Geometry (jsbml-spatial 1.6.1 API)

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase
  - - org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
    - - org.sbml.jsbml.ext.spatial.Geometry

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, SpatialNamedSBase, NamedSBase, SBase, TreeNodeWithChangeSupport
```
public class Geometry
extends AbstractSpatialNamedSBase
```
Since:

1.0

Author:

Alex Thomas, Andreas Dräger, Piero Dalle Pezze

See Also:

Serialized Form

Field Summary
- Fields inherited from class org.sbml.jsbml.AbstractSBase
  ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName
- Fields inherited from class org.sbml.jsbml.AbstractTreeNode
  listOfListeners, parent, resourceBundle

Constructor Summary

Constructors
Constructor	Description
`Geometry()`
`Geometry(int level, int version)`
`Geometry(java.lang.String id, int level, int version)`
`Geometry(Geometry sb)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`addAdjacentDomain(AdjacentDomains adjacentDomains)`	Adds a new `AdjacentDomains` to the `listOfAdjacentDomains`.
`boolean`	`addCoordinateComponent(CoordinateComponent coordinateComponents)`	Adds a new `CoordinateComponent` to the listOfCoordinateComponents.
`boolean`	`addDomain(Domain domain)`	Adds a new `Domain` to the listOfDomains.
`boolean`	`addDomainType(DomainType domainType)`	Adds a new `DomainType` to the listOfDomainTypes.
`boolean`	`addGeometryDefinition(GeometryDefinition geometryDefinition)`	Adds a new `GeometryDefinition` to the listOfGeometryDefinitions.
`boolean`	`addSampledField(SampledField sampledField)`	Adds a new `SampledField` to the listOfSampledFields.
`Geometry`	`clone()`
`AdjacentDomains`	`createAdjacentDomain()`	Creates a new AdjacentDomain element and adds it to the ListOfAdjacentDomains list
`AdjacentDomains`	`createAdjacentDomain(java.lang.String id)`	Creates a new `AdjacentDomains` element and adds it to the `listOfAdjacentDomains` list
`AnalyticGeometry`	`createAnalyticGeometry()`
`AnalyticGeometry`	`createAnalyticGeometry(java.lang.String id)`
`CoordinateComponent`	`createCoordinateComponent()`	Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list
`CoordinateComponent`	`createCoordinateComponent(java.lang.String id)`	Creates a new `CoordinateComponent` element and adds it to the ListOfCoordinateComponents list
`CSGeometry`	`createCSGeometry()`
`CSGeometry`	`createCSGeometry(java.lang.String id)`
`Domain`	`createDomain()`	Creates a new Domain element and adds it to the ListOfDomains list
`Domain`	`createDomain(java.lang.String id)`	Creates a new `Domain` element and adds it to the ListOfDomains list
`DomainType`	`createDomainType()`	Creates a new DomainType element and adds it to the ListOfDomainTypes list
`DomainType`	`createDomainType(java.lang.String id)`	Creates a new `DomainType` element and adds it to the ListOfDomainTypes list
`MixedGeometry`	`createMixedGeometry()`
`MixedGeometry`	`createMixedGeometry(java.lang.String id)`	Creates a new `GeometryDefinition` element and adds it to the ListOfGeometryDefinitions list
`ParametricGeometry`	`createParametricGeometry()`
`ParametricGeometry`	`createParametricGeometry(java.lang.String id)`
`SampledField`	`createSampledField()`	Creates a new SampledField element and adds it to the ListOfSampledFields list
`SampledField`	`createSampledField(java.lang.String id)`	Creates a new `SampledField` element and adds it to the ListOfSampledFields list
`SampledFieldGeometry`	`createSampledFieldGeometry()`	Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
`SampledFieldGeometry`	`createSampledFieldGeometry(java.lang.String id)`	Creates a new `GeometryDefinition` element and adds it to the ListOfGeometryDefinitions list
`boolean`	`equals(java.lang.Object object)`
`AdjacentDomains`	`getAdjacentDomains(int i)`	Gets an element from the `listOfAdjacentDomains` at the given index.
`AdjacentDomains`	`getAdjacentDomains(java.lang.String id)`	Gets an element from the listOfAdjacentDomains, with the given id.
`int`	`getAdjacentDomainsCount()`	Returns the number of `AdjacentDomains`s in this `Geometry`.
`boolean`	`getAllowsChildren()`
`javax.swing.tree.TreeNode`	`getChildAt(int index)`
`int`	`getChildCount()`
`CoordinateComponent`	`getCoordinateComponent(int i)`	Gets an element from the `listOfCoordinateComponents` at the given index.
`CoordinateComponent`	`getCoordinateComponent(java.lang.String id)`	Gets an element from the listOfCoordinateComponents, with the given id.
`int`	`getCoordinateComponentCount()`	Returns the number of `CoordinateComponent`s in this `Geometry`.
`GeometryKind`	`getCoordinateSystem()`	Returns the value of coordinateSystem
`Domain`	`getDomain(int i)`	Gets an element from the `listOfDomains` at the given index.
`Domain`	`getDomain(java.lang.String id)`	Gets an element from the listOfDomains, with the given id.
`int`	`getDomainCount()`	Returns the number of `Domain`s in this `Geometry`.
`DomainType`	`getDomainType(int i)`	Gets an element from the `listOfDomainTypes` at the given index.
`DomainType`	`getDomainType(java.lang.String id)`	Gets an element from the listOfDomainTypes, with the given id.
`int`	`getDomainTypeCount()`	Returns the number of `DomainType`s in this `Geometry`.
`GeometryDefinition`	`getGeometryDefinition(int i)`	Gets an element from the `listOfGeometryDefinitions` at the given index.
`GeometryDefinition`	`getGeometryDefinition(java.lang.String id)`	Gets an element from the listOfGeometryDefinitions, with the given id.
`int`	`getGeometryDefinitionCount()`	Returns the number of `GeometryDefinition`s in this `Geometry`.
