Serialized Form (jsbml-spatial 1.1 API)

Package org.sbml.jsbml.ext.spatial
- Class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase extends org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -1814806955800042477L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialId
```
String spatialId
```
- Class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin extends org.sbml.jsbml.ext.AbstractSBasePlugin implements Serializable
  
  serialVersionUID:
  
  -75143209163226722L
- Class org.sbml.jsbml.ext.spatial.AdjacentDomains extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  1600690320824551145L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domain1
```
String domain1
```
    - domain2
```
String domain2
```
- Class org.sbml.jsbml.ext.spatial.AdvectionCoefficient extends ParameterType implements Serializable
  
  serialVersionUID:
  
  8982184068116596444L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - coordinate
```
CoordinateKind coordinate
```
- Class org.sbml.jsbml.ext.spatial.AnalyticGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -6680739495215471035L
  - Serialized Fields
    - listOfAnalyticVolumes
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfAnalyticVolumes
```
- Class org.sbml.jsbml.ext.spatial.AnalyticVolume extends org.sbml.jsbml.AbstractMathContainer implements Serializable
  
  serialVersionUID:
  
  1757917501241390228L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - value
```
Double value
```
- Class org.sbml.jsbml.ext.spatial.BoundaryCondition extends ParameterType implements Serializable
  
  serialVersionUID:
  
  -6986768113234565819L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - boundaryDomainType
```
String boundaryDomainType
```
    - coordinateBoundary
```
String coordinateBoundary
```
    - type
```
BoundaryConditionKind type
```
- Class org.sbml.jsbml.ext.spatial.CompartmentMapping extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -4623759168043277022L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - unitSize
```
Double unitSize
```
- Class org.sbml.jsbml.ext.spatial.CoordinateComponent extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -3561130269969678307L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - type
```
CoordinateKind type
```
    - boundaryMaximum
```
Boundary boundaryMaximum
```
    - boundaryMinimum
```
Boundary boundaryMinimum
```
    - unit
```
String unit
```
- Class org.sbml.jsbml.ext.spatial.CoordinateReference extends org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7651871640808157489L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      Deprecated.
      
      A Logger for this class.
    - coordinate
```
CoordinateKind coordinate
```
      Deprecated.
- Class org.sbml.jsbml.ext.spatial.CSGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -3162376343741365280L
  - Serialized Fields
    - listOfCSGObjects
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - ordinal
```
Integer ordinal
```
    - csgNode
```
CSGNode csgNode
```
- Class org.sbml.jsbml.ext.spatial.CSGPrimitive extends CSGNode implements Serializable
  
  serialVersionUID:
  
  -6783804853380306509L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - primitiveType
```
PrimitiveKind primitiveType
```
- Class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive extends CSGNode implements Serializable
  
  serialVersionUID:
  
  303742063326104808L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - csgObjectRef
```
String csgObjectRef
```
- Class org.sbml.jsbml.ext.spatial.CSGRotation extends CSGTransformation implements Serializable
  
  serialVersionUID:
  
  -4799604235135248586L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - scaleX
```
Double scaleX
```
    - scaleY
```
Double scaleY
```
    - scaleZ
```
Double scaleZ
```
- Class org.sbml.jsbml.ext.spatial.CSGSetOperator extends CSGNode implements Serializable
  
  serialVersionUID:
  
  3448308755493169761L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - operationType
```
SetOperation operationType
```
    - complementA
```
String complementA
```
    - complementB
```
String complementB
```
    - listOfCSGNodes
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
```
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
- Class org.sbml.jsbml.ext.spatial.Domain extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  7959434109047369076L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - domainType
```
String domainType
```
    - listOfInteriorPoints
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfInteriorPoints
```
- Class org.sbml.jsbml.ext.spatial.DomainType extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -1429902642364213170L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialDimensions
```
Integer spatialDimensions
```
- Class org.sbml.jsbml.ext.spatial.Geometry extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  9115597691155572976L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - listOfCoordinateComponents
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfCoordinateComponents
```
    - listOfDomainTypes
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfDomainTypes
```
    - listOfDomains
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfDomains
```
    - listOfAdjacentDomains
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfAdjacentDomains
```
    - listOfGeometryDefinitions
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfGeometryDefinitions
```
    - listOfSampledFields
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfSampledFields
```
    - coordinateSystem
```
GeometryKind coordinateSystem
```
- Class org.sbml.jsbml.ext.spatial.GeometryDefinition extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  211166389798247646L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - isActive
```
Boolean isActive
```
- Class org.sbml.jsbml.ext.spatial.InteriorPoint extends org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  5525511951071345435L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfGeometryDefinitions
```
    - listOfOrdinalMappings
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfOrdinalMappings
```
- Class org.sbml.jsbml.ext.spatial.OrdinalMapping extends org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -7174553771288567408L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - geometryDefinition
```
String geometryDefinition
```
    - ordinal
```
Integer ordinal
```
- Class org.sbml.jsbml.ext.spatial.ParameterType extends org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  1359841900912406174L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfParametricObjects
```
- Class org.sbml.jsbml.ext.spatial.ParametricObject extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8093810090391511545L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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 org.sbml.jsbml.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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
```
org.sbml.jsbml.xml.XMLNode data
```
- Class org.sbml.jsbml.ext.spatial.SampledFieldGeometry extends GeometryDefinition implements Serializable
  
  serialVersionUID:
  
  -1541677165317653439L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - listOfSampledVolumes
```
org.sbml.jsbml.ListOf<T extends org.sbml.jsbml.SBase> listOfSampledVolumes
```
    - sampledField
```
String sampledField
```
- Class org.sbml.jsbml.ext.spatial.SampledVolume extends AbstractSpatialNamedSBase implements Serializable
  
  serialVersionUID:
  
  -8253664900275697978L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
```
HashMap<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 org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -3467717442431545263L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - 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
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - spatialRef
```
String spatialRef
```
- Class org.sbml.jsbml.ext.spatial.TransformationComponent extends org.sbml.jsbml.AbstractSBase implements Serializable
  
  serialVersionUID:
  
  -2905551100912455549L
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
      A Logger for this class.
    - components
```
Double[] components
```
    - componentsLength
```
Integer componentsLength
```

Serialized Form

Package org.sbml.jsbml.ext.spatial

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

Serialized Fields

logger

spatialId

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

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

Serialized Fields

logger

domain1

domain2

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

Serialized Fields

logger

coordinate

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

Serialized Fields

listOfAnalyticVolumes

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

Serialized Fields

logger

spatialId

domainType

functionType

ordinal

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

Serialized Fields

logger

value

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

Serialized Fields

logger

boundaryDomainType

coordinateBoundary

type

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

Serialized Fields

logger

domainType

unitSize

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

Serialized Fields

logger

type

boundaryMaximum

boundaryMinimum

unit

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

Serialized Fields

logger

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

logger

domainType

ordinal

csgNode

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

Serialized Fields

logger

primitiveType

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

Serialized Fields

logger

csgObjectRef

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

Serialized Fields

logger

rotateAxisX

rotateAxisY

rotateAxisZ