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

A

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

ABOVE - org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition

abs(double, MathContainer) - Static method in class org.sbml.jsbml.ASTNode

Creates and returns an ASTNode that computes the absolute value of the given double value.

abs(int, MathContainer) - Static method in class org.sbml.jsbml.ASTNode

Creates and returns an ASTNode that computes the absolute value of the given integer value.

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

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

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

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

The absolute value represented by the given ASTNode.

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

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

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

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

Deprecated.

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

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

The absolute value represented by the given ASTNode2.

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

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

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

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

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

RegularExpression Id.

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Refers to the absolute part of a RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

absoluteX1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Deprecated.

Made obsolete by the introduction of RelAbsVector

absoluteX2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

absoluteY1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Deprecated.

Made obsolete by the introduction of RelAbsVector

absoluteY2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Deprecated.

Made obsolete by the introduction of RelAbsVector

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

Deprecated.

Made obsolete by the introduction of RelAbsVector

absoluteZ1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Deprecated.

Made obsolete by the introduction of RelAbsVector

absoluteZ2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Deprecated.

Made obsolete by the introduction of RelAbsVector

AbstractASTNode - Class in org.sbml.jsbml.math

A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.

AbstractASTNode() - Constructor for class org.sbml.jsbml.math.AbstractASTNode

Creates an empty AbstractTreeNode without a pointer to its containing MathContainer.

AbstractASTNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.AbstractASTNode

Constructor for cloning AbstractTreeNode

AbstractASTNode(MathContainer) - Constructor for class org.sbml.jsbml.math.AbstractASTNode

Creates an empty AbstractTreeNode with a pointer to the specified MathContainer.

AbstractASTNodePlugin - Class in org.sbml.jsbml.ext

AbstractASTNodePlugin() - Constructor for class org.sbml.jsbml.ext.AbstractASTNodePlugin

AbstractASTNodePlugin(ASTNode) - Constructor for class org.sbml.jsbml.ext.AbstractASTNodePlugin

AbstractASTNodePlugin(ASTNodePlugin) - Constructor for class org.sbml.jsbml.ext.AbstractASTNodePlugin

This method will need to be further tested

AbstractConstraint<T> - Class in org.sbml.jsbml.validator.offline.constraints

Abstract generic mother class for all the constraints.

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

Abstract mother class for all constraints declarations.

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

AbstractDistribSBase - Class in org.sbml.jsbml.ext.distrib

AbstractDistribSBase() - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(String) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(AbstractDistribSBase) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractFBCSBasePlugin - Class in org.sbml.jsbml.ext.fbc

Represents the basic properties of all SBasePlugin in the FBC package.

AbstractFBCSBasePlugin() - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

AbstractFBCSBasePlugin(AbstractFBCSBasePlugin) - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

AbstractFBCSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

AbstractLayoutBuilder<P,NodeT,ArcT> - Class in org.sbml.jsbml.ext.render.director

This abstract class combines the interfaces LayoutBuilder and LayoutFactory.

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

AbstractMathContainer - Class in org.sbml.jsbml

Base class for all the SBML components which contain MathML nodes.

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

Creates a MathContainer instance.

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

Creates a MathContainer instance from a level and version.

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

Creates a new MathContainer instance.

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

Creates a MathContainer instance from a given MathContainer.

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

Creates a MathContainer instance from an ASTNode, level and version.

AbstractNamedSBase - Class in org.sbml.jsbml

Base abstract class for all the SBML components with an id and a name (optional or not) in SBML Level 3 Version 1 or lower.

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

Creates a new AbstractNamedSBase instance.

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

Creates an AbstractNamedSBase from a level and version.

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

Creates an AbstractNamedSBase with the given identifier.

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

Creates an AbstractNamedSBase from an id, level and version.

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

Creates an AbctractNamedSBase from an id, name, level and version.

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

Creates an AbstractNamedSBase from a given AbstractNamedSBase.

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

This abstract class is used by Deletion and Port classes.

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

Creates an AbstractNamedSBaseRef.

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

Creates an AbstractNamedSBaseRef from a level and version.

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

Creates an AbstractNamedSBaseRef with the given identifier.

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

Creates an AbstractNamedSBaseRef from an id, level and version.

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

Creates an AbstractNamedSBaseRef from an id, name, level and version.

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

Creates an AbstractNamedSBaseRef from a given AbstractNamedSBaseRef.

AbstractNamedSBaseWithUnit - Class in org.sbml.jsbml

This simple implementation of the interfaces NamedSBaseWithDerivedUnit and SBaseWithUnit defines elements that can be addressed by their identifier and are or can be associated with a defined Unit or UnitDefinition.

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

Initializes a new object of type AbstractNamedSBaseWithUnit whose identifier and name are set to null and whose level and version are set to -1 each.

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

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

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

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

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

AbstractReaderWriter - Class in org.sbml.jsbml.xml.parsers

Contains some code shared by most of the L3 packages parsers.

AbstractReaderWriter() - Constructor for class org.sbml.jsbml.xml.parsers.AbstractReaderWriter

AbstractReferenceGlyph - Class in org.sbml.jsbml.ext.layout

Abstract super class for all kinds of glyphs that graphically represent an instance of NamedSBase.

AbstractReferenceGlyph() - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Creates a new instance of AbstractReferenceGlyph.

AbstractReferenceGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Creates a new instance of AbstractReferenceGlyph.

AbstractReferenceGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Creates a new instance of AbstractReferenceGlyph.

AbstractReferenceGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Creates a new instance of AbstractReferenceGlyph.

AbstractReferenceGlyph(AbstractReferenceGlyph) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Creates a new instance of AbstractReferenceGlyph from the given glyph.

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

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

Creates a AbstractRenderPlugin instance.

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

Clone constructor

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

Creates an AbstractRenderPlugin instance

AbstractSBase - Class in org.sbml.jsbml

The base class for each SBase component.

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

Creates an AbstractSBase instance.

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

Creates an AbstractSBase instance with the given SBML Level and Version.

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

Creates an AbstractSBase with the given identifier.

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

Creates an AbstractSBase from an id, level and version.

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

Creates an AbstractSBase from an id, name, level and version.

AbstractSBase(SBase) - Constructor for class org.sbml.jsbml.AbstractSBase

Creates an AbstractSBase instance from a given AbstractSBase.

AbstractSBasePlugin - Class in org.sbml.jsbml.ext

AbstractSBasePlugin() - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin

AbstractSBasePlugin(SBasePlugin) - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin

This method will need to be further tested

AbstractSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin

AbstractSBGNnode<T> - Class in org.sbml.jsbml.ext.render.director

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

AbstractSBGNNodeWithCloneMarker<T> - Class in org.sbml.jsbml.ext.render.director

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

AbstractSBGNProcessNode<T> - Class in org.sbml.jsbml.ext.render.director

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

AbstractSpatialNamedSBase - Class in org.sbml.jsbml.ext.spatial

The base class for each spatial class.

AbstractSpatialNamedSBase() - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

Creates a new AbstractSpatialNamedSBase instance.

AbstractSpatialNamedSBase(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

Creates a new AbstractSpatialNamedSBase instance.

AbstractSpatialNamedSBase(String) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

Creates a new AbstractSpatialNamedSBase instance.

AbstractSpatialNamedSBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

Creates a new AbstractSpatialNamedSBase instance.

AbstractSpatialNamedSBase(SpatialNamedSBase) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

Creates a new AbstractSpatialNamedSBase instance.

AbstractSpatialSBasePlugin - Class in org.sbml.jsbml.ext.spatial

AbstractSpatialSBasePlugin() - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

AbstractSpatialSBasePlugin(AbstractSpatialSBasePlugin) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

AbstractSpatialSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

AbstractTreeNode - Class in org.sbml.jsbml

A basic implementation of the TreeNode interface.

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

Creates an empty AbstractTreeNode without child nodes and an empty list of TreeNodeChangeListeners.

AbstractTreeNode(TreeNode) - Constructor for class org.sbml.jsbml.AbstractTreeNode

Constructor for cloning.

