Serialized Form (jsbml-spatial 1.2-beta1 API)

Package org.sbml.jsbml.ext.spatial
- Class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -1814806955800042477L
  - Serialized Fields
    - spatialId
```
String spatialId
```
- Class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin extends AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -75143209163226722L
- Class org.sbml.jsbml.ext.spatial.AdjacentDomains extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  1600690320824551145L
  - Serialized Fields
    - domain1
```
String domain1
```
    - domain2
```
String domain2
```
- Class org.sbml.jsbml.ext.spatial.AdvectionCoefficient extends ParameterType implements Serializable
  
  serialVersionUID:
  
  8982184068116596444L
  - Serialized Fields
    - coordinate
```
CoordinateKind coordinate
```
- Class org.sbml.jsbml.ext.spatial.AnalyticGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -6680739495215471035L
  - Serialized Fields
    - listOfAnalyticVolumes
```
ListOf<T extends SBase> listOfAnalyticVolumes
```
- Class org.sbml.jsbml.ext.spatial.AnalyticVolume extends AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  1757917501241390228L
  - Serialized Fields
    - spatialId
```
String spatialId
```
    - domainType
```
String domainType
```
    - functionType
```
FunctionKind functionType
```
    - ordinal
```
Integer ordinal
```
- Class org.sbml.jsbml.ext.spatial.Boundary extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -5283759970799753982L
  - Serialized Fields
    - value
```
Double value
```
- Class org.sbml.jsbml.ext.spatial.BoundaryCondition extends ParameterType implements Serializable
  
  serialVersionUID:
  
  -6986768113234565819L
  - Serialized Fields
    - boundaryDomainType
```
String boundaryDomainType
```
    - coordinateBoundary
```
String coordinateBoundary
```
    - type
```
BoundaryConditionKind type
```
- Class org.sbml.jsbml.ext.spatial.CompartmentMapping extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -4623759168043277022L
  - Serialized Fields
    - domainType
```
String domainType
```
    - unitSize
```
Double unitSize
```
- Class org.sbml.jsbml.ext.spatial.CoordinateComponent extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -3561130269969678307L
  - Serialized Fields
    - type
```
CoordinateKind type
```
    - boundaryMaximum
```
Boundary boundaryMaximum
```
    - boundaryMinimum
```
Boundary boundaryMinimum
```
    - unit
```
String unit
```
- Class org.sbml.jsbml.ext.spatial.CoordinateReference extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7651871640808157489L
  - Serialized Fields
    - coordinate
```
CoordinateKind coordinate
```
      Deprecated.
- Class org.sbml.jsbml.ext.spatial.CSGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -3162376343741365280L
  - Serialized Fields
    - listOfCSGObjects
```
ListOf<T extends SBase> listOfCSGObjects
```
- Class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  1247170964151052926L
  - Serialized Fields
    - forwardTransformation
```
TransformationComponent forwardTransformation
```
    - reverseTransformation
```
TransformationComponent reverseTransformation
```
- Class org.sbml.jsbml.ext.spatial.CSGNode extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  5499821335582691196L
- Class org.sbml.jsbml.ext.spatial.CSGObject extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  1385748485171648666L
  - Serialized Fields
    - domainType
```
String domainType
```
    - ordinal
```
Integer ordinal
```
    - csgNode
```
CSGNode csgNode
```
- Class org.sbml.jsbml.ext.spatial.CSGPrimitive extends CSGNode implements Serializable
  
  serialVersionUID:
  
  -6783804853380306509L
  - Serialized Fields
    - primitiveType
```
PrimitiveKind primitiveType
```
- Class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive extends CSGNode implements Serializable
  
  serialVersionUID:
  
  303742063326104808L
  - Serialized Fields
    - csgObjectRef
```
String csgObjectRef
```
- Class org.sbml.jsbml.ext.spatial.CSGRotation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  -4799604235135248586L
  - Serialized Fields
    - rotateAxisX
```
Double rotateAxisX
```
    - rotateAxisY
```
Double rotateAxisY
```
    - rotateAxisZ
```
Double rotateAxisZ
```
    - rotateAngleInRadians
```
Double rotateAngleInRadians
```
- Class org.sbml.jsbml.ext.spatial.CSGScale extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  7021488698800177528L
  - Serialized Fields
    - scaleX
```
Double scaleX
```
    - scaleY
```
Double scaleY
```
    - scaleZ
```
Double scaleZ
```
- Class org.sbml.jsbml.ext.spatial.CSGSetOperator extends CSGNode implements Serializable
  
  serialVersionUID:
  
  3448308755493169761L
  - Serialized Fields
    - operationType
```
SetOperation operationType
```
    - complementA
```
String complementA
```
    - complementB
```
String complementB
```
    - listOfCSGNodes
```
ListOf<T extends SBase> listOfCSGNodes
```
- Class org.sbml.jsbml.ext.spatial.CSGTransformation extends CSGNode implements Serializable
  
  serialVersionUID:
  
