A-Index (JSBML 1.1 API Specification)

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

A

about - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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(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.
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
absoluteCx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteCy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteCz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteFx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteFy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteFz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteHeight - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteR - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteRx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteRy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteWidth - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteX - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteX1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteX2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteY - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteY1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteY2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteZ - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteZ1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
absoluteZ2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
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.
AbstractFBCSBasePlugin - Class in org.sbml.jsbml.ext.fbc
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
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(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.
AbstractMathContainer(int, int) - Constructor for class org.sbml.jsbml.AbstractMathContainer: Creates a MathContainer instance from a level and version.
AbstractNamedSBase - Class in org.sbml.jsbml: The base class for each SBML element with an optional id and name.
AbstractNamedSBase() - Constructor for class org.sbml.jsbml.AbstractNamedSBase: Creates an AbstractNamedSBase.
AbstractNamedSBase(AbstractNamedSBase) - Constructor for class org.sbml.jsbml.AbstractNamedSBase: Creates an AbstractNamedSBase from a given AbstractNamedSBase.
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.
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 AbstractNamedSBase.
AbstractNamedSBaseRef(AbstractNamedSBaseRef) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef: Creates an AbstractNamedSBase from a given AbstractNamedSBase.
AbstractNamedSBaseRef(int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef: Creates an AbstractNamedSBase from a level and version.
AbstractNamedSBaseRef(String) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef: Creates an AbstractNamedSBase with the given identifier.
AbstractNamedSBaseRef(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef: Creates an AbctractNamedSBase from an id, level and version.
AbstractNamedSBaseRef(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef: Creates an AbctractNamedSBase from an id, name, level and version.
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(AbstractNamedSBaseWithUnit) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
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
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
AbstractReferenceGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
AbstractReferenceGlyph(AbstractReferenceGlyph) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
AbstractReferenceGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
AbstractReferenceGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
AbstractRenderPlugin - Class in org.sbml.jsbml.ext.render
AbstractRenderPlugin(SBase) - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Creates an AbstractRenderPlugin instance
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
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(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(SBase) - 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
AbstractSpatialNamedSBase - Class in org.sbml.jsbml.ext.spatial
AbstractSpatialNamedSBase() - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
AbstractSpatialNamedSBase(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
AbstractSpatialNamedSBase(SpatialNamedSBase) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
AbstractSpatialNamedSBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
AbstractSpatialNamedSBase(String) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
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.
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.distrib.DrawFromDistribution
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.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.SpeciesReferenceFilter
accepts(Object) - Method in class org.sbml.jsbml.util.filters.XMLNodeFilter
activeObjective - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
add(Layout) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin: Adds the given Layout to the listOfLayouts.
add(int, T) - Method in class org.sbml.jsbml.ListOf
add(T) - Method in class org.sbml.jsbml.ListOf
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(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) - 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(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLAttributes: Adds an attribute with the given XMLTriple/value pair to this XMLAttributes set.
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) - Method in class org.sbml.jsbml.xml.XMLNamespaces: Appends an XML namespace URI with an empty prefix to this list of namespace declarations.
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(Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf
addAll(int, 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>, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.math.ASTUnknown
addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - 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 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(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(CurveSegment) - Method in class org.sbml.jsbml.ext.layout.Curve
addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.layout.Curve
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.
addCVTerm - 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.
addDeclaredNamespace - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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.
addDistribInput(DistribInput) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution: Adds a new DistribInput to the listOfDistribInputs.
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.
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(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.
addExtension - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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.SpeciesType: Adds a new InSpeciesTypeBond to the SpeciesType.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.
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, String, String) - Method in class org.sbml.jsbml.SBMLDocument: Deprecated.
use SBase.addDeclaredNamespace(String, String)
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.
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.
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(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.
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.
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.
addSpeciesFeatureChange(SpeciesFeatureChange) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Adds a new SpeciesFeatureChange to the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges.
addSpeciesFeatureType(SpeciesFeatureType) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Adds a new SpeciesFeatureType to the SpeciesType.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.listOfSpeciesReferencesGlyphs.
addSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Adds a SpeciesType.
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.SpeciesType: Adds a new SpeciesTypeComponentIndex to the SpeciesType.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.SpeciesType: Adds a new SpeciesTypeInstance to the SpeciesType.listOfSpeciesTypeInstances.
addStyle(Style) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
addSubGlyph(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: Adds a new GraphicalObject to the listOfSubGlyphs.
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, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.math.ASTUnknown
addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - 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 interface org.sbml.jsbml.util.TreeNodeWithChangeSupport: Adds a listener to this TreeNodeWithChangeSupport object and optionally also to all of its child nodes.
addUnit(String) - Method in class org.sbml.jsbml.UnitDefinition
addUnit(Unit) - Method in class org.sbml.jsbml.UnitDefinition: Adds an Unit to this UnitDefinition.
addUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition: Convenient method to add a new unit object with the given kind that will have the same level/version combination than this UnitDefinition object.
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.
addValue(String, double) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler: Adds a new string,double pair to the idToValue.
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
adjacentDomains - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
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 - Class in org.sbml.jsbml.ext.spatial
AdvectionCoefficient() - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
AdvectionCoefficient(AdvectionCoefficient) - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
AdvectionCoefficient(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
advectionCoefficient - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
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(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.
AlgebraicRule(int, int) - Constructor for class org.sbml.jsbml.AlgebraicRule: Creates an AlgebraicRule instance from level and version.
all_L3_namespaces - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
AnalyticGeometry - Class in org.sbml.jsbml.ext.spatial
AnalyticGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry
AnalyticGeometry(AnalyticGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry
AnalyticGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry
analyticGeometry - 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
AnalyticVolume(AnalyticVolume) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume
AnalyticVolume(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume
analyticVolume - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
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 - Class in org.sbml.jsbml.ext.fbc: Introduced to FBC in version 2.
And() - Constructor for class org.sbml.jsbml.ext.fbc.And
And(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.And
And(And) - Constructor for class org.sbml.jsbml.ext.fbc.And
and - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
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(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 - 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.
and(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
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
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
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(Annotation) - Constructor for class org.sbml.jsbml.Annotation: Creates a new Annotation instance by cloning the given Annotation.
Annotation(List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation: Creates an Annotation instance from a list of CVTerm objects.
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(XMLNode) - Constructor for class org.sbml.jsbml.Annotation
annotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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
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.
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(T) - Method in class org.sbml.jsbml.ListOf: Adds item to the end of this ListOf.
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(String) - Method in class org.sbml.jsbml.xml.XMLToken: Appends characters to this XML text content.
appendAnnotation(String) - Method in class org.sbml.jsbml.AbstractSBase
appendAnnotation(XMLNode) - 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 interface org.sbml.jsbml.SBase: Appends the given annotation to the 'annotation' subelement of this object.
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(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase: Appends notes to the existing notes.
appendNotes(String) - Method in interface org.sbml.jsbml.SBase: Appends 'notes' to the notes String of this object.
appendNotes(XMLNode) - Method in interface org.sbml.jsbml.SBase: Appends 'notes' to the notes of this object.
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(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
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
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arccosh of n
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arcus-cotangens of a double value.
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arccoth of n
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arccosecant of a double value
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arccsch of n
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arcsecant of a double value
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arcsech of n
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(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
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
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arcsinh of n
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(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
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
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(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
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(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the arctanh of n
AREA - Static variable in class org.sbml.jsbml.UnitDefinition: Identifier of the (for SBML Level 2) predefined UnitDefinition area.
area(int, int) - Static method in class org.sbml.jsbml.UnitDefinition: Predefined unit for area.
areaUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
areCompatible(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition: Predicate returning true or false depending on whether two UnitDefinition objects are compatible.
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.
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: Predicate returning true or false depending on whether two UnitDefinition objects are equivalent.
areIdentical(Unit, Unit) - Static method in class org.sbml.jsbml.Unit: Predicate returning true or false depending on whether two Unit objects are identical.
areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition: Predicate returning true or false depending on whether two UnitDefinition objects are identical.