AbstractValidationFunction<T> - Class in org.sbml.jsbml.validator.offline.constraints

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

accept(SBase) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

accept(SBase) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

accept(SBase) - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

accept(SBase) - Method in class org.sbml.jsbml.KineticLaw

accept(SBase) - Method in class org.sbml.jsbml.Model

accept(SBase) - Method in interface org.sbml.jsbml.util.IdManager

Returns true if this IdManager can register or unregister the given SBase.

accepts(Object) - Method in class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.AndFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.BoundaryConditionFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.CVTermFilter

accepts(Object) - Method in interface org.sbml.jsbml.util.filters.Filter

This method checks whether the given object is of the correct type and has the desired properties set to be acceptable.

accepts(Object) - Method in class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.IdFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.MetaIdFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.NameFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.OrFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.SBOFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.SIdFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter

accepts(Object) - Method in class org.sbml.jsbml.util.filters.XMLNodeFilter

ACTIVATOR - org.sbml.jsbml.ext.layout.SpeciesReferenceRole

activeObjective - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

add(int, T) - Method in class org.sbml.jsbml.ListOf

add(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Appends an XML namespace URI with an empty prefix to this list of namespace declarations.

add(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Adds an attribute (a name/value pair) to this XMLAttributes set optionally with a prefix and URI defining a namespace.

add(String, String) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Appends an XML namespace prefix and URI pair to this list of namespace declarations.

add(String, String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Adds an attribute (a name/value pair) to this XMLAttributes set optionally with a prefix and URI defining a namespace.

add(String, String, String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Adds an attribute (a name/value pair) to this XMLAttributes set optionally with a prefix and URI defining a namespace.

add(Layout) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

Adds the given Layout to the listOfLayouts.

add(SBMLError) - Method in class org.sbml.jsbml.SBMLErrorLog

Adds an error.

add(Option) - Method in class org.sbml.jsbml.SBMLErrorLog

Adds an option.

add(AnyConstraint<T>) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup

Adds a constraint to the group.

add(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Adds an attribute with the given XMLTriple/value pair to this XMLAttributes set.

add(T) - Method in class org.sbml.jsbml.ListOf

addAdditionalGraphicalObject(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.Layout

Adds an arbitrary additional GraphicalObject.

addAdjacentDomain(AdjacentDomains) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Adds a new AdjacentDomains to the Geometry.listOfAdjacentDomains.

addAll(int, Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf

addAll(Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf

addAllAssociations(List<Association>) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Sets the given ListOf<Association>.

addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.math.ASTUnknown

addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Adds recursively all given TreeNodeChangeListener instances to this element.

addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown

addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAnalyticVolume(AnalyticVolume) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

Adds a new AnalyticVolume to the listOfAnalyticVolumes.

addAssociation(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Adds a new Association to the LogicalOperator.listOfAssociations.

addAttr(String, String) - Method in class org.sbml.jsbml.xml.XMLToken

Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.

addAttr(String, String, String) - Method in class org.sbml.jsbml.xml.XMLToken

Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.

addAttr(String, String, String, String) - Method in class org.sbml.jsbml.xml.XMLToken

Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.

addAttr(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLToken

Adds an attribute with the given XMLTriple/value pair to the attribute set in this XMLToken.

addAttributes(Map<String, String>) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

Adds an attribute to this attributes HashMap.

addChangedMath(ChangedMath) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

Adds a new ChangedMath to the listOfChangedMaths.

addChild(ASTNode) - Method in class org.sbml.jsbml.ASTNode

Adds a child to this node.

addChild(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Identical to calling LogicalOperator.addAssociation(Association).

addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode

Adds a child to this node.

addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction

Adds a child to this node.

addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode

addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode

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

addChild(XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode

Adds a child to this XMLNode.

addChildElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Adds the given element to the end of the list of children elements.

addColorDefinition(ColorDefinition) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

addCompartment(Compartment) - Method in class org.sbml.jsbml.Model

Adds a Compartment instance to the listOfCompartments of this Model.

addCompartmentGlyph(CompartmentGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout

Adds a new CompartmentGlyph to the Layout.listOfCompartmentGlyphs.

addCompartmentReference(CompartmentReference) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Adds a new CompartmentReference to the MultiCompartmentPlugin.listOfCompartmentReferences.

addCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

addConstantId(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

Add an id to the list

addConstraint(Constraint) - Method in class org.sbml.jsbml.Model

Adds a Constraint instance to the listOfConstraints of this Model.

addCoordinateComponent(CoordinateComponent) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Adds a new CoordinateComponent to the listOfCoordinateComponents.

addCreator(Creator) - Method in class org.sbml.jsbml.History

Adds a Creator instance to this History.

addCSGNode(CSGNode) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Adds a new CSGNode to the listOfCSGNodes.

addCSGObject(CSGObject) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Adds a new CSGObject to the listOfCSGObjects.

addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.layout.Curve

addCurveSegment(int, CurveSegment) - Method in interface org.sbml.jsbml.ext.layout.ICurve

addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon

addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve

addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.layout.Curve

addCurveSegment(CurveSegment) - Method in interface org.sbml.jsbml.ext.layout.ICurve

addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon

Adds a new CurveSegment to the Polygon.listOfCurveSegments.

addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Adds a new CurveSegment to the RenderCurve.listOfCurveSegments.

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

addCVTerm(CVTerm) - Method in class org.sbml.jsbml.AbstractSBase

addCVTerm(CVTerm) - Method in class org.sbml.jsbml.Annotation

Adds a CVTerm.

addCVTerm(CVTerm) - Method in interface org.sbml.jsbml.SBase

Adds a CVTerm.

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

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

Adds an additional name space to the set of declared namespaces of this SBase.

addDeclaredNamespace(String, String) - Method in class org.sbml.jsbml.Annotation

Adds an additional namespace to the set of declared namespaces of this SBase.

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

Adds an additional name space to the set of declared namespaces of this SBase.

addDeletion(Deletion) - Method in class org.sbml.jsbml.ext.comp.Submodel

Adds a new Deletion to the listOfDeletions.

addDimension(Dimension) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Adds a new Dimension to the listOfDimensions.

addDomain(Domain) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Adds a new Domain to the listOfDomains.

addDomainType(DomainType) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Adds a new DomainType to the listOfDomainTypes.

addDynElement(DynElement) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Adds a new DynElement to the listOfDynElements.

addElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.Polygon

addElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.RenderCurve

addElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Adds a new Transformation2D to the listOfElements.

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdjacentDomainsConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdvectionCoefficientConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticGeometryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticVolumeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ArraysSBasePluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConditionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundingBoxConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ColorDefinitionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentMappingConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBasePluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBMLDocumentPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration

Adds all error codes which are needed for a check the attribute to the set.

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CoordinateComponentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGeometryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGHomogeneousTransformationConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGObjectConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGPrimitiveConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGRotationConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGScaleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGSetOperatorConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGTranslationConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CubicBezierConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CurveConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DefaultValuesConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DelayConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DeletionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DiffusionCoefficientConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionsConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EllipseConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExternalModelDefinitionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionDefinitionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneralGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryDefinitionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GlobalRenderInformationConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientBaseConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientStopConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalObjectConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive1DConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive2DConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ImageConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InteriorPointConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.KineticLawConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LinearGradientConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineEndingConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineSegmentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalRenderInformationConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalStyleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MixedGeometryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrdinalMappingConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricGeometryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricObjectConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PointConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PolygonConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PortConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RadialGradientConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RateRuleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RectangleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReferenceGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCubicBezierConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCurveConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGraphicalObjectPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGroupConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderInformationBaseConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderLayoutPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderListOfLayoutsPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderPointConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedByConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedElementConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RuleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldGeometryConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledVolumeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialCompartmentPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialParameterPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialPointsConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialReactionPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSpeciesPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSymbolReferenceConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.StyleConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SubmodelConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextGlyphConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.Transformation2DConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationComponentConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitDefinitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdjacentDomainsConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdvectionCoefficientConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticGeometryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticVolumeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ArraysSBasePluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConditionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundingBoxConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ColorDefinitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentMappingConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBasePluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBMLDocumentPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration

Adds all error codes which are needed for a check in this category to the set.