`ListOf<AdjacentDomains>`	`getListOfAdjacentDomains()`	Returns the listOfAdjacentDomains.
`ListOf<CoordinateComponent>`	`getListOfCoordinateComponents()`	Returns the listOfCoordinateComponents.
`ListOf<Domain>`	`getListOfDomains()`	Returns the listOfDomains.
`ListOf<DomainType>`	`getListOfDomainTypes()`	Returns the listOfDomainTypes.
`ListOf<GeometryDefinition>`	`getListOfGeometryDefinitions()`	Returns the listOfGeometryDefinitions.
`ListOf<SampledField>`	`getListOfSampledFields()`	Returns the listOfSampledFields.
`int`	`getNumAdjacentDomains()`	Returns the number of `AdjacentDomains`s in this `Geometry`.
`int`	`getNumCoordinateComponents()`	Returns the number of `CoordinateComponent`s in this `Geometry`.
`int`	`getNumDomains()`	Returns the number of `Domain`s in this `Geometry`.
`int`	`getNumDomainTypes()`	Returns the number of `DomainType`s in this `Geometry`.
`int`	`getNumGeometryDefinitions()`	Returns the number of `GeometryDefinition`s in this `Geometry`.
`int`	`getNumSampledFields()`	Returns the number of `SampledField`s in this `Geometry`.
`SampledField`	`getSampledField(int i)`	Gets an element from the `listOfSampledFields` at the given index.
`SampledField`	`getSampledField(java.lang.String id)`	Gets an element from the listOfSampledFields, with the given id.
`int`	`getSampledFieldCount()`	Returns the number of `SampledField`s in this `Geometry`.
`int`	`hashCode()`
`boolean`	`isSetCoordinateSystem()`	Returns whether coordinateSystem is set
`boolean`	`isSetListOfAdjacentDomains()`	Returns `true`, if listOfAdjacentDomains contains at least one element.
`boolean`	`isSetListOfCoordinateComponents()`	Returns `true`, if listOfCoordinateComponents contains at least one element.
`boolean`	`isSetListOfDomains()`	Returns `true`, if listOfDomains contains at least one element.
`boolean`	`isSetListOfDomainTypes()`	Returns `true`, if listOfDomainTypes contains at least one element.
`boolean`	`isSetListOfGeometryDefinitions()`	Returns `true`, if listOfGeometryDefinitions contains at least one element.
`boolean`	`isSetListOfSampledFields()`	Returns `true`, if listOfSampledFields contains at least one element.
`boolean`	`readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)`
`void`	`removeAdjacentDomain(int i)`	Removes an element from the listOfAdjacentDomains at the given index.
`void`	`removeAdjacentDomain(java.lang.String id)`
`boolean`	`removeAdjacentDomain(AdjacentDomains adjacentDomains)`	Removes an element from the listOfAdjacentDomains.
`void`	`removeCoordinateComponent(int i)`	Removes an element from the listOfCoordinateComponents at the given index.
`void`	`removeCoordinateComponent(java.lang.String id)`
`boolean`	`removeCoordinateComponent(CoordinateComponent coordinateComponents)`	Removes an element from the listOfCoordinateComponents.
`void`	`removeDomain(int i)`	Removes an element from the listOfDomains at the given index.
`void`	`removeDomain(java.lang.String id)`
`boolean`	`removeDomain(Domain domain)`	Removes an element from the listOfDomains.
`void`	`removeDomainType(int i)`	Removes an element from the listOfDomainTypes at the given index.
`void`	`removeDomainType(java.lang.String id)`
`boolean`	`removeDomainType(DomainType domainType)`	Removes an element from the listOfDomainTypes.
`void`	`removeGeometryDefinition(int i)`	Removes an element from the listOfGeometryDefinitions at the given index.
`void`	`removeGeometryDefinition(java.lang.String id)`
`boolean`	`removeGeometryDefinition(GeometryDefinition geometryDefinition)`	Removes an element from the listOfGeometryDefinitions.
`void`	`removeSampledField(int i)`	Removes an element from the listOfSampledFields at the given index.
`void`	`removeSampledField(java.lang.String id)`
`boolean`	`removeSampledField(SampledField sampledField)`	Removes an element from the listOfSampledFields.
`void`	`setCoordinateSystem(GeometryKind coordinateSystem)`	Sets the value of coordinateSystem
`void`	`setListOfAdjacentDomains(ListOf<AdjacentDomains> listOfAdjacentDomains)`	Sets the given `ListOf<AdjacentDomain>`.
`void`	`setListOfCoordinateComponents(ListOf<CoordinateComponent> listOfCoordinateComponents)`	Sets the given `ListOf<CoordinateComponent>`.
`void`	`setListOfDomains(ListOf<Domain> listOfDomains)`	Sets the given `ListOf<Domain>`.
`void`	`setListOfDomainTypes(ListOf<DomainType> listOfDomainTypes)`	Sets the given `ListOf<DomainType>`.
`void`	`setListOfGeometryDefinitions(ListOf<GeometryDefinition> listOfGeometryDefinitions)`	Sets the given `ListOf<GeometryDefinition>`.
`void`	`setListOfSampledFields(ListOf<SampledField> listOfSampledFields)`	Sets the given `ListOf<SampledField>`.
`boolean`	`unsetCoordinateSystem()`	Unsets the variable coordinateSystem
`boolean`	`unsetListOfAdjacentDomains()`	Returns `true`, if listOfAdjacentDomains contain at least one element, otherwise `false`
`boolean`	`unsetListOfCoordinateComponents()`	Returns `true`, if listOfCoordinateComponents contain at least one element, otherwise `false`
`boolean`	`unsetListOfDomains()`	Returns `true`, if listOfDomains contain at least one element, otherwise `false`
`boolean`	`unsetListOfDomainTypes()`	Returns `true`, if listOfDomainTypes contain at least one element, otherwise `false`
`boolean`	`unsetListOfGeometryDefinitions()`	Returns `true`, if listOfGeometryDefinitions contain at least one element, otherwise `false`
`boolean`	`unsetListOfSampledFields()`	Returns `true`, if listOfSampledFields contain at least one element, otherwise `false`
`java.util.Map<java.lang.String,java.lang.String>`	`writeXMLAttributes()`

Methods inherited from class org.sbml.jsbml.AbstractSBase
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
getSpatialId, initDefaults, isSetSpatialId, setSpatialId, unsetSpatialId

Methods inherited from interface org.sbml.jsbml.NamedSBase
getId, getName, isIdMandatory, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface javax.swing.tree.TreeNode
children, getIndex, getParent, isLeaf

- Constructor Detail
  - Geometry
```
public Geometry()
```
  - Geometry
```
public Geometry(Geometry sb)
```
    Parameters:
    
    sb -
  - Geometry
```
public Geometry(java.lang.String id,
                int level,
                int version)
```
    Parameters:
    
    id -
    
    level -
    
    version -
  - Geometry
```
public Geometry(int level,
                int version)
```
    Parameters:
    
    level -
    
    version -
- Method Detail
  - clone
```
public Geometry clone()
```
    Specified by:
    
    clone in interface SBase
    
    Specified by:
    
    clone in class AbstractSpatialNamedSBase
  - equals
```
public boolean equals(java.lang.Object object)
```
    Specified by:
    
    equals in interface SBase
    
    Overrides:
    
    equals in class AbstractSpatialNamedSBase
  - getCoordinateSystem
```
public GeometryKind getCoordinateSystem()
```
    Returns the value of coordinateSystem
    
    Returns:
    
    the value of coordinateSystem
  - isSetCoordinateSystem
```
public boolean isSetCoordinateSystem()
```
    Returns whether coordinateSystem is set
    
    Returns:
    
    whether coordinateSystem is set
  - setCoordinateSystem
```
public void setCoordinateSystem(GeometryKