A B C D E F G H I L M N O P R S T U V W

A

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

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

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

Adds a new AdjacentDomains to the Geometry.listOfAdjacentDomains.

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

Adds a new AnalyticVolume to the listOfAnalyticVolumes.

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

Adds a new CoordinateComponent to the listOfCoordinateComponents.

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.

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.

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.

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

Adds a new InteriorPoint to the listOfInteriorPoints.

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

Adds a new OrdinalMapping to the listOfOrdinalMappings.

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

Adds a new ParametricObject to the listOfParametricObjects.

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.

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

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

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

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.

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

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

B

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

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

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

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

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

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

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

BoundaryConditionKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

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

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

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

C

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

clone() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

clone() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

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

clones this class

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

CompressionKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

coord1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

coord2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

coord3 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

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

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

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

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

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

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

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

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

CoordinateKind - Enum in org.sbml.jsbml.ext.spatial

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

Deprecated.

Not present in spec 0.90, as be moved into DiffusionCoefficient.

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

Deprecated.

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

Deprecated.

coordinateReference1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

coordinateReference2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

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

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

Creates a new AdjacentDomain element and adds it to the ListOfAdjacentDomains list

createAdjacentDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new AdjacentDomains element and adds it to the Geometry.listOfAdjacentDomains list

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

createAnalyticGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

createAnalyticGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

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

Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list

createAnalyticVolume(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list

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

Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list

createCoordinateComponent(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list

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

createCSGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

createCSGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

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

createCSGHomogeneousTransformation(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGHomogeneousTransformation element and adds it to the ListOfCSGNodes list

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

Creates a new CSGObject element and adds it to the ListOfCSGObjects list

createCSGObject(String) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Creates a new CSGObject element and adds it to the ListOfCSGObjects list

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

Creates a new CSGNode element and adds it to the ListOfCSGNodes list

createCSGPrimitive(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGPrimitive element and adds it to the ListOfCSGNodes list

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

createCSGPseudoPrimitive(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGPseudoPrimitive element and adds it to the ListOfCSGNodes list

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

createCSGRotation(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGRotation element and adds it to the ListOfCSGNodes list

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

createCSGScale(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGScale element and adds it to the ListOfCSGNodes list

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

createCSGSetOperator(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGSetOperator element and adds it to the ListOfCSGNodes list

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

createCSGTranslation(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Creates a new CSGTranslation element and adds it to the ListOfCSGNodes list

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

Creates a new Domain element and adds it to the ListOfDomains list

createDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new Domain element and adds it to the ListOfDomains list

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

Creates a new DomainType element and adds it to the ListOfDomainTypes list

createDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new DomainType element and adds it to the ListOfDomainTypes list

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

Creates a new Geometry, adds it to this object and returns a pointer to it.

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

Creates a new InteriorPoint element and adds it to the ListOfInteriorPoints list

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

createMixedGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list

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

createMixedGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list

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

Creates a new OrdinalMapping element and adds it to the ListOfOrdinalMappings list

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

createParametricGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

createParametricGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

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

Creates a new ParametricObject element and adds it to the ListOfParametricObjects list

createParametricObject(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Creates a new ParametricObject element and adds it to the ListOfParametricObjects list

createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

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

Creates a new SampledField element and adds it to the ListOfSampledFields list

createSampledField(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new SampledField element and adds it to the ListOfSampledFields list

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

Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list

createSampledFieldGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list

createSampledFieldGeometry(String) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list

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

Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list

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

Creates a new SampledVolume element and adds it to the ListOfSampledVolumes list

createSampledVolume(String) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Creates a new SampledVolume element and adds it to the ListOfSampledVolumes list

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

D

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

DataKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

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

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

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

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

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

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

DiffusionKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

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

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

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

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

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

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

domain1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

domain2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

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

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

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

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

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

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

E

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

F

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

FunctionKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

G

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

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

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

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

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

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

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

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

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

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

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

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

GeometryKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

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

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

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

Returns the value of SpatialPoints.arrayData.

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

Returns the value of arrayDataLength.

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

Returns the value of boundaryDomainType

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

Returns the value of boundaryMaximum

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

Returns the value of boundaryMinimum

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.Domain

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

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

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

getCompartmentMapping() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

Returns the value of compartmentMapping

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

Returns the value of complementA

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

Returns the value of complementB

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

Returns the value of components

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

Returns the value of componentsLength

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

Returns the value of compression.

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

Returns the value of compression

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

Returns the value of compression.

getCoord1() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns the value of coord1

getCoord2() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns the value of coord2

getCoord3() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns the value of coord3

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

Returns the value of coordinate

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

Deprecated.

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

Returns the value of coordinateBoundary

getCoordinateReference1() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns the value of coordinateReference1

getCoordinateReference2() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns the value of coordinateReference2

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

Returns the value of coordinateSystem

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

Returns the value of csgNode

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

Returns the value of csgNode

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

Returns the value of csgObjectRef

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

Returns the value of data

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

Returns the value of data

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

Returns the value of dataType.

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

Returns the value of dataType

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

Returns the value of dataType.

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

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

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

Returns the value of diffusionKind

getDomain1() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Returns the value of domain1

getDomain2() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Returns the value of domain2

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

Returns the value of domainType

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

Returns the value of domainType

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

Returns the value of domainType

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

Returns the value of domainType

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

Returns the value of domain

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

Returns the value of domainType

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

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

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

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

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

Returns the value of forwardTransformation

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

Returns the value of functionType

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

Returns the value of geometry

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

Returns the value of geometryDefinition

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

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

Returns the value of interpolation

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

Returns the value of isActive

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

Returns the value of isLocal

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

Returns the listOfAdjacentDomains.

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

Returns the listOfAnalyticVolumes.

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

Returns the listOfCoordinateComponents.

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

Returns the listOfCSGNodes.

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

Returns the listOfCSGObjects.

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

Returns the listOfDomains.

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

Returns the listOfDomainTypes.

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

Returns the listOfGeometryDefinitions.

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

Returns the listOfGeometryDefinitions.

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

Returns the listOfInteriorPoints.

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

Returns the listOfOrdinalMappings.

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

Returns the listOfParametricObjects.

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

Returns the listOfSampledFields.

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

Returns the listOfSampledVolumes.

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

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

Returns the value of maxValue

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

Returns the value of minValue

getModel() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.spatial.SpatialConstants

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getNumSamples1() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of numSamples1

getNumSamples2() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of numSamples2

getNumSamples3() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of numSamples3

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

Returns the value of operationType

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

Returns the value of ordinal

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

Returns the value of ordinal

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

Returns the value of ordinal

getPackageName() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getParamType() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getParent() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getParent() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

Returns the value of ParametricObject.pointIndex.

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

Deprecated.

Returns the value of pointIndex

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

Returns the value of pointIndexLength.

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

Returns the value of polygonType

getPrefix() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

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

Returns the value of primitiveType

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

Returns the value of reverseTransformation

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

Returns the value of rotateAngleInRadians

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

Returns the value of rotateAxisX

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

Returns the value of rotateAxisY

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

Returns the value of rotateAxisZ

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

Returns the value of sampledField

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

Returns the value of sampledValue

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

Returns the value of SampledField.samples.

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

Returns the value of SampledField.samplesLength.

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

Returns the value of scaleX

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

Returns the value of scaleY

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

Returns the value of scaleZ

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

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

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

Returns the value of spatialDimension

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

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

getSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase

Returns the value of spatialId

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

Returns the value of ParametricGeometry.spatialPoints.

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

Returns the value of SpatialSymbolReference.spatialRef.

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

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

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

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

Returns the value of translateX

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

Returns the value of translateY

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

Returns the value of translateZ

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

Returns the value of type

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

Returns the value of type

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

Returns the value of unit

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

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

Returns the value of unitSize

getURI() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

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

Returns the value of value

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

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

H

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

hashCode() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

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

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

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

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

I

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

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

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

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Deprecated.

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Deprecated.