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CoordinateComponentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGeometryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGHomogeneousTransformationConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGObjectConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGPrimitiveConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGRotationConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGScaleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGSetOperatorConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGTranslationConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CubicBezierConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CurveConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DefaultValuesConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DelayConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DeletionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DiffusionCoefficientConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionsConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EllipseConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExternalModelDefinitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionDefinitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneralGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryDefinitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GlobalRenderInformationConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientBaseConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientStopConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalObjectConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive1DConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive2DConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ImageConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InteriorPointConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.KineticLawConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LinearGradientConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineEndingConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineSegmentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalRenderInformationConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalStyleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MixedGeometryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrdinalMappingConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricGeometryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricObjectConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PointConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PolygonConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PortConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RadialGradientConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RateRuleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RectangleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReferenceGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCubicBezierConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCurveConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGraphicalObjectPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGroupConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderInformationBaseConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderLayoutPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderListOfLayoutsPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderPointConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedByConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedElementConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RuleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldGeometryConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledVolumeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialCompartmentPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialParameterPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialPointsConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialReactionPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSpeciesPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSymbolReferenceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.StyleConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SubmodelConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextGlyphConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.Transformation2DConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationComponentConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitDefinitionConstraints

addEvent(Event) - Method in class org.sbml.jsbml.Model

Adds an Event instance to the listOfEvents of this Model.

addEventAssignment(EventAssignment) - Method in class org.sbml.jsbml.Event

Adds a new EventAssignment to the listOfEventAssignments.

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

addExtension(String, ASTNodePlugin) - Method in class org.sbml.jsbml.ASTNode

Adds a ASTNodePlugin object to this ASTNode.

addExtension(String, SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase

addExtension(String, SBasePlugin) - Method in interface org.sbml.jsbml.SBase

Adds a SBasePlugin extension object to this SBase.

addExternalModelDefinition(ExternalModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Adds a new ExternalModelDefinition to the listOfExternalModelDefinitions.

addFilter(Filter) - Method in class org.sbml.jsbml.util.filters.AndFilter

addFluxBound(FluxBound) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

addFluxObjective(FluxObjective) - Method in class org.sbml.jsbml.ext.fbc.Objective

Adds a new FluxObjective to the listOfFluxObjectives.

addFunctionDefinition(FunctionDefinition) - Method in class org.sbml.jsbml.Model

Adds a FunctionDefinition instance to the listOfFunctionDefinitions of this Model.

addFunctionTerm(FunctionTerm) - Method in class org.sbml.jsbml.ext.qual.Transition

addGeneProduct(GeneProduct) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Adds a new GeneProduct to the FBCModelPlugin.listOfGeneProducts.

addGeneralGlyph(GeneralGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout

Adds a GeneralGlyph object.

addGeometryDefinition(GeometryDefinition) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Adds a new GeometryDefinition to the listOfGeometryDefinitions.

addGeometryDefinition(GeometryDefinition) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Adds a new GeometryDefinition to the listOfGeometryDefinitions.

addGlobalRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

addGradientBase(GradientBase) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

addGradientStop(GradientStop) - Method in class org.sbml.jsbml.ext.render.GradientBase

addGraphicalObject(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.Layout

Adds an arbitrary additional GraphicalObject.

addGroup(Group) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Adds a new element to the listOfGroups.

addIndex(Index) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Adds a new Index to the listOfIndices.

addInitialAssignment(InitialAssignment) - Method in class org.sbml.jsbml.Model

Adds an InitialAssignment instance to the listOfInitialAssignments of this Model.

addInput(Input) - Method in class org.sbml.jsbml.ext.qual.Transition

addInSpeciesTypeBond(InSpeciesTypeBond) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Adds a new InSpeciesTypeBond to the MultiSpeciesType.listOfInSpeciesTypeBonds.

addInteriorPoint(InteriorPoint) - Method in class org.sbml.jsbml.ext.spatial.Domain

Adds a new InteriorPoint to the listOfInteriorPoints.

addLayout(Layout) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

Adds the given Layout to the listOfLayouts.

addLayoutedEdge(SpeciesReferenceGlyph, ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add a layouted edge to the input of the algorithm.

addLayoutedGlyph(GraphicalObject) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add a fully layouted glyph (i.e. glyph with boundingbox, dimensions and position) to the input of the algorithm.

addLineEnding(LineEnding) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

addLocalParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw

Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.

addLocalRenderInformation(LocalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

addLocalStyle(LocalStyle) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

addMember(Member) - Method in class org.sbml.jsbml.ext.groups.Group

Adds a new Member to the Group.listOfMembers.

addModelDefinition(ModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Adds a new ModelDefinition to the listOfModelDefinitions.

addModifiedDate(Date) - Method in class org.sbml.jsbml.History

Adds a Date of modification to this History.

addModifier(ModifierSpeciesReference) - Method in class org.sbml.jsbml.Reaction

Adds a ModifierSpeciesReference instance to this Reaction.

addNamespace(String) - Method in class org.sbml.jsbml.xml.XMLToken

Appends an XML namespace URI to this XMLToken.

addNamespace(String, String) - Method in class org.sbml.jsbml.xml.XMLToken

Appends an XML namespace prefix and URI pair to this XMLToken.

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

Deprecated.

use SBase.addDeclaredNamespace(String, String)

addNestedCVTerm(CVTerm) - Method in class org.sbml.jsbml.CVTerm

Adds a new CVTerm to the CVTerm.listOfNestedCVTerms.

addObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Adds a new Objective to the listOfObjectives.

addOrdinalMapping(OrdinalMapping) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Adds a new OrdinalMapping to the listOfOrdinalMappings.

addOutput(Output) - Method in class org.sbml.jsbml.ext.qual.Transition

addOutwardBindingSite(OutwardBindingSite) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Adds a new OutwardBindingSite to the MultiSpeciesPlugin.listOfOutwardBindingSites.

addParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

use KineticLaw.addLocalParameter(LocalParameter).

addParameter(Parameter) - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

A KineticLaw can only contain instances of LocalParameters. Please use KineticLaw.addLocalParameter(LocalParameter) and create an instance of LocalParameter for your purposes.

addParameter(Parameter) - Method in class org.sbml.jsbml.Model

Adds a Parameter instance to the listOfParameters of this Model.

addParametricObject(ParametricObject) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Adds a new ParametricObject to the listOfParametricObjects.

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

addPlugin(String, ASTNodePlugin) - Method in class org.sbml.jsbml.ASTNode

Adds a ASTNodePlugin object to this ASTNode.

addPlugin(String, SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase

addPlugin(String, SBasePlugin) - Method in interface org.sbml.jsbml.SBase

Adds a SBasePlugin extension object to this SBase.

addPort(Port) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Adds a new Port to the listOfPorts.

addPossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Adds a new PossibleSpeciesFeatureValue to the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

addPredefinedUnitDefinitions(Model) - Static method in class org.sbml.jsbml.util.SBMLtools

addProduct(SpeciesReference) - Method in class org.sbml.jsbml.Reaction

Adds a SpeciesReference instance to the listOfProducts of this Reaction.

addQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Adds a QualitativeSpecies to the model.

addReactant(SpeciesReference) - Method in class org.sbml.jsbml.Reaction

Adds a SpeciesReference instance to the listOfReactants of this Reaction.

addReaction(Reaction) - Method in class org.sbml.jsbml.Model

Adds a Reaction instance to the listOfReactions of this Model.

addReactionGlyph(ReactionGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout

Adds a ReactionGlyph to this layout

addReferenceGlyph(ReferenceGlyph) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

Appends the specified element to the end of the GeneralGlyph.listOfReferenceGlyphs.

addReplacedElement(ReplacedElement) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Adds a new element to listOfReplacedElements.

addResource(int, String) - Method in class org.sbml.jsbml.CVTerm

Adds a resource to the CVTerm at the specified index.

addResource(String) - Method in class org.sbml.jsbml.CVTerm

Adds a resource to the CVTerm.

addResources(String...) - Method in class org.sbml.jsbml.CVTerm

Adds list of resources to the CVTerm.

addResources(CVTerm.Qualifier, String...) - Method in class org.sbml.jsbml.AbstractSBase

Adds all the given resources to the first CVTerm with the given CVTerm.Qualifier or, if no such term exists yet, creates one.

addResources(CVTerm.Qualifier, String...) - Method in class org.sbml.jsbml.Annotation

Adds all the given resources to the first CVTerm with the given CVTerm.Qualifier or, if no such term exists yet, creates one.

addResourceURI(String) - Method in class org.sbml.jsbml.CVTerm

Adds a resource to the CVTerm.

