Uses of Class
org.sbml.jsbml.AbstractSBase

Packages that use AbstractSBase

Package	Description
org.sbml.jsbml	Pure Java™ implementation of the data structures to represent all SBML constructs.
org.sbml.jsbml.ext.arrays
org.sbml.jsbml.ext.comp	Provides classes for the Hierarchical Model Composition package.
org.sbml.jsbml.ext.distrib
org.sbml.jsbml.ext.dyn	Provides classes for the Dynamic Structures package.
org.sbml.jsbml.ext.fbc	Provides classes for the Flux Balance Constraints package (FBC).
org.sbml.jsbml.ext.groups	Provides classes for the Groups package.
org.sbml.jsbml.ext.layout	Provides classes for the Layout package.
org.sbml.jsbml.ext.multi	Provides classes for the Multi package.
org.sbml.jsbml.ext.qual	Provides classes for the Qualitative Models package.
org.sbml.jsbml.ext.render	Provides classes for the render package, see the specification at sbml.org.
org.sbml.jsbml.ext.req
org.sbml.jsbml.ext.spatial	Provides classes for the Spatial Geometries and Processes package.
org.sbml.jsbml.util	A collection of handy utilities when working with JSBML classes, such as classes for String manipulation or mathematical operations.

Uses of AbstractSBase in org.sbml.jsbml

Subclasses of AbstractSBase in org.sbml.jsbml

Modifier and Type	Class and Description
class	AbstractMathContainer Base class for all the SBML components which contain MathML nodes.
class	AbstractNamedSBase Base abstract class for all the SBML components with an id and a name (optional or not) in SBML Level 3 Version 1 or lower.
class	AbstractNamedSBaseWithUnit 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.
class	AlgebraicRule Represents the algebraicRule XML element of a SBML file.
class	AssignmentRule Represents the assignmentRule XML element of a SBML file.
class	Compartment Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation.
class	CompartmentType Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
class	Constraint Represents the constraint XML element of a SBML file.
class	Delay Represents the delay subnode of an event element.
class	Event Represents the event XML element of a SBML file.
class	EventAssignment Represents the eventAssignment XML element of a SBML file.
class	ExplicitRule An explicit Rule is a rule that explicitly declares its variable element.
class	FunctionDefinition Represents the functionDefinition XML element of a SBML file.
class	InitialAssignment Represents the initialAssignment XML element of a SBML file.
class	KineticLaw Represents the kineticLaw XML element of a SBML file.
class	ListOf<T extends SBase> This list implementation is a Java List that extends AbstractSBase.
class	LocalParameter A local parameter can only be used to specify a constant within a KineticLaw.
class	Model JSBML implementation of SBML's Model construct.
class	ModifierSpeciesReference Represents the modifierSpeciesReference XML element of a SBML file.
class	Parameter Represents a globally valid parameter in the model, i.e., a variable that may change during a simulation or that provides a constant value.
class	Priority This class represents the priority element in SBML.
class	QuantityWithUnit This object represents an element with identifier and name, a value, and a defined unit.
class	RateRule Represents the rateRule XML element of a SBML file.
class	Reaction Represents the reaction XML element of a SBML file.
class	Rule The base class for the AlgebraicRule, RateRule, AssignmentRule.
class	SBMLDocument Represents the 'sbml' root node of a SBML file.
class	SimpleSpeciesReference The base class of SpeciesReference and ModifierSpeciesReference.
class	Species Represents the species XML element of a SBML file.
class	SpeciesReference Represents the speciesReference XML element of a SBML file.
class	SpeciesType Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
class	StoichiometryMath Deprecated. Since SBML Level 3 Version 1 use AssignmentRule with instances of SpeciesReference as Variable instead.
class	Symbol The base class for Compartment, Species, Parameter.
class	Trigger Represents the trigger XML element of a SBML file.
class	Unit Represents the unit XML element of a SBML file.
class	UnitDefinition Represents the unitDefinition XML element of a SBML file.

Methods in org.sbml.jsbml that return AbstractSBase

Modifier and Type	Method and Description
abstract AbstractSBase	AbstractSBase.clone()

Uses of AbstractSBase in org.sbml.jsbml.ext.arrays

Subclasses of AbstractSBase in org.sbml.jsbml.ext.arrays

Modifier and Type	Class and Description
class	Dimension The Dimension is used to indicate the parent SBase is arrayed.
class	Index The Index is used to referenced an arrayed element specified in an attribute.

Uses of AbstractSBase in org.sbml.jsbml.ext.comp

Subclasses of AbstractSBase in org.sbml.jsbml.ext.comp

Modifier and Type	Class and Description
class	AbstractNamedSBaseRef This abstract class is used by Deletion and Port classes.
class	Deletion Defines a deletion operation to be applied when a submodel instantiates a model definition.
class	ExternalModelDefinition The ExternalModelDefinition objects are model definitions - in and of themselves, they are definitions of the models but not uses of those models.
class	ModelDefinition Holder class for model definitions, which are Models.
class	Port The Port allows a modeler to design a Submodel such that other models interact with the Submodel through designated interfaces.
class	ReplacedBy Indicates when the parent object is to be replaced by another object.
class	ReplacedElement Points to a submodel object that should be considered "replaced".
class	SBaseRef Contains the machinery for constructing references to specific components within enclosed models or even within external models located in other files.
class	Submodel Submodels are instantiations of models contained within other models.

Uses of AbstractSBase in org.sbml.jsbml.ext.distrib

Subclasses of AbstractSBase in org.sbml.jsbml.ext.distrib

Modifier and Type	Class and Description
class	AbstractDistribSBase
class	Uncertainty The Uncertainty class is a collection of zero or more statistical measures related to the uncertainty of the parent SBML element.
class	UncertParameter Defines one uncertainty statistic about the parent element.
class	UncertSpan The UncertSpan class defines a span of values that define an uncertainty statistic such as confidence interval or range.

Uses of AbstractSBase in org.sbml.jsbml.ext.dyn

Subclasses of AbstractSBase in org.sbml.jsbml.ext.dyn

Modifier and Type	Class and Description
class	DynElement
class	SpatialComponent

Methods in org.sbml.jsbml.ext.dyn that return AbstractSBase

Modifier and Type	Method and Description
AbstractSBase	SpatialComponent.clone()
AbstractSBase	DynElement.clone()

Uses of AbstractSBase in org.sbml.jsbml.ext.fbc

Subclasses of AbstractSBase in org.sbml.jsbml.ext.fbc

Modifier and Type	Class and Description
class	And This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.
class	FluxBound Deprecated. Only defined in FBC Version 1.
class	FluxObjective The FluxObjective class is a relatively simple container for a model variable weighted by a signed linear coefficient.
class	GeneProduct Defines a single gene product.
class	GeneProductAssociation Contains a single Association.
class	GeneProductRef References a GeneProduct.
class	ListOfObjectives ListOfObjectives adds an additional required attribute: 'activeObjective'.
class	LogicalOperator Represents a collection of genes in a logical expression.
class	Objective An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction).
class	Or This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.

Uses of AbstractSBase in org.sbml.jsbml.ext.groups

Subclasses of AbstractSBase in org.sbml.jsbml.ext.groups

Modifier and Type	Class and Description
class	Group
class	ListOfMemberConstraint Deprecated. This class was removed from the specifications as of version 0.7 (2015-11-24) as no software wanted to implement support for it. It might be added back in a future version of the specifications if somebody want to implement it.
class	ListOfMembers
class	Member
class	MemberConstraint Deprecated. This class was removed from the specifications as of version 0.7 (2015-11-24) as no software wanted to implement support for it. It might be added back in a future version of the specifications if somebody want to implement it.

Uses of AbstractSBase in org.sbml.jsbml.ext.layout

Subclasses of AbstractSBase in org.sbml.jsbml.ext.layout

Modifier and Type	Class and Description
class	AbstractReferenceGlyph Abstract super class for all kinds of glyphs that graphically represent an instance of NamedSBase.
class	BoundingBox The BoundingBox class specifies the required elements position and dimension.
class	CompartmentGlyph The CompartmentGlyph class is derived from GraphicalObject and inherits its attributes.
class	CubicBezier Represents smooth curves in the Layout package.
class	Curve The Curve class describes how to connect elements in a diagram defined with the use of the Layout package.
class	CurveSegment Parent class to LineSegment and CubicBezier.
class	Dimensions A Dimensions is specified via the required attributes width, height and an optional attribute depth, all of which are of type double.
class	GeneralGlyph The GeneralGlyph is used to facilitate the representation of elements other than Compartment, Species and Reaction and thus can be used for the display of relationships of Rule or elements defined by other SBML packages.
class	GraphicalObject All the more specific layout elements (CompartmentGlyph, GeneralGlyph, SpeciesGlyph, ReactionGlyph, ReferenceGlyph, TextGlyph, and SpeciesReferenceGlyph) are derived from the class GraphicalObject.
class	Layout The Layout class stores layout information for some or all elements of the Model as well as additional objects that need not be connected to the Model.
class	LineSegment The LineSegment class consists of the mandatory attribute xsi:type and two child elements of type Point.
class	Point The representation of a point in the "layout" package.
class	ReactionGlyph Analogous to how a Reaction object has to at least have one reactant or product, the ReactionGlyph has to at least have one SpeciesReferenceGlyph stored in the ReactionGlyph.listOfSpeciesReferenceGlyphs.
class	ReferenceGlyph The ReferenceGlyph element describes the graphical connection between an arbitrary GraphicalObject (or derived element) and a GeneralGlyph (which would be an arrow or some curve in most cases).
class	SpeciesGlyph The SpeciesGlyph class has an optional species attribute, in addition to to the attributes from GraphicalObject.
class	SpeciesReferenceGlyph The SpeciesReferenceGlyph class describes the graphical connection between a SpeciesGlyph and a ReactionGlyph (which would be an arrow or some curve in most cases).
class	TextGlyph The TextGlyph class describes the position and dimension of text labels.

Uses of AbstractSBase in org.sbml.jsbml.ext.multi

Subclasses of AbstractSBase in org.sbml.jsbml.ext.multi

Modifier and Type	Class and Description
class	BindingSiteSpeciesType A BindingSiteSpeciesType object is a binding site, and therefore its instance can further define the bindingStatus attribute and can participate a binding internally and explicitly in an InSpeciesTypeBond object, or externally and implicitly defined by an OutwardBindingSite object.
class	CompartmentReference
class	InSpeciesTypeBond Defines a bond existing within a MultiSpeciesType.
class	IntraSpeciesReaction
class	MultiSpeciesType The element MultiSpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 Core any more.
class	OutwardBindingSite A binding site not involved in any InSpeciesTypeBond object in the MultiSpeciesType referenced by a Species is an outwardBindingSite.
class	PossibleSpeciesFeatureValue Each state feature (SpeciesFeatureType) also requires the definition of all the possible values it can take.
class	SpeciesFeature Defines the state of a component in a species by selecting values from the listOfPossibleSpeciesFeatureValues of the referenced SpeciesFeatureType.
class	SpeciesFeatureType A species type (MultiSpeciesType) can carry any number of features (SpeciesFeatureType), which are characteristic properties specific for this type of species (Species).
class	SpeciesFeatureValue
class	SpeciesTypeComponentIndex Provides a way to identify or index a component within a MultiSpeciesType.
class	SpeciesTypeComponentMapInProduct A speciesTypeComponentMapInProduct defines the mapping between a component in a reactant and a component in a product.
class	SpeciesTypeInstance Provides a way to construct MultiSpeciesTypes and Species with multiple components.
class	SubListOfSpeciesFeature Allows to regroup a set of SpeciesFeature that have a specific Relation between them.