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

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

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

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

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

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

InterpolationKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

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

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

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

isRequired() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

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

Returns whether SpatialPoints.arrayData is set.

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

Returns whether arrayDataLength is set.

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

Returns whether boundaryDomainType is set

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

Returns whether boundaryMaximum is set

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

Returns whether boundaryMinimum is set

isSetCompartmentMapping() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

Returns whether compartmentMapping is set

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

Returns whether complementA is set

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

Returns whether complementB is set

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

Returns whether components is set

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

Returns whether componentsLength is set

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

Returns whether compression is set.

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

Returns whether compression is set

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

Returns whether compression is set.

isSetCoord1() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns whether coord1 is set

isSetCoord2() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns whether coord2 is set

isSetCoord3() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns whether coord3 is set

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

Returns whether coordinate is set

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

Deprecated.

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

Returns whether coordinateBoundary is set

isSetCoordinateReference1() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns whether coordinateReference1 is set

isSetCoordinateReference2() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns whether coordinateReference2 is set

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

Returns whether coordinateSystem is set

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

Returns whether csgNode is set

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

Returns whether csgNode is set

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

Returns whether csgObjectRef is set

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

Returns whether data is set

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

Returns whether dataType is set.

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

Returns whether dataType is set

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

Returns whether dataType is set.

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

Returns whether diffusionKind is set

isSetDomain1() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Returns whether domain1 is set

isSetDomain2() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Returns whether domain2 is set

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

Returns whether domainType is set

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

Returns whether domainType is set

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

Returns whether domainType is set

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

Returns whether domainType is set

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

Returns whether domain is set

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

Returns whether domainType is set

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

Returns whether forwardTransformation is set

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

Returns whether functionType is set

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

Returns whether geometry is set

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

Returns whether geometryDefinition is set

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

Returns whether interpolation is set

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

Returns whether isActive is set

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

Returns whether isLocal is set

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

Returns true, if listOfAdjacentDomains contains at least one element.

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

Returns true, if listOfAnalyticVolumes contains at least one element.

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

Returns true, if listOfCoordinateComponents contains at least one element.

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

Returns true, if listOfCSGNodes contains at least one element.

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

Returns true, if listOfCSGObjects contains at least one element.

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

Returns true, if listOfDomains contains at least one element.

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

Returns true, if listOfDomainTypes contains at least one element.

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

Returns true, if listOfGeometryDefinitions contains at least one element.

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

Returns true, if listOfGeometryDefinitions contains at least one element.

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

Returns true, if listOfInteriorPoints contains at least one element.

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

Returns true, if listOfOrdinalMappings contains at least one element.

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

Returns true, if listOfParametricObjects contains at least one element.

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

Returns true, if listOfSampledFields contains at least one element.

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

Returns true, if listOfSampledVolumes contains at least one element.

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

Returns whether maxValue is set

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

Returns whether minValue is set

isSetNumSamples1() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns whether numSamples1 is set

isSetNumSamples2() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns whether numSamples2 is set

isSetNumSamples3() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns whether numSamples3 is set

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

Returns whether operationType is set

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

Returns whether ordinal is set

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

Returns whether ordinal is set

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

Returns whether ordinal is set

isSetParamType() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

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

Returns whether ParametricObject.pointIndex is set.

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

Deprecated.

Returns whether pointIndex is set

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

Returns whether pointIndexLength is set.

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

Returns whether polygonType is set

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

Returns whether primitiveType is set

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

Returns whether reverseTransformation is set

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

Returns whether rotateAngleInRadians is set

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

Returns whether rotateAxisX is set

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

Returns whether rotateAxisY is set

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

Returns whether rotateAxisZ is set

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

Returns whether sampledField is set

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

Returns whether sampledValue is set

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

Returns whether SampledField.samples is set.

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

Returns whether SampledField.samplesLength is set.

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

Returns whether scaleX is set

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

Returns whether scaleY is set

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

Returns whether scaleZ is set

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

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

Returns whether spatialDimension is set

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

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

isSetSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase

Returns whether spatialId is set

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

Returns whether ParametricGeometry.spatialPoints is set.

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

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

Returns whether SpatialSymbolReference.spatialRef is set.

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

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

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

Returns whether translateX is set

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

Returns whether translateY is set

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

Returns whether translateZ is set

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

Returns whether type is set

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

Returns whether type is set

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

Returns whether unit is set

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

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

Returns whether unitSize is set

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

Returns whether value is set

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

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

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

L

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

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

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

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

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

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

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

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

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

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

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

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

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

M

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

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

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

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

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

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

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

N

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

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

The latest namespace URI of this parser, this value can change between releases.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURIrequired - Static variable in class org.sbml.jsbml.xml.parsers.SpatialParser

The name space of required elements.

numSamples1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

numSamples2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

numSamples3 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

O

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

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

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

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

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

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

org.sbml.jsbml.ext.spatial - package org.sbml.jsbml.ext.spatial

Provides classes for the Spatial Geometries and Processes package.

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

P

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

PolygonKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

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

PrimitiveKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

R

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.Boundary

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference

Deprecated.

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGScale

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.Domain

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.DomainType

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.PolygonObject

Deprecated.

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SampledField

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

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

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

Removes an element from the listOfAdjacentDomains.

removeAdjacentDomain(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Removes an element from the listOfAdjacentDomains at the given index.

removeAdjacentDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

Removes an element from the listOfAnalyticVolumes.

removeAnalyticVolume(int) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

Removes an element from the listOfAnalyticVolumes at the given index.

removeAnalyticVolume(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

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

Removes an element from the listOfCoordinateComponents.

removeCoordinateComponent(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Removes an element from the listOfCoordinateComponents at the given index.

removeCoordinateComponent(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

Removes an element from the listOfCSGNodes.

removeCSGNode(int) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Removes an element from the listOfCSGNodes at the given index.

removeCSGNode(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

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

Removes an element from the listOfCSGObjects.

removeCSGObject(int) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Removes an element from the listOfCSGObjects at the given index.

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

Removes an element from the listOfDomains.

removeDomain(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Removes an element from the listOfDomains at the given index.

removeDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

Removes an element from the listOfDomainTypes.

removeDomainType(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Removes an element from the listOfDomainTypes at the given index.

removeDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

Removes an element from the listOfGeometryDefinitions.

removeGeometryDefinition(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Removes an element from the listOfGeometryDefinitions at the given index.

removeGeometryDefinition(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

Removes an element from the listOfGeometryDefinitions.

removeGeometryDefinition(int) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Removes an element from the listOfGeometryDefinitions at the given index.

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

Removes an element from the listOfInteriorPoints.

removeInteriorPoint(int) - Method in class org.sbml.jsbml.ext.spatial.Domain

Removes an element from the listOfInteriorPoints at the given index.

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

Removes an element from the listOfOrdinalMappings.

removeOrdinalMapping(int) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Removes an element from the listOfOrdinalMappings at the given index.

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

Removes an element from the listOfParametricObjects.

removeParametricObject(int) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Removes an element from the listOfParametricObjects at the given index.

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

Removes an element from the listOfSampledFields.

removeSampledField(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Removes an element from the listOfSampledFields at the given index.

removeSampledField(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

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

Removes an element from the listOfSampledVolumes.

removeSampledVolume(int) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Removes an element from the listOfSampledVolumes at the given index.

removeSampledVolume(String) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

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

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

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

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

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

S

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setArrayData(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Sets the value of arrayData

setArrayDataLength(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Sets the value of arrayDataLength

setBoundaryDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Sets the value of boundaryDomainType

setBoundaryMaximum(Boundary) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Sets the value of boundaryMaximum

setBoundaryMinimum(Boundary) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Sets the value of boundaryMinimum

setCompartmentMapping(CompartmentMapping) - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