addRule(Rule) - Method in class org.sbml.jsbml.Model

Adds a Rule instance to the listOfRules of this Model.

addSampledField(SampledField) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Adds a new SampledField to the listOfSampledFields.

addSampledVolume(SampledVolume) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Adds a new SampledVolume to the listOfSampledVolumes.

addSemanticsAnnotation(XMLNode) - Method in class org.sbml.jsbml.ASTNode

Adds the given XMLNode as a MathML <semantics> element to this ASTNode.

addSpatialComponent(SpatialComponent) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Adds a new SpatialComponent to the ListOfSpatialComponents.

addSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Adds a QualitativeSpecies instance to the listOfSpecies of this Model.

addSpecies(Species) - Method in class org.sbml.jsbml.Model

Adds a Species instance to the listOfSpecies of this Model.

addSpeciesFeature(SpeciesFeature) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Adds a new SpeciesFeature to the MultiSpeciesPlugin.listOfSpeciesFeatures.

addSpeciesFeatureType(SpeciesFeatureType) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Adds a new SpeciesFeatureType to the MultiSpeciesType.listOfSpeciesFeatureTypes.

addSpeciesFeatureValue(SpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Adds a new SpeciesFeatureValue to the SpeciesFeature.listOfSpeciesFeatureValues.

addSpeciesGlyph(SpeciesGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout

addSpeciesReferenceGlyph(SpeciesReferenceGlyph) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

Appends the specified element to the end of the ReactionGlyph.listOfSpeciesReferenceGlyphs.

addSpeciesType(MultiSpeciesType) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Adds a MultiSpeciesType.

addSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Adds a new SpeciesTypeComponentIndex to the MultiSpeciesType.listOfSpeciesTypeComponentIndexes.

addSpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Adds a new SpeciesTypeComponentMapInProduct to the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

addSpeciesTypeInstance(SpeciesTypeInstance) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Adds a new SpeciesTypeInstance to the MultiSpeciesType.listOfSpeciesTypeInstances.

addStrokeDash(Short) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

addStyle(Style) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

Adds the given style to the list of styles

addSubGlyph(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

Adds a new GraphicalObject to the listOfSubGlyphs.

addSubListOfSpeciesFeature(SubListOfSpeciesFeature) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Adds a new SubListOfSpeciesFeature to the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures.

addSubmodel(Submodel) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Adds a new Submodel to the listOfSubmodels.

addTextGlyph(TextGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout

addTransition(Transition) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.AbstractTreeNode

addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.math.ASTUnknown

addTreeNodeChangeListener(TreeNodeChangeListener) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Adds recursively a listener to the TreeNodeWithChangeSupport object and all of its sub-elements.

addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode

addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown

addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Adds a listener to this TreeNodeWithChangeSupport object and optionally also to all of its child nodes.

addUncertainty(Uncertainty) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Adds a new Uncertainty to the DistribSBasePlugin.listOfUncertainties.

addUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Adds a new UncertParameter to the Uncertainty.listOfUncertParameters.

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

Adds a new UncertParameter to the UncertParameter.listOfUncertParameters.

addUnit(String) - Method in class org.sbml.jsbml.UnitDefinition

Adds a new Unit instance, created from the given unit Unit.Kind, to this UnitDefinition.

addUnit(Unit) - Method in class org.sbml.jsbml.UnitDefinition

Adds a Unit to this UnitDefinition.

addUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition

Adds a new Unit instance, with the given kind, to this UnitDefinition.

addUnitDefinition(UnitDefinition) - Method in class org.sbml.jsbml.Model

Adds an UnitDefinition instance to the Model.listOfUnitDefinitions of this Model.

addUnitDefinitionIfNotContained(Model, UnitDefinition) - Static method in class org.sbml.jsbml.JSBML

Adds the given UnitDefinition to the given model or returns the identifier of an equivalent UnitDefinition that is already part of the model.

addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition) - Method in class org.sbml.jsbml.Model

Checks whether an identical UnitDefinition like the given UnitDefinition is already in this Model's Model.listOfUnitDefinitions.

addUnlayoutedEdge(SpeciesReferenceGlyph, ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add an unlayouted edge to the input of the algorithm.

addUnlayoutedGlyph(GraphicalObject) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add a glyph with missing layout information (i.e. no dimensions or no position specified) to the input of the algorithm.

addValidationListener(ValidationListener) - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Adds a ValidationListener to this context.

addValue(String, double) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Adds a new string,double pair to the idToValue.

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

AdjacentDomains - Class in org.sbml.jsbml.ext.spatial

AdjacentDomains() - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains

Creates a AdjacentDomains instance.

AdjacentDomains(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains

Creates a AdjacentDomains instance with a level and version.

AdjacentDomains(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains

AdjacentDomains(AdjacentDomains) - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains

Clone constructor

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

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

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

adjustBeginLineColumn(int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

adjustBeginLineColumn(int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

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

AdvectionCoefficient - Class in org.sbml.jsbml.ext.spatial

AdvectionCoefficient() - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

AdvectionCoefficient(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

AdvectionCoefficient(AdvectionCoefficient) - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

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

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

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

AlgebraicRule - Class in org.sbml.jsbml

Represents the algebraicRule XML element of a SBML file.

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

Creates an AlgebraicRule instance.

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

Creates an AlgebraicRule instance from level and version.

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

Creates an AlgebraicRule instance from a given AlgebraicRule instance.

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

Creates an AlgebraicRule instance from math, level and version.

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

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

all_L3_namespaces - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

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

String that can be added to an SBase user objects, if it is associated with the value true, then the getters and setters will allow to set some invalid values instead of throwing exceptions.

allowedCnType - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

allowedCsymbolURI - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

allowedCsymbolURIL2 - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

allowedCsymbolURIL3V1 - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

alpha - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to elemental rotation of an object about the X coordinate axis

AMPERE - org.sbml.jsbml.Unit.Kind

The ampere unit.

analyseSBMLerrorLog(List<SBMLError>) - Static method in class org.sbml.jsbml.validator.offline.LoggingValidationContext

Goes through the list of SBMLError given to determined which check categories should be ignored.

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

AnalyticGeometry - Class in org.sbml.jsbml.ext.spatial

AnalyticGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry

AnalyticGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry

AnalyticGeometry(AnalyticGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry

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

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

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

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

AnalyticVolume - Class in org.sbml.jsbml.ext.spatial

AnalyticVolume() - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume

Creates a new AnalyticVolume instance.

AnalyticVolume(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume

Creates a new AnalyticVolume instance.

AnalyticVolume(AnalyticVolume) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume

Creates a new AnalyticVolume instance.

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

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

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

and - org.sbml.jsbml.ext.multi.Relation

and - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

Introduced to FBC in version 2.

and(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

and(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

and(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

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

Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_AND and adds the given nodes as children.

And - Class in org.sbml.jsbml.ext.fbc

This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.

And() - Constructor for class org.sbml.jsbml.ext.fbc.And

Creates a new And instance.

And(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.And

Creates a new And instance.

And(And) - Constructor for class org.sbml.jsbml.ext.fbc.And

Creates a new And instance.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

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

AndFilter - Class in org.sbml.jsbml.util.filters

A Filter that accepts an item only if all of its internal filters also accept the given item.

AndFilter() - Constructor for class org.sbml.jsbml.util.filters.AndFilter

AndFilter(Filter...) - Constructor for class org.sbml.jsbml.util.filters.AndFilter

anisotropic - org.sbml.jsbml.ext.spatial.DiffusionKind

Anisotropic

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

Annotation - Class in org.sbml.jsbml

An Annotation represents the annotations of an SBase element.

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

Creates an Annotation instance.

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

Creates an Annotation instance from a String containing non RDF annotation.

Annotation(String, List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation

Creates an Annotation instance from a String containing non RDF annotation and a list of CVTerm.

Annotation(List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation

Creates an Annotation instance from a list of CVTerm objects.

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

Creates a new Annotation instance by cloning the given Annotation.

Annotation(XMLNode) - Constructor for class org.sbml.jsbml.Annotation

AnnotationElement - Class in org.sbml.jsbml

A common super class for all those elements that can be part of an Annotation.

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

Creates a new empty AnnotationElement without any children, an empty list of TreeNodeChangeListeners, and a parent that is null.

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

Clone constructor.

