment rules

EventAssignCompartmentMismatch - org.sbml.jsbml.SBMLException.Code

Mismatched units in event assignment for compartment

EventAssignment - Class in org.sbml.jsbml

Represents the eventAssignment XML element of a SBML file.

EventAssignment() - Constructor for class org.sbml.jsbml.EventAssignment

Creates an EventAssignment instance.

EventAssignment(int, int) - Constructor for class org.sbml.jsbml.EventAssignment

Creates an EventAssignment instance from a level and version.

EventAssignment(EventAssignment) - Constructor for class org.sbml.jsbml.EventAssignment

Creates an EventAssignment instance from a given EventAssignment.

EventAssignmentConstraints - Class in org.sbml.jsbml.validator.offline.constraints

EventAssignmentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints

EventAssignmentForConstantEntity - org.sbml.jsbml.SBMLException.Code

Cannot assign to a constant component in an event assignment

EventAssignParameterMismatch - org.sbml.jsbml.SBMLException.Code

Mismatched units in event assignment for parameter

EventAssignSpeciesMismatch - org.sbml.jsbml.SBMLException.Code

Mismatched units in event assignment for species

EventConstraints - Class in org.sbml.jsbml.validator.offline.constraints

EventConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.EventConstraints

EventNotValidComponent - org.sbml.jsbml.SBMLException.Code

Events not supported in this Level+Version of SBML

exp(ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Returns a new ASTNode that represents Euler's constant raised by the power of the given exponent.

exp(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

exp(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

exp(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

exp(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

exp(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Returns a new ASTPowerNode that represents Euler's constant raised by the power of the given exponent.

exp(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

exp(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

exp(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

exp(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

exp(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

expandFunctionDefinition(MathContainer) - Static method in class org.sbml.jsbml.util.converters.ExpandFunctionDefinitionConverter

Expands the FunctionDefinition used in the given MathContainer.

expandFunctionDefinition(Model, ASTNode) - Static method in class org.sbml.jsbml.util.converters.ExpandFunctionDefinitionConverter

Expands the FunctionDefinition used in the given ASTNode.

ExpandFunctionDefinitionConverter - Class in org.sbml.jsbml.util.converters

Expands user-defined FunctionDefinition in an SBML document.

ExpandFunctionDefinitionConverter() - Constructor for class org.sbml.jsbml.util.converters.ExpandFunctionDefinitionConverter

expectedTokenSequences - Variable in exception org.sbml.jsbml.math.parser.ParseException

Each entry in this array is an array of integers.

expectedTokenSequences - Variable in exception org.sbml.jsbml.text.parser.ParseException

Each entry in this array is an array of integers.

ExplicitRule - Class in org.sbml.jsbml

An explicit Rule is a rule that explicitly declares its variable element.

ExplicitRule() - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule.

ExplicitRule(int, int) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule

ExplicitRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule

ExplicitRule(ASTNode, Variable) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule with the given ASTNode element for the assignment to the given Variable or the derivative of the Variable.

ExplicitRule(ExplicitRule) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule

ExplicitRule(Parameter) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule

ExplicitRule(Parameter, ASTNode) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule

ExplicitRule(Variable) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates an ExplicitRule instance from a given Variable.

ExplicitRule(Variable, ASTNode) - Constructor for class org.sbml.jsbml.ExplicitRule

Creates a new ExplicitRule

ExplicitRuleConstraints - Class in org.sbml.jsbml.validator.offline.constraints

ExplicitRuleConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints

EXPNUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

EXPNUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

RegularExpression Id.

exponent - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

ExtendedSBaseValidator - Class in org.sbml.jsbml.ext.arrays.validator

Validates a given SBase object in the context of a given model and makes sure that the SBase object is in accordance with the arrays package specification.

ExtendedSBaseValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.ExtendedSBaseValidator

extension - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

EXTENT - Static variable in class org.sbml.jsbml.UnitDefinition

Identifier of the (for SBML Level 3) UnitDefinition extent.

extentConversionFactor - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

extentUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

ExternalModelDefinition - Class in org.sbml.jsbml.ext.comp

The ExternalModelDefinition objects are model definitions - in and of themselves, they are definitions of the models but not uses of those models.

ExternalModelDefinition() - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Creates an ExternalModelDefinition instance

ExternalModelDefinition(String) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Creates a ExternalModelDefinition instance with an id.

ExternalModelDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Creates a ExternalModelDefinition instance with an id, level, and version.

ExternalModelDefinition(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Creates a ExternalModelDefinition instance with an id, name, level, and version.

ExternalModelDefinition(ExternalModelDefinition) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Clone constructor

ExternalModelDefinitionConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the ExternalModelDefinition class.

ExternalModelDefinitionConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ExternalModelDefinitionConstraints

externalParameter - org.sbml.jsbml.ext.distrib.UncertParameter.Type

This type is uniquely described by an appropriate definitionURL, and is provided to allow a modeler to encode externally-provided parameters not otherwise explicitly handled by this specification.

extractPackageVersion(String) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil

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