  5388780141573233538L
  - Serialized Fields
    - csgNode
```
CSGNode csgNode
```
- Class org.sbml.jsbml.ext.spatial.CSGTranslation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  7030963917812170311L
  - Serialized Fields
    - translateX
```
Double translateX
```
    - translateY
```
Double translateY
```
    - translateZ
```
Double translateZ
```
- Class org.sbml.jsbml.ext.spatial.DiffusionCoefficient extends ParameterType implements Serializable
  
  serialVersionUID:
  
  1233063375698575897L
  - Serialized Fields
    - diffusionKind
```
DiffusionKind diffusionKind
```
    - coordinateReference1
```
CoordinateKind coordinateReference1
```
    - coordinateReference2
```
CoordinateKind coordinateReference2
```
- Class org.sbml.jsbml.ext.spatial.Domain extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  7959434109047369076L
  - Serialized Fields
    - domainType
```
String domainType
```
    - listOfInteriorPoints
```
ListOf<T extends SBase> listOfInteriorPoints
```
- Class org.sbml.jsbml.ext.spatial.DomainType extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -1429902642364213170L
  - Serialized Fields
    - spatialDimensions
```
Integer spatialDimensions
```
- Class org.sbml.jsbml.ext.spatial.Geometry extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  9115597691155572976L
  - Serialized Fields
    - listOfCoordinateComponents
```
ListOf<T extends SBase> listOfCoordinateComponents
```
    - listOfDomainTypes
```
ListOf<T extends SBase> listOfDomainTypes
```
    - listOfDomains
```
ListOf<T extends SBase> listOfDomains
```
    - listOfAdjacentDomains
```
ListOf<T extends SBase> listOfAdjacentDomains
```
    - listOfGeometryDefinitions
```
ListOf<T extends SBase> listOfGeometryDefinitions
```
    - listOfSampledFields
```
ListOf<T extends SBase> listOfSampledFields
```
    - coordinateSystem
```
GeometryKind coordinateSystem
```
- Class org.sbml.jsbml.ext.spatial.GeometryDefinition extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  211166389798247646L
  - Serialized Fields
    - isActive
```
Boolean isActive
```
- Class org.sbml.jsbml.ext.spatial.InteriorPoint extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  5525511951071345435L
  - Serialized Fields
    - coord1
```
Double coord1
```
    - coord2
```
Double coord2
```
    - coord3
```
Double coord3
```
- Class org.sbml.jsbml.ext.spatial.MixedGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -7544034155315224945L
  - Serialized Fields
    - listOfGeometryDefinitions
```
ListOf<T extends SBase> listOfGeometryDefinitions
```
    - listOfOrdinalMappings
```
ListOf<T extends SBase> listOfOrdinalMappings
```
- Class org.sbml.jsbml.ext.spatial.OrdinalMapping extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7174553771288567408L
  - Serialized Fields
    - geometryDefinition
```
String geometryDefinition
```
    - ordinal
```
Integer ordinal
```
- Class org.sbml.jsbml.ext.spatial.ParameterType extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  1359841900912406174L
  - Serialized Fields
    - spId
```
String spId
```
      Refers to SpIdRef in the documentation
    - speciesRef
```
String speciesRef
```
      Refers to species object that the parameter is associated with
- Class org.sbml.jsbml.ext.spatial.ParametricGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  5947368889263003716L
  - Serialized Fields
    - spatialPoints
```
SpatialPoints spatialPoints
```
    - listOfParametricObjects
```
ListOf<T extends SBase> listOfParametricObjects
```
- Class org.sbml.jsbml.ext.spatial.ParametricObject extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8093810090391511545L
  - Serialized Fields
    - polygonType
```
PolygonKind polygonType
```
    - domainType
```
String domainType
```
    - compression
```
CompressionKind compression
```
    - pointIndex
```
String pointIndex
```
    - pointIndexLength
```
Integer pointIndexLength
```
    - dataType
```
DataKind dataType
```
- Class org.sbml.jsbml.ext.spatial.PolygonObject extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -4878021358939009394L
  - Serialized Fields
    - pointIndex
```
Integer[] pointIndex
```
      Deprecated.
- Class org.sbml.jsbml.ext.spatial.SampledField extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  4345673559248715940L
  - Serialized Fields
    - numSamples1
```
Integer numSamples1
```
    - numSamples2
```
Integer numSamples2
```
    - numSamples3
```
Integer numSamples3
```
    - interpolation
```
InterpolationKind interpolation
```
    - compression
```
CompressionKind compression
```
    - samples
```
String samples
```
    - samplesLength
```
Integer samplesLength
```
    - dataType
```
DataKind dataType
```
    - data
```
XMLNode data
```
- Class org.sbml.jsbml.ext.spatial.SampledFieldGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -1541677165317653439L
  - Serialized Fields
    - listOfSampledVolumes
```
ListOf<T extends SBase> listOfSampledVolumes
```
    - sampledField
```
String sampledField
```
- Class org.sbml.jsbml.ext.spatial.SampledVolume extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8253664900275697978L
  - Serialized Fields
    - domainType
```
String domainType
```
    - sampledValue
```
Double sampledValue
```
    - minValue
```
Double minValue
```
    - maxValue
```
Double maxValue
```
- Class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  1363097365327594433L
  - Serialized Fields
    - compartmentMapping
```
CompartmentMapping compartmentMapping
```
- Class org.sbml.jsbml.ext.spatial.SpatialModelPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  8449591192464040411L
  - Serialized Fields
    - geometry
```
Geometry geometry
```
    - spatialIdMap
```
Map<K,V> spatialIdMap
```
- Class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -3766260342134204275L
  - Serialized Fields
    - param
```
ParameterType param
```
- Class org.sbml.jsbml.ext.spatial.SpatialPoints extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -3467717442431545263L
  - Serialized Fields
    - compression
```
CompressionKind compression
```
    - arrayDataLength
```
Integer arrayDataLength
```
    - dataType
```
DataKind dataType
```
    - arrayData
```
String arrayData
```
- Class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -2154884901226244123L
  - Serialized Fields
    - isLocal
```
Boolean isLocal
```
- Class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin extends AbstractSpatialSBasePlugin implements Serializable
  
  serialVersionUID:
  
  1636970127352490380L
  - Serialized Fields
    - spatial
```
Boolean spatial
```
- Class org.sbml.jsbml.ext.spatial.SpatialSymbolReference extends ParameterType implements Serializable
  
  serialVersionUID:
  
  -8906622500258765056L
  - Serialized Fields
    - spatialRef
```
String spatialRef
```
- Class org.sbml.jsbml.ext.spatial.TransformationComponent extends AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -2905551100912455549L
  - Serialized Fields
    - components
```
Double[] components
```
    - componentsLength
```
Integer componentsLength
```

Serialized Form

Package org.sbml.jsbml.ext.spatial

Class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase extends AbstractSBase implements Serializable

Serialized Fields

spatialId

Class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin extends AbstractSBasePlugin implements Serializable

Class org.sbml.jsbml.ext.spatial.AdjacentDomains extends AbstractSpatialNamedSBase implements Serializable

Serialized Fields

domain1

domain2

Class org.sbml.jsbml.ext.spatial.AdvectionCoefficient extends ParameterType implements Serializable

Serialized Fields

coordinate

Class org.sbml.jsbml.ext.spatial.AnalyticGeometry extends GeometryDefinition implements Serializable

Serialized Fields

listOfAnalyticVolumes

Class org.sbml.jsbml.ext.spatial.AnalyticVolume extends AbstractMathContainer implements Serializable

Serialized Fields

spatialId

domainType

functionType

ordinal

Class org.sbml.jsbml.ext.spatial.Boundary extends AbstractSpatialNamedSBase implements Serializable

Serialized Fields

value

Class org.sbml.jsbml.ext.spatial.BoundaryCondition extends ParameterType implements Serializable

Serialized Fields

boundaryDomainType

coordinateBoundary

type

Class org.sbml.jsbml.ext.spatial.CompartmentMapping extends AbstractSpatialNamedSBase implements Serializable

Serialized Fields

domainType

unitSize

Class org.sbml.jsbml.ext.spatial.CoordinateComponent extends AbstractSpatialNamedSBase implements Serializable

Serialized Fields

type

boundaryMaximum

boundaryMinimum

unit

Class org.sbml.jsbml.ext.spatial.CoordinateReference extends AbstractSBase implements Serializable

Serialized Fields

coordinate

Class org.sbml.jsbml.ext.spatial.CSGeometry extends GeometryDefinition implements Serializable

Serialized Fields

listOfCSGObjects

Class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation extends CSGTransformation implements Serializable

Serialized Fields

forwardTransformation

reverseTransformation

Class org.sbml.jsbml.ext.spatial.CSGNode extends AbstractSpatialNamedSBase implements Serializable

Class org.sbml.jsbml.ext.spatial.CSGObject extends AbstractSpatialNamedSBase implements Serializable

Serialized Fields

domainType

ordinal

csgNode

Class org.sbml.jsbml.ext.spatial.CSGPrimitive extends CSGNode implements Serializable

Serialized Fields

primitiveType

Class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive extends CSGNode implements Serializable

Serialized Fields

csgObjectRef

Class org.sbml.jsbml.ext.spatial.CSGRotation extends CSGTransformation implements Serializable

Serialized Fields

rotateAxisX

rotateAxisY

rotateAxisZ

rotateAngleInRadians

Class org.sbml.jsbml.ext.spatial.CSGScale extends CSGTransformation implements Serializable

Serialized Fields

scaleX

scaleY

scaleZ

Class org.sbml.jsbml.ext.spatial.CSGSetOperator extends CSGNode implements Serializable

Serialized Fields

operationType

complementA

complementB

listOfCSGNodes

Class org.sbml.jsbml.ext.spatial.CSGTransformation extends CSGNode implements Serializable