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

AnnotationNotesNotAllowedLevel1 - org.sbml.jsbml.SBMLException.Code

Annotation on <sbml> not permitted in SBML Level 1

AnnotationReader - Interface in org.sbml.jsbml.xml.parsers

The interface to implement for the SBML parsers reading SBML annotations.

AnnotationWriter - Interface in org.sbml.jsbml.xml.parsers

The interface to implement for the SBML parsers writing SBML annotations.

ANY - org.sbml.jsbml.ext.render.Style.Type

AnyConstraint<T> - Interface in org.sbml.jsbml.validator.offline.constraints

Basic interface which must be implemented by every kind of constraint.

append(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Appends the variable data to pointIndex.

append(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Appends the variable data to samples.

append(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Appends the variable data to arrayData.

append(String) - Method in class org.sbml.jsbml.xml.XMLToken

Appends characters to this XML text content.

append(StringBuffer, Object...) - Static method in class org.sbml.jsbml.util.StringTools

Takes the given StringBuffer as input and appends every further Object to it.

append(StringBuilder, Object...) - Static method in class org.sbml.jsbml.util.StringTools

append(T) - Method in class org.sbml.jsbml.ListOf

Adds item to the end of this ListOf.

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

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

Appends the given annotation to the 'annotation' subelement of this object.

appendAnnotation(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase

appendAnnotation(XMLNode) - Method in interface org.sbml.jsbml.SBase

Appends the given annotation to the 'annotation' subelement of this object.

appendCobraNotes(SBase, Properties) - Static method in class org.sbml.jsbml.util.CobraUtil

appendNonRDFAnnotation(String) - Method in class org.sbml.jsbml.Annotation

Appends some 'annotation' to the non RDF annotation XMLNode of this object.

appendNonRDFAnnotation(XMLNode) - Method in class org.sbml.jsbml.Annotation

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

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

Appends 'notes' to the notes String of this object.

appendNotes(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase

Appends notes to the existing notes.

appendNotes(XMLNode) - Method in interface org.sbml.jsbml.SBase

Appends 'notes' to the notes of this object.

ApplyCiMustBeModelComponent - org.sbml.jsbml.SBMLException.Code

<ci>'s value is not a component in this model

ApplyCiMustBeUserFunction - org.sbml.jsbml.SBMLException.Code

<ci> does not refer to a function definition

applyToAll - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arccosh(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arccosh of n

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arccot(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arcus-cotangens of a double value.

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arccoth(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arccoth of n

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arccsc(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arccosecant of a double value

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arccsch(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arccsch of n

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arcsec(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arcsecant of a double value

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arcsech(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arcsech of n

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arcsinh(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arcsinh of n

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

arctanh(double) - Static method in class org.sbml.jsbml.util.Maths

Computes the arctanh of n

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

area(int, int) - Static method in class org.sbml.jsbml.UnitDefinition

Returns the predefined unit for area.

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

Identifier of the (for SBML Level 2) predefined UnitDefinition area.

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

areCompatible(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition

Returns true or false depending on whether two UnitDefinition objects are compatible.

areEquivalent(Unit.Kind, Unit.Kind) - Static method in enum org.sbml.jsbml.Unit.Kind

Tests whether the both given unit kinds are equivalent, i.e., it also considers METRE and METER and LITRE and LITER.

areEquivalent(UnitDefinition, String) - Static method in class org.sbml.jsbml.UnitDefinition

Checks whether the given UnitDefinition and the UnitDefinition or Unit represented by the given String are equivalent.

areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition

Returns true or false depending on whether two UnitDefinition objects are equivalent.

areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns true or false depending on whether two UnitDefinition objects are equivalent.

areEquivalent(Unit, String) - Static method in class org.sbml.jsbml.Unit

Checks whether the given Unit and the Unit represented by the given String are equivalent.

areEquivalent(Unit, Unit) - Static method in class org.sbml.jsbml.Unit

Predicate returning true or false depending on whether Unit objects are equivalent.

areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition

Returns true or false depending on whether two UnitDefinition objects are identical.

areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns true or false depending on whether two UnitDefinition objects are identical.

areIdentical(Unit, Unit) - Static method in class org.sbml.jsbml.Unit

Predicate returning true or false depending on whether two Unit objects are identical.

ArgsToEqNeedSameType - org.sbml.jsbml.SBMLException.Code

Arguments to <eq> or <neq> have inconsistent data types

arithmeticOperation(ASTNode.Type, ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates a new ASTArithmeticOperatorNode of type operator and adds the given nodes as children.

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

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

arrayDimension - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

ARRAYS_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010101: To conform to the arrays Package specification for SBML Level 3 Version 1, an SBML document must declare 'http://www.sbml.org/sbml/level3/version1/arrays/version1' as the XMLNamespace to use for elements of this package.

ARRAYS_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010102: Wherever they appear in an SBML document, elements and attributes from the arrays Package must use the 'http://www.sbml.org/sbml/level3/version1/arrays/version1' namespace, declaring so either explicitly or implicitly.

ARRAYS_10201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010201: In all SBML documents using the arrays Package, the <sbml> object must have the 'arrays:required' attribute.

ARRAYS_10202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010202: The value of attribute 'arrays:required' on the <sbml> object must be of data type 'boolean'.

ARRAYS_10203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010203: The value of attribute 'arrays:required' on the <sbml> object must be set to 'true'.

ARRAYS_10204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010204: Wherever MathML content appears in an SBML document, the MathML content must be placed within a math element, and that math element must be either explicitly or implicitly declared to be in the XML namespace http://www.w3.org/1998/Math/MathML Reference: L3V1 Arrays V1 Section 3.4

ARRAYS_10205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010205: The following is a list of the additional MathML 2.0 elements permitted in the Arrays package: vector and selector.

ARRAYS_10206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010206: The first argument of aMathML selector must be aMathML vector object or a valid identifier to an SBase object extended with a list of Dimension objects.

ARRAYS_10207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010207: The first argument of a MathML selector must have a number of dimensions equal to the number of arguments to the selector minus 1.

ARRAYS_10208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010208: The arguments of a MathML selector other than the first argument must be statically computable.

ARRAYS_10209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010209: The arguments of a MathML selector other than the first argument must be evaluated to a scalar value.

ARRAYS_10210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010210: For each possible value of each Dimension id (i.e., 0 to size-1 of the Dimension referred to) that appears in the second and later arguments of the selector, there should be no array out - of - bounds problems.Namely, it must evaluate to a non - negative integer that is less than the size of the corresponding Dimension for the object being indexed where the last argument refers to dimension 0, next to last to dimension 1 Reference: L3V1 Arrays V1 Section 3.5

ARRAYS_10211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010211: All mathematical operations must be performed on scalar values rather than vectors.

ARRAYS_10212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010212: For MathML operations with two or more operands involving MathML vectors or SBase objects with a list of Dimension objects, the number of dimensions and their sizemust agree for all operands unless the operand is a scalar type(i.e., it does not have a list of Dimension objects).

ARRAYS_10213 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010213: No SBase is allowed to have value of type vector.

ARRAYS_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010301: (Extends validation rule #10301 in the SBML Level 3 Core specification.

ARRAYS_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8010302: The value of a 'arrays:id' must conform to the syntax of the <sbml> data type 'SId' Reference: L3V1 Arrays V1 Section

ARRAYS_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020101: Any object derived from the extended SBase class (defined in the Arrays package) may contain at most one instance of a ListOfDimensions.

ARRAYS_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020102: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfDimensions> container object may only contain <dimension> objects.

ARRAYS_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020103: The ListOfDimensions associated with an SBase object must have a Dimension object with arrays:arrayDimension attribute set to 0 ... n-1 before adding a Dimension object with arrays : arrayDimension attribute set to n.

ARRAYS_20104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020104: The ListOfDimensions associated with an SBase object must not have multiple Dimension objects with the same arrays:arrayDimension attribute.

ARRAYS_20105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020105: A <listOfDimensions> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

ARRAYS_20106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020106: ListOf objects are not permitted to have a ListOfDimensions.

ARRAYS_20107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020107: InSBML Level 3 Core, Models, FunctionDefinitions, Units, UnitDefinitions, KineticLaws, LocalParameters, Triggers, Priorities, and Delays are not permitted to have a ListOfDimensions.

ARRAYS_20108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020108: The Dimension and Index objects are not permitted to have a ListOfDimensions.

ARRAYS_20109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020109: Any object derived from the extended SBase class (defined in the Arrays package) may contain at most one instance of a ListOfIndices.

ARRAYS_20110 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020110: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfIndices> container object may only contain <index> objects.

ARRAYS_20111 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020111: The ListOfIndices associated with an SBase object must have a Index object with arrays:arrayDimension attribute set to 0, 1, .

ARRAYS_20112 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020112: The ListOfIndices in an SBase object must not have multiple Index objects with the same pair of values arrays:arrayDimension and arrays:referencedAttribute attributes.

ARRAYS_20113 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020113: A <listOfIndices> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

ARRAYS_20114 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020114: Only SBML objects that include defined attributes of type SIdRef are permitted to have a ListOfIndices.

ARRAYS_20115 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020115: SBase objects containg SIdRef must have a ListOfIndices if the referenced SBase is an array.

ARRAYS_20116 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020116: SBase objects containg SIdRef with a ListOfDimensions should have a ListOfIndices containing as many Index objects for this particular arrays:referencedAttribute as the number of Dimension objects the referenced object contains.

ARRAYS_20117 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020117: Reference: L3V1 Arrays V1

ARRAYS_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020201: A <dimension> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

ARRAYS_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020202: A <dimension> object must have the required attributes 'arrays:size' and 'arrays:arrayDimension', and may have the optional attributes 'arrays:id' and 'arrays:name'.

ARRAYS_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020203: The attribute 'arrays:arrayDimension' on a <dimension> must have a value of data type 'integer'.

ARRAYS_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020204: The value of the attribute 'arrays:size' of a <dimension> object must be the identifier of an existing <sBase> object defined in the enclosing <model> object.

ARRAYS_20205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020205: The value of the Parameter referenced by the arrays:size attribute must be a non-negative scalar constant integer.

ARRAYS_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020301: An <index> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

ARRAYS_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020302: An <index> object must have the required attributes 'arrays:referencedAttribute' and 'arrays:arrayDimension'.

ARRAYS_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020303: The attribute 'arrays:referencedAttribute' on an <index> must have a value of data type 'string'.

ARRAYS_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020304: The attribute 'arrays:arrayDimension' on an <index> must have a value of data type 'integer'.

ARRAYS_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020305: The object referenced by the SIdRef indicated by the arrays:referencedAttribute attribute must include an arrays:arrayDimension matching the arrays:arrayDimension for the Index Reference: L3V1 Arrays V1 Section 3.4

ARRAYS_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020306: An <index> object must contain one and only one instance of the ASTNode element.

ARRAYS_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020307: The MathML math element in an Index object must be statically computable.

ARRAYS_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020308: For each possible value of each Dimension id (i.e., 0 to size-1 of the Dimension referred to) that appears in theMathML math element, there should be no array out of bounds problems.

ARRAYS_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020309: An <index> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

ARRAYS_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020402: A <dimension> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

ARRAYS_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 8020403: The attribute 'arrays:name' on a <dimension> must have a value of data type 'string'.

ArraysCompiler - Class in org.sbml.jsbml.ext.arrays.compiler

This compiler is used to evaluate an ASTNode object to a real number.

ArraysCompiler() - Constructor for class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Constructs an ArraysCompiler object.

ArraysCompiler(ArraysCompiler) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Clone constructor

ArraysConstants - Class in org.sbml.jsbml.ext.arrays

This is where the constants that are frequently used in the arrays package are defined.

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

ArraysConstraint - Class in org.sbml.jsbml.ext.arrays.validator.constraints

An ArraysConstraint object ensures that a given Model doesn't violate a certain validation rule defined in the arrays specification.

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

Constructs an ArraysConstraint.

ArraysConstraint(Model) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Constructs an ArraysConstraint with a model.

ArraysFlattening - Class in org.sbml.jsbml.ext.arrays.flattening

ArraysFlattening() - Constructor for class org.sbml.jsbml.ext.arrays.flattening.ArraysFlattening

ArraysMath - Class in org.sbml.jsbml.ext.arrays.util

ArraysMath() - Constructor for class org.sbml.jsbml.ext.arrays.util.ArraysMath

ArraysMathCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

ArraysMathCheck(Model, MathContainer) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysMathCheck

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

This checks a given MathContainer object math is in accordance with the arrays package specification.

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

ArraysParser - Class in org.sbml.jsbml.xml.parsers

ArraysParser() - Constructor for class org.sbml.jsbml.xml.parsers.ArraysParser

ArraysSBasePlugin - Class in org.sbml.jsbml.ext.arrays

The ArraysSBasePlugin class extends the SBase class by adding an optional ListOfDimensions child and a single optional Index child.

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

Creates an new ArraysSBasePlugin instance.

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

Clone constructor

ArraysSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Creates an new ArraysSBasePlugin instance.

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

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

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

Contains some utility methods for the Arrays package validation.

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

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

The ArraysValidator is used to ensure that an SBMLDocument does not violate any validation rules specified in the Arrays Package Specifications.

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

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

Assignment - Interface in org.sbml.jsbml

An Assignment can be seen as a mathematical equation with a Variable on the left hand side and an equation on the right hand side that assigns a value to the Variable.

ASSIGNMENT_CYCLE_VALIDATION_FOUND_CYCLE_IDS - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation

Key to store a set of ids in the ValidationContext so that we do not report several times the same cycle.

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

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

AssignmentCycleValidation - Class in org.sbml.jsbml.validator.offline.constraints.helper

Validates rule SBMLErrorCodes.CORE_20906.

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

assignmentLevel - org.sbml.jsbml.ext.qual.OutputTransitionEffect

The level of the QualitativeSpecies is set to the resultLevel of the selected term.

AssignmentRule - Class in org.sbml.jsbml

Represents the assignmentRule XML element of a SBML file.

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

Creates an AssignmentRule instance.

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

Creates an AssignmentRule instance with the given level and version.

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

Creates a cloned AssignmentRule instance from a given AssignmentRule.

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

Creates an AssignmentRule instance from a given math, level and version.

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

Creates an AssignmentRule instance from a given math and Parameter.

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

Creates an AssignmentRule instance from a given math and Variable.

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

Creates a cloned AssignmentRule instance from a given ExplicitRule.

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

Creates an AssignmentRule instance from a given Parameter.

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

Creates an AssignmentRule instance from a given math and Parameter.

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

Creates an AssignmentRule instance from a given variable.

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

Creates an AssignmentRule instance from a given variable and math.

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

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

AssignmentToConstantEntity - org.sbml.jsbml.SBMLException.Code

Cannot reassign a constant in an assignment rule

AssignmentVariableFilter - Class in org.sbml.jsbml.util.filters

This filter only accepts instances of Assignment with the variable as given in the constructor of this object.

AssignmentVariableFilter() - Constructor for class org.sbml.jsbml.util.filters.AssignmentVariableFilter

AssignmentVariableFilter(String) - Constructor for class org.sbml.jsbml.util.filters.AssignmentVariableFilter

AssignRuleCompartmentMismatch - org.sbml.jsbml.SBMLException.Code

Mismatched units in assignment rule for compartment

AssignRuleParameterMismatch - org.sbml.jsbml.SBMLException.Code

Mismatched units in assignment rule for parameter

AssignRuleSpeciesMismatch - org.sbml.jsbml.SBMLException.Code

Mismatched units in assignment rule for species

associatedSpecies - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

Introduced to FBC in version 2.

association - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

Introduced to FBC in version 2.

Association - Interface in org.sbml.jsbml.ext.fbc

Represents either a single gene, or a collection of genes in a logical expression and is only ever instantiated as one of its subclasses: GeneProductRef, And and Or.

AssociationNode<T> - Interface in org.sbml.jsbml.ext.render.director

ASTArithmeticOperatorNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing an arithmetic operator in a mathematical expression.

ASTArithmeticOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode

Creates a new ASTArithmeticOperatorNode without a pointer to its containing MathContainer.

ASTArithmeticOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode

Creates a new ASTArithmeticOperatorNode without a pointer to its containing MathContainer but of the specified ASTNode.Type.

ASTArithmeticOperatorNode(ASTNode.Type, MathContainer) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode

Creates a new ASTArithmeticOperatorNode of type ASTNode.Type and container MathContainer.

ASTArithmeticOperatorNode(ASTArithmeticOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode

Copy constructor; Creates a deep copy of the given ASTArithmeticOperatorNode.