Sets the value of compartmentMapping

setComplementA(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Sets the value of complementA

setComplementB(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Sets the value of complementB

setComponents(Double...) - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

Sets the value of components

setCompression(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of compression

setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of compression

setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of compression

setCompression(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Sets the value of compression

setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Sets the value of compression

setCoord1(double) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Sets the value of coord1

setCoord2(double) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Sets the value of coord2

setCoord3(double) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Sets the value of coord3

setCoordinate(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

Sets the value of coordinate

setCoordinate(String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference

Deprecated.

setCoordinate(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference

Deprecated.

setCoordinateBoundary(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Sets the value of coordinateBoundary

setCoordinateReference1(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Sets the value of coordinateReference1

setCoordinateReference2(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Sets the value of coordinateReference2

setCoordinateSystem(GeometryKind) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the value of coordinateSystem

setCSGNode(CSGNode) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

Sets the value of csgNode

setCSGNode(CSGNode) - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

Sets the value of csgNode

setCsgObjectRef(String) - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

Sets the value of csgObjectRef

setData(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of data

setData(XMLNode) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of data

setDataType(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of dataType

setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of dataType

setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of dataType

setDataType(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Sets the value of dataType

setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Sets the value of dataType

setDiffusionKind(DiffusionKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Sets the value of diffusionKind

setDomain1(String) - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

setDomain2(String) - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Sets the value of domain2

setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

Sets the value of domainType

setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

Sets the value of domainType

setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

Sets the value of domainType

setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.Domain

Sets the value of domainType

setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of domain

setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Sets the value of domainType

setForwardTransformation(TransformationComponent) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

Sets the value of forwardTransformation

setFunctionType(FunctionKind) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

Sets the value of functionType

setGeometry(Geometry) - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

Sets the value of geometry

setGeometryDefinition(String) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

Sets the value of geometryDefinition

setInterpolation(InterpolationKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of interpolation

setIsActive(boolean) - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition

Sets the value of isActive

setIsLocal(boolean) - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

Sets the value of isLocal

setListOfAdjacentDomains(ListOf<AdjacentDomains>) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the given ListOf<AdjacentDomain>.

setListOfAnalyticVolumes(ListOf<AnalyticVolume>) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

Sets the given ListOf<AnalyticVolume>.

setListOfCoordinateComponents(ListOf<CoordinateComponent>) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the given ListOf<CoordinateComponent>.

setListOfCSGNodes(ListOf<CSGNode>) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Sets the given ListOf<CSGNode>.

setListOfCSGObjects(ListOf<CSGObject>) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Sets the given ListOf<CSGObject>.

setListOfDomains(ListOf<Domain>) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the given ListOf<Domain>.

setListOfDomainTypes(ListOf<DomainType>) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the given ListOf<DomainType>.

setListOfGeometryDefinitions(ListOf<GeometryDefinition>) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the given ListOf<GeometryDefinition>.

setListOfGeometryDefinitions(ListOf<GeometryDefinition>) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Sets the given ListOf<GeometryDefinition>.

setListOfInteriorPoints(ListOf<InteriorPoint>) - Method in class org.sbml.jsbml.ext.spatial.Domain

Sets the given ListOf<InteriorPoint>.

setListOfOrdinalMappings(ListOf<OrdinalMapping>) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Sets the given ListOf<OrdinalMapping>.

setListOfParametricObjects(ListOf<ParametricObject>) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Sets the given ListOf<ParametricObject>.

setListOfSampledFields(ListOf<SampledField>) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Sets the given ListOf<SampledField>.

setListOfSampledVolumes(ListOf<SampledVolume>) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Sets the given ListOf<SampledVolume>.

setMaxValue(double) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Sets the value of maxValue

setMinValue(double) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Sets the value of minValue

setNumSamples1(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of numSamples1

setNumSamples2(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of numSamples2

setNumSamples3(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of numSamples3

SetOperation - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

setOperationType(SetOperation) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Sets the value of operationType

setOrdinal(int) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

Sets the value of ordinal

setOrdinal(int) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

Sets the value of ordinal

setOrdinal(int) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

Sets the value of ordinal

setParamType(ParameterType) - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

setPointIndex(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of pointIndex

setPointIndex(Integer...) - Method in class org.sbml.jsbml.ext.spatial.PolygonObject

Deprecated.