Methods in org.sbml.jsbml.ext.multi that return AbstractSBase

Modifier and Type	Method and Description
AbstractSBase	PossibleSpeciesFeatureValue.clone()

Uses of AbstractSBase in org.sbml.jsbml.ext.qual

Subclasses of AbstractSBase in org.sbml.jsbml.ext.qual

Modifier and Type	Class and Description
class	FunctionTerm Each FunctionTerm is also associated with a result and in addition to a Boolean function inside a Math element that can be used to set the conditions under which this term is selected.
class	Input Each Input refers to a QualitativeSpecies that participates in the corresponding Transition.
class	Output Each Output refers to a QualitativeSpecies that participates in (is affected by) the corresponding Transition.
class	QualitativeSpecies Similarly to the Species in SBML, the components of qualitative models refer to pools of entities that are considered indistinguishable and are each located in a specific Compartment.
class	Transition A Transition defines the changes in level associated with the QualitativeSpecies that occur when a Transition is enabled.

Uses of AbstractSBase in org.sbml.jsbml.ext.render

Subclasses of AbstractSBase in org.sbml.jsbml.ext.render

Modifier and Type	Class and Description
class	ColorDefinition
class	DefaultValues Encodes default values within the containing ListOfGlobalRenderInformation or ListOfLocalRenderInformation.
class	Ellipse Encodes an ellipse.
class	GlobalRenderInformation
class	GradientBase
class	GradientStop
class	GraphicalPrimitive1D
class	GraphicalPrimitive2D
class	Image
class	LinearGradient
class	LineEnding
class	ListOfGlobalRenderInformation Derives from the ListOf class and contains one or more objects of type GlobalRenderInformation.
class	ListOfLocalRenderInformation Derives from the ListOf class and contains one or more objects of type LocalRenderInformation.
class	ListOfRenderInformation<T extends RenderInformationBase> Derives from the ListOf class and contains one or more objects of type RenderInformationBase.
class	LocalRenderInformation
class	LocalStyle
class	Polygon
class	RadialGradient
class	Rectangle
class	RenderCubicBezier
class	RenderCurve Implements the curve concept from the SBML render extension.
class	RenderCurveSegment Parent class to RenderPoint and RenderCubicBezier.
class	RenderGroup The RenderGroup class from the SBML render extension is used to group graphical primitives together to create composite representations from simple primitives.
class	RenderInformationBase
class	RenderPoint
class	Style
class	Text
class	Transformation
class	Transformation2D

Uses of AbstractSBase in org.sbml.jsbml.ext.req

Subclasses of AbstractSBase in org.sbml.jsbml.ext.req

Modifier and Type	Class and Description
class	ChangedMath Declares which package has modified the value or the mathematical meaning of an SBase and in which way.

Uses of AbstractSBase in org.sbml.jsbml.ext.spatial

Subclasses of AbstractSBase in org.sbml.jsbml.ext.spatial

Modifier and Type	Class and Description
class	AbstractSpatialNamedSBase The base class for each spatial class.
class	AdjacentDomains
class	AdvectionCoefficient
class	AnalyticGeometry
class	AnalyticVolume
class	Boundary
class	BoundaryCondition
class	CompartmentMapping
class	CoordinateComponent
class	CoordinateReference Deprecated. Not present in spec 0.90, as be moved into DiffusionCoefficient.
class	CSGeometry
class	CSGHomogeneousTransformation
class	CSGNode
class	CSGObject
class	CSGPrimitive
class	CSGPseudoPrimitive
class	CSGRotation
class	CSGScale
class	CSGSetOperator
class	CSGTransformation
class	CSGTranslation
class	DiffusionCoefficient
class	Domain
class	DomainType
class	Geometry
class	GeometryDefinition
class	InteriorPoint
class	MixedGeometry
class	OrdinalMapping
class	ParameterType Top level class for all possible child of a SpatialParameterPlugin.
class	ParametricGeometry
class	ParametricObject
class	PolygonObject Deprecated.
class	SampledField
class	SampledFieldGeometry
class	SampledVolume
class	SpatialPoints
class	SpatialSymbolReference
class	TransformationComponent

Uses of AbstractSBase in org.sbml.jsbml.util

Subclasses of AbstractSBase in org.sbml.jsbml.util

Modifier and Type	Class and Description
class	ListOfWithName<T extends SBase> Deprecated. since JSBML 1.2 and the introduction of ListOf.setOtherListName(String), this class is not necessary any more.