ASTArithmeticOperatorNode(MathContainer) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode

Creates a new ASTArithmeticOperatorNode with a pointer to the specified MathContainer..

ASTBinaryFunctionNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a function with two parameters

ASTBinaryFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode

Creates a new ASTBinaryFunctionNode.

ASTBinaryFunctionNode(ASTBinaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode

Copy constructor; Creates a deep copy of the given ASTBinaryFunctionNode.

ASTBinaryFunctionNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode

Creates a new ASTBinaryFunctionNode with the specified children.

ASTBoolean - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a boolean

ASTBoolean() - Constructor for class org.sbml.jsbml.math.ASTBoolean

ASTBoolean(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTBoolean

Creates a new ASTBoolean.

ASTBoolean(ASTBoolean) - Constructor for class org.sbml.jsbml.math.ASTBoolean

Copy constructor; Creates a deep copy of the given ASTBoolean.

ASTCiFunctionNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML ci element in a mathematical expression.

ASTCiFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTCiFunctionNode

Creates a new ASTCiFunctionNode.

ASTCiFunctionNode(ASTCiFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTCiFunctionNode

Copy constructor; Creates a deep copy of the given ASTCiFunctionNode.

ASTCiNumberNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML ci element in a mathematical expression.

ASTCiNumberNode() - Constructor for class org.sbml.jsbml.math.ASTCiNumberNode

Creates a new ASTCiNumberNode.

ASTCiNumberNode(ASTCiNumberNode) - Constructor for class org.sbml.jsbml.math.ASTCiNumberNode

Copy constructor; Creates a deep copy of the given ASTCiNumberNode.

ASTCnExponentialNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing an exponent in a mathematical expression

ASTCnExponentialNode() - Constructor for class org.sbml.jsbml.math.ASTCnExponentialNode

Creates a new ASTCnExponentialNode that lacks a pointer to its containing MathContainer.

ASTCnExponentialNode(ASTCnExponentialNode) - Constructor for class org.sbml.jsbml.math.ASTCnExponentialNode

Copy constructor; Creates a deep copy of the given ASTCnExponentialNode.

ASTCnIntegerNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing an Integer in a mathematical expression

ASTCnIntegerNode() - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode

Creates a new ASTCnIntegerNode that lacks a pointer to its containing MathContainer.

ASTCnIntegerNode(int) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode

Creates a new ASTCnIntegerNode with int value.

ASTCnIntegerNode(ASTCnIntegerNode) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode

Copy constructor; Creates a deep copy of the given ASTCnIntegerNode.

ASTCnNumberNode<T> - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML cn element in a mathematical expression. cn elements are used to specify actual numerical constants.

ASTCnNumberNode() - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode

Creates a new ASTCnNumberNode that lacks a pointer to its containing MathContainer.

ASTCnNumberNode(String) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode

Creates a new ASTCnNumberNode that lacks a pointer to its containing MathContainer and has a variable String.

ASTCnNumberNode(ASTCnNumberNode<T>) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode

Copy constructor; Creates a deep copy of the given ASTCnNumberNode.

ASTCnRationalNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a rational number in a mathematical expression

ASTCnRationalNode() - Constructor for class org.sbml.jsbml.math.ASTCnRationalNode

Creates a new ASTCnRationalNode that lacks a pointer to its containing MathContainer.

ASTCnRationalNode(ASTCnRationalNode) - Constructor for class org.sbml.jsbml.math.ASTCnRationalNode

Copy constructor; Creates a deep copy of the given ASTCnRationalNode.

ASTCnRealNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a real number in a mathematical expression

ASTCnRealNode() - Constructor for class org.sbml.jsbml.math.ASTCnRealNode

Creates a new ASTCnRealNode that lacks a pointer to its containing MathContainer.

ASTCnRealNode(double) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode

Creates a new ASTCnRealNode that lacks a pointer to its containing MathContainer but has the specified real value.

ASTCnRealNode(ASTCnRealNode) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode

Copy constructor; Creates a deep copy of the given ASTCnRealNode.

ASTConstantNumber - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a constant number in a mathematical expression.

ASTConstantNumber() - Constructor for class org.sbml.jsbml.math.ASTConstantNumber

Creates a new ASTConstantNumber.

ASTConstantNumber(double) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber

Creates a new ASTConstantNumber with double value.

ASTConstantNumber(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber

Creates a new ASTConstantNumber of type ASTNode.Type.

ASTConstantNumber(ASTConstantNumber) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber

Copy constructor; Creates a deep copy of the given ASTConstantNumber.

ASTCSymbolAvogadroNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing avogadro's number

ASTCSymbolAvogadroNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

Creates a new ASTCSymbolAvogadroNode.

ASTCSymbolAvogadroNode(ASTCSymbolAvogadroNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

Copy constructor; Creates a deep copy of the given ASTCSymbolAvogadroNode.

ASTCSymbolBaseNode - Interface in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML element that contains a definitionURL and name attribute.

ASTCSymbolDelayNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the delay function

ASTCSymbolDelayNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolDelayNode

Creates a new ASTCSymbolDelayNode.

ASTCSymbolDelayNode(ASTCSymbolDelayNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolDelayNode

Copy constructor; Creates a deep copy of the given ASTCSymbolDelayNode.

ASTCSymbolNode - Interface in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML csymbol element in a mathematical expression.

ASTCSymbolTimeNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the time function

ASTCSymbolTimeNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolTimeNode

Creates a new ASTCSymbolTimeNode.

ASTCSymbolTimeNode(ASTCSymbolTimeNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolTimeNode

Copy constructor; Creates a deep copy of the given ASTCSymbolTimeNode.

ASTDivideNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the divide function

ASTDivideNode() - Constructor for class org.sbml.jsbml.math.ASTDivideNode

Creates a new ASTDivideNode.

ASTDivideNode(ASTDivideNode) - Constructor for class org.sbml.jsbml.math.ASTDivideNode

Copy constructor; Creates a deep copy of the given ASTDivideNode.

ASTDivideNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTDivideNode

Creates a new ASTDivideNode with the specified numerator ASTNode2 and denominator ASTNode2.

ASTFactory - Class in org.sbml.jsbml.math

A collection of static methods that can be used to create new abstract syntax trees or alter the topology of existing ones.

ASTFactory() - Constructor for class org.sbml.jsbml.math.ASTFactory

ASTFunction - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a function in a mathematical expression.

ASTFunction() - Constructor for class org.sbml.jsbml.math.ASTFunction

Creates a new ASTFunction that lacks a pointer to its containing MathContainer.

ASTFunction(ASTFunction) - Constructor for class org.sbml.jsbml.math.ASTFunction

Copy constructor; Creates a deep copy of the given ASTFunction.

ASTFunction(MathContainer) - Constructor for class org.sbml.jsbml.math.ASTFunction

Creates a new ASTFunction with a pointer to the specified MathContainer.

ASTHyperbolicNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a hyperbolic function

ASTHyperbolicNode() - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode

Creates a new ASTHyperbolicNode.

ASTHyperbolicNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode

Creates a new ASTHyperbolicNode of type ASTNode.Type

ASTHyperbolicNode(ASTHyperbolicNode) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode

Copy constructor; Creates a deep copy of the given ASTHyperbolicNode.

ASTLambdaFunctionNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a lambda function in a mathematical expression.

ASTLambdaFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTLambdaFunctionNode

Creates a new ASTLambdaFunctionNode.

ASTLambdaFunctionNode(ASTLambdaFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTLambdaFunctionNode

Copy constructor; Creates a deep copy of the given ASTLambdaFunctionNode.

ASTLogarithmNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the logarithm function

ASTLogarithmNode() - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode

Creates a new ASTLogarithmNode.

ASTLogarithmNode(ASTLogarithmNode) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode

Copy constructor; Creates a deep copy of the given ASTLogarithmNode.

ASTLogarithmNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode

Creates a new ASTLogarithmNode with base 10 and value ASTNode2

ASTLogarithmNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode

Creates a new ASTLogarithmNode with base ASTNode2 and value ASTNode2

ASTLogicalOperatorNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a logical operator in a mathematical expression.

ASTLogicalOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode

Creates a new ASTLogicalOperatorNode.

ASTLogicalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode

Creates a new ASTLogicalOperatorNode of type ASTNode.Type.