Sets the value of pointIndex

setPointIndexLength(int) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of pointIndexLength

setPolygonType(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of polygonType

setPolygonType(PolygonKind) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Sets the value of polygonType

setPrimitiveType(String) - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

Sets the value of primitiveType

setPrimitiveType(PrimitiveKind) - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

Sets the value of primitiveType

setReverseTransformation(TransformationComponent) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

Sets the value of reverseTransformation

setRotateAngleInRadians(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Sets the value of rotateAngleInRadians

setRotateAxisX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Sets the value of rotateAxisX

setRotateAxisY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Sets the value of rotateAxisY

setRotateAxisZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Sets the value of rotateAxisZ

setSampledField(String) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Sets the value of sampledField

setSampledValue(double) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Sets the value of sampledValue

setSamples(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of samples

setSamplesLength(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of samplesLength

setSamplesLength(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField

Sets the value of samplesLength

setScaleX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGScale

Sets the value of scaleX

setScaleY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGScale

Sets the value of scaleY

setScaleZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGScale

Sets the value of scaleZ

setSpatial(boolean) - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

setSpatialDimensions(int) - Method in class org.sbml.jsbml.ext.spatial.DomainType

Sets the value of spatialDimension

setSpatialId(String) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

setSpatialId(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

setSpatialId(String) - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase

Sets the value of spatialId

setSpatialPoints(SpatialPoints) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Sets the value of spatialPoints

setSpatialRef(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference

Sets the value of spatialRef

setSpeciesReference(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

setSpId(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

setTranslateX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Sets the value of translateX

setTranslateY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Sets the value of translateY

setTranslateZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Sets the value of translateZ

setType(BoundaryConditionKind) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Sets the value of type

setType(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

setType(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Sets the value of type

setUnits(String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Sets the value of unit

setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

setUnits(Unit) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

setUnitSize(double) - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

Sets the value of unitSize

setValue(double) - Method in class org.sbml.jsbml.ext.spatial.Boundary

Sets the value of value

setVariable(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

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

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

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

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

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

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

Contains some constants related to the spatial package.

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

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

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

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

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

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

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

SpatialNamedSBase - Interface in org.sbml.jsbml.ext.spatial

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

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

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

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

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

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

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

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

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

Creates an SpatialPoints instance

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

Creates a SpatialPoints instance with a level and version.

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

Clone constructor

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

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

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

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

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

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

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

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

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

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

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

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

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

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

T

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

toString() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

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

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

toString() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

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

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

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

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

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

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

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

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

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

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

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

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

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

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

U

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

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

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

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

Unsets the variable arrayData.

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

Unsets the variable arrayDataLength.

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

Unsets the variable boundaryDomainType

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

Unsets the variable boundaryMaximum

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

Unsets the variable boundaryMinimum

unsetCompartmentMapping() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

Unsets the variable compartmentMapping

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

Unsets the variable complementA

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

Unsets the variable complementB

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

Unsets the variable components

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

Unsets the variable compression.

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

Unsets the variable compression

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

Unsets the variable compression.

unsetCoord1() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Unsets the variable coord1

unsetCoord2() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Unsets the variable coord2

unsetCoord3() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Unsets the variable coord3

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

Unsets the variable coordinate

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

Unsets the variable coordinateBoundary

unsetCoordinateReference1() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Unsets the variable coordinateReference1

unsetCoordinateReference2() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Unsets the variable coordinateReference2

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

Unsets the variable coordinateSystem

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

Unsets the variable csgNode

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

Unsets the variable csgNode

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

Unsets the variable csgObjectRef

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

Unsets the variable data

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

Unsets the variable dataType.

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

Unsets the variable dataType

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

Unsets the variable dataType.

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

Unsets the variable diffusionKind

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

Unsets the variable domain

unsetDomain1() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Unsets the variable domain1

unsetDomain2() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Unsets the variable domain2

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

Unsets the variable domainType

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

Unsets the variable domainType

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

Unsets the variable domainType

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

Unsets the variable domainType

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

Unsets the variable domainType

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

Unsets the variable forwardTransformation

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

Unsets the variable functionType

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

Unsets the variable geometry

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

Unsets the variable geometryDefinition

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

Unsets the variable interpolation

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

Unsets the variable isActive

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

Unsets the variable isLocal

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

Returns true, if listOfAdjacentDomains contain at least one element, otherwise false

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

Returns true, if listOfAnalyticVolumes contain at least one element, otherwise false

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

Returns true, if listOfCoordinateComponents contain at least one element, otherwise false

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

Returns true, if listOfCSGNodes contain at least one element, otherwise false

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

Returns true, if listOfCSGObjects contain at least one element, otherwise false

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

Returns true, if listOfDomains contain at least one element, otherwise false

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

Returns true, if listOfDomainTypes contain at least one element, otherwise false

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

Returns true, if listOfGeometryDefinitions contain at least one element, otherwise false

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

Returns true, if listOfGeometryDefinitions contain at least one element, otherwise false

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

Returns true, if listOfInteriorPoints contain at least one element, otherwise false

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

Returns true, if listOfOrdinalMappings contain at least one element, otherwise false

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

Returns true, if listOfParametricObjects contain at least one element, otherwise false

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

Returns true, if listOfSampledFields contain at least one element, otherwise false

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

Returns true, if listOfSampledVolumes contain at least one element, otherwise false

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

Unsets the variable maxValue

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

Unsets the variable minValue

unsetNumSamples1() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Unsets the variable numSamples1

unsetNumSamples2() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Unsets the variable numSamples2

unsetNumSamples3() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Unsets the variable numSamples3

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

Unsets the variable operationType

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

Unsets the variable ordinal

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

Unsets the variable ordinal

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

Unsets the variable ordinal

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

Unsets the variable pointIndex.

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

Deprecated.

Unsets the variable pointIndex

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

Unsets the variable pointIndexLength.

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

Unsets the variable polygonType

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

Unsets the variable primitiveType

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

Unsets the variable reverseTransformation

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

Unsets the variable rotateAngleInRadians

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

Unsets the variable rotateAxisX

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

Unsets the variable rotateAxisY

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

Unsets the variable rotateAxisZ

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

Unsets the variable sampledField

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

Unsets the variable sampledValue

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

Unsets the variable samples.

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

Unsets the variable samplesLength.

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

Unsets the variable scaleX

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

Unsets the variable scaleY

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

Unsets the variable scaleZ

unsetSpatialDimension() - Method in class org.sbml.jsbml.ext.spatial.DomainType

Unsets the variable spatialDimension

unsetSpatialId() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

unsetSpatialId() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

unsetSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase

Unsets the variable spatialId

unsetSpatialPoints() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Unsets the variable spatialPoints.

unsetSpatialRef() - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference

Unsets the variable spatialRef.

unsetTranslateX() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Unsets the variable translateX

unsetTranslateY() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Unsets the variable translateY

unsetTranslateZ() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Unsets the variable translateZ

unsetType() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Unsets the variable type

unsetType() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Unsets the variable type

unsetUnits() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Unsets the variable unit

unsetUnitSize() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

Unsets the variable unitSize

unsetValue() - Method in class org.sbml.jsbml.ext.spatial.Boundary

Unsets the variable value

V

value - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.BoundaryConditionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.CompressionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.CoordinateKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.DataKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.DiffusionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.FunctionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.GeometryKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.InterpolationKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.PolygonKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.PrimitiveKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.SetOperation

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.sbml.jsbml.ext.spatial.BoundaryConditionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.CompressionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.CoordinateKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.DataKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.DiffusionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.FunctionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.GeometryKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.InterpolationKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.PolygonKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.PrimitiveKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.SetOperation

Returns an array containing the constants of this enum type, in the order they are declared.

variable - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

W

writeCharacters(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.Boundary

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference

Deprecated.

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGScale

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.Domain

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.DomainType

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.Geometry

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.PolygonObject

Deprecated.

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SampledField

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

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