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
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 ArraysSBasePlugin instance
ArraysSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Creates an ArraysSBasePlugin with a level and a version.
ArraysSBasePlugin(ArraysSBasePlugin) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Clone constructor
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.
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(AssignmentRule) - Constructor for class org.sbml.jsbml.AssignmentRule: Creates a cloned AssignmentRule instance from a given AssignmentRule.
AssignmentRule(ExplicitRule) - Constructor for class org.sbml.jsbml.AssignmentRule: Creates a cloned AssignmentRule instance from a given ExplicitRule.
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(int, int) - Constructor for class org.sbml.jsbml.AssignmentRule: Creates an AssignmentRule instance with the given level and version.
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.
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
associatedSpecies - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
Association - Interface in org.sbml.jsbml.ext.fbc
association - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
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(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..
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.
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(ASTBoolean) - Constructor for class org.sbml.jsbml.math.ASTBoolean: Copy constructor; Creates a deep copy of the given ASTBoolean.
ASTBoolean(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTBoolean: Creates a new 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(ASTCnIntegerNode) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode: Copy constructor; Creates a deep copy of the given ASTCnIntegerNode.
ASTCnIntegerNode(int) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode: Creates a new ASTCnIntegerNode with int value.
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(ASTCnNumberNode<T>) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode: Copy constructor; Creates a deep copy of the given ASTCnNumberNode.
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.
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(ASTCnRealNode) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode: Copy constructor; Creates a deep copy of the given ASTCnRealNode.
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.
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(ASTConstantNumber) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber: Copy constructor; Creates a deep copy of the given 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.
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(ASTHyperbolicNode) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode: Copy constructor; Creates a deep copy of the given ASTHyperbolicNode.
ASTHyperbolicNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode: Creates a new ASTHyperbolicNode of type ASTNode.Type
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(ASTLogicalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode: Copy constructor; Creates a deep copy of the given ASTLogicalOperatorNode.
ASTLogicalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode: Creates a new ASTLogicalOperatorNode of type ASTNode.Type.
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(ASTNode) - Constructor for class org.sbml.jsbml.ASTNode: Copy constructor; Creates a deep copy of the given ASTNode.
ASTNode(CallableSBase) - 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(CallableSBase, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode: Creates and returns a new ASTNode referring to the given CallableSBase.
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, 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(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(MathContainer) - Constructor for class org.sbml.jsbml.ASTNode: Creates and returns a new ASTNode.
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.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.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(T, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
ASTNode2Value(UnitDefinition, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
ASTNodeCompiler - Interface in org.sbml.jsbml.util.compilers: A compiler for abstract syntax trees.
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(ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
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(long, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
ASTNodeValue(int, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
ASTNodeValue(CallableSBase, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
ASTNodeValue(Node, 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(UnitDefinition, 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(ASTQualifierNode) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode: Copy constructor; Creates a deep copy of the given ASTQualifierNode.
ASTQualifierNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode: Creates a new ASTQualifierNode of the given type ASTNode.Type
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(ASTRelationalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode: Copy constructor; Creates a deep copy of the given ASTRelationalOperatorNode.
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.
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(ASTTrigonometricNode) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode: Copy constructor; Creates a deep copy of the given ASTTrigonometricNode.
ASTTrigonometricNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode: Creates a new ASTTrigonometricNode of type ASTNode.Type.
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(ASTUnaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode: Copy constructor; Creates a deep copy of the given ASTUnaryFunctionNode.
ASTUnaryFunctionNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode: Creates a new ASTUnaryFunctionNode of type ASTNode.Type
ASTUnknown - Class in org.sbml.jsbml.math: An ASTNode2 with specified neutral behavior.
AVOGADRO_L3V1 - Static variable in class org.sbml.jsbml.util.Maths: Avogadro's constant of 6.02214179 ⋅ 10²³ mol^-1.

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