ASTLogicalOperatorNode(ASTLogicalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode

Copy constructor; Creates a deep copy of the given ASTLogicalOperatorNode.

ASTMinusNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the minus operator

ASTMinusNode() - Constructor for class org.sbml.jsbml.math.ASTMinusNode

Creates a new ASTMinusNode.

ASTMinusNode(ASTMinusNode) - Constructor for class org.sbml.jsbml.math.ASTMinusNode

Copy constructor; Creates a deep copy of the given ASTMinusNode.

ASTMinusNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTMinusNode

Creates a new ASTMinusNode with two children

ASTNode - Class in org.sbml.jsbml

A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.

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

Creates a new ASTNode of unspecified type and without a pointer to its containing MathContainer.

ASTNode(char) - Constructor for class org.sbml.jsbml.ASTNode

Creates a new ASTNode representing an operator, i.e., an internal node.

ASTNode(char, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode

Creates a new ASTNode representing an operator, i.e., an internal node.

ASTNode(double) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode.

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

Creates and returns a new ASTNode.

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

Creates and returns a new ASTNode.

ASTNode(double, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode.

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

Creates and returns a new ASTNode with the given integer value.

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

Creates and returns a new ASTNode with the given integer value with the given associated ASTNode.unitId for the given MathContainer as its parent SBML object.

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

Creates and returns a new ASTNode with the given integer value for the given MathContainer as its parent SBML object.

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

Creates and returns a new ASTNode with the given name.

ASTNode(String, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode with the given name.

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

Copy constructor; Creates a deep copy of the given ASTNode.

ASTNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.ASTNode

Creates a new ASTNode of the given ASTNode.Type but without a pointer to its MathContainer.

ASTNode(ASTNode.Type, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode.

ASTNode(CallableSBase) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode referring to the given CallableSBase.

ASTNode(CallableSBase, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode referring to the given CallableSBase.

ASTNode(ASTNode2) - Constructor for class org.sbml.jsbml.ASTNode

Create a new node of type ASTNode from the given ASTNode2

ASTNode(MathContainer) - Constructor for class org.sbml.jsbml.ASTNode

Creates and returns a new ASTNode.

ASTNODE_CN_TYPE_ATTRIBUTE - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

ASTNode.Type - Enum in org.sbml.jsbml

An enumeration of all possible types that can be represented by an abstract syntax tree node.

ASTNode2 - Interface in org.sbml.jsbml.math

A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.

ASTNode2Compiler - Interface in org.sbml.jsbml.math.compiler

A compiler for abstract syntax trees.

ASTNode2Value<T> - Class in org.sbml.jsbml.math.compiler

When interpreting ASTNode2s, the ASTNode2Compiler takes elements of this class as arguments and performs its operations on it.

ASTNode2Value(ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value

ASTNode2Value(UnitDefinition, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value

ASTNode2Value(T, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value

ASTNodeCompiler - Interface in org.sbml.jsbml.util.compilers

A compiler for abstract syntax trees.

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

Validation constraints related to ASTNode.

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

ASTNodePlugin - Interface in org.sbml.jsbml.ext

Defines the methods necessary for an ASTNode or ASTNode2 Plugin.

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

Returns a simple tree view of the ASTNode internal, including mainly node type and hierarchy.

ASTNodeValue - Class in org.sbml.jsbml.util.compilers

When interpreting ASTNodes, the ASTNodeCompiler takes elements of this class as arguments and performs its operations on it.

ASTNodeValue(boolean, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(double, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(float, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(int, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(long, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(Number, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(String, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(CallableSBase, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(UnitDefinition, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNodeValue(Node, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue

ASTNumber - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a number in a mathematical expression.

ASTNumber() - Constructor for class org.sbml.jsbml.math.ASTNumber

Creates a new ASTNumber that lacks a pointer to its containing MathContainer.

ASTNumber(ASTNumber) - Constructor for class org.sbml.jsbml.math.ASTNumber

Copy constructor; Creates a deep copy of the given ASTNumber.

ASTPiecewiseFunctionNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML piecewise element in a mathematical expression.

ASTPiecewiseFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTPiecewiseFunctionNode

Creates a new ASTPiecewiseFunctionNode.

ASTPiecewiseFunctionNode(ASTPiecewiseFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTPiecewiseFunctionNode

Copy constructor; Creates a deep copy of the given ASTPiecewiseFunctionNode.

ASTPlusNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the plus operator

ASTPlusNode() - Constructor for class org.sbml.jsbml.math.ASTPlusNode

Creates a new ASTPlusNode.

ASTPlusNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTPlusNode

Creates a new ASTPlusNode with two children

ASTPlusNode(ASTPlusNode) - Constructor for class org.sbml.jsbml.math.ASTPlusNode

Copy constructor; Creates a deep copy of the given ASTPlusNode.

ASTPowerNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the power function

ASTPowerNode() - Constructor for class org.sbml.jsbml.math.ASTPowerNode

Creates a new ASTPowerNode.

ASTPowerNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTPowerNode

Creates a new ASTPowerNode with the specified basis and exponent.

ASTPowerNode(ASTPowerNode) - Constructor for class org.sbml.jsbml.math.ASTPowerNode

Copy constructor; Creates a deep copy of the given ASTPowerNode.

ASTQualifierNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a MathML qualifier element in a mathematical expression.

ASTQualifierNode() - Constructor for class org.sbml.jsbml.math.ASTQualifierNode

Creates a new ASTQualifierNode.

ASTQualifierNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode

Creates a new ASTQualifierNode of the given type ASTNode.Type

ASTQualifierNode(ASTQualifierNode) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode

Copy constructor; Creates a deep copy of the given ASTQualifierNode.

ASTRelationalOperatorNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a relational operator in a mathematical expression.

ASTRelationalOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode

Creates a new ASTRelationalOperatorNode without a pointer to its containing MathContainer.

ASTRelationalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode

Creates a new ASTRelationalOperatorNode without a pointer to its containing MathContainer but with the specified ASTNode.Type.

ASTRelationalOperatorNode(ASTRelationalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode

Copy constructor; Creates a deep copy of the given ASTRelationalOperatorNode.

ASTRootNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a root function

ASTRootNode() - Constructor for class org.sbml.jsbml.math.ASTRootNode

Creates a new ASTRootNode.

ASTRootNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTRootNode

Creates a new ASTRootNode with the specified radicand and a root exponent of 2.

ASTRootNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTRootNode

Creates a new ASTRootNode with the specified radicand and rootExponent.

ASTRootNode(ASTRootNode) - Constructor for class org.sbml.jsbml.math.ASTRootNode

Copy constructor; Creates a deep copy of the given ASTRootNode.

ASTTimesNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing the times operator

ASTTimesNode() - Constructor for class org.sbml.jsbml.math.ASTTimesNode

Creates a new ASTTimesNode.

ASTTimesNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTTimesNode

Creates a new ASTTimesNode with two children

ASTTimesNode(ASTTimesNode) - Constructor for class org.sbml.jsbml.math.ASTTimesNode

Copy constructor; Creates a deep copy of the given ASTTimesNode.

ASTTrigonometricNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a trigonometric function

ASTTrigonometricNode() - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode

Creates a new ASTTrigonometricNode.

ASTTrigonometricNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode

Creates a new ASTTrigonometricNode of type ASTNode.Type.

ASTTrigonometricNode(ASTTrigonometricNode) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode

Copy constructor; Creates a deep copy of the given ASTTrigonometricNode.

ASTUnaryFunctionNode - Class in org.sbml.jsbml.math

An Abstract Syntax Tree (AST) node representing a function with only one parameter

ASTUnaryFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode

Creates a new ASTUnaryFunctionNode.

ASTUnaryFunctionNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode

Creates a new ASTUnaryFunctionNode of type ASTNode.Type

ASTUnaryFunctionNode(ASTUnaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode

Copy constructor; Creates a deep copy of the given ASTUnaryFunctionNode.

ASTUnknown - Class in org.sbml.jsbml.math

An ASTNode2 with specified neutral behavior.

AVOGADRO - org.sbml.jsbml.Unit.Kind

This unit is DIMENSIONLESS multiplied with Avogadro's number.

AVOGADRO_L3V1 - Static variable in class org.sbml.jsbml.util.Maths

Avogadro's constant of 6.02214179 ⋅ 10²³ mol^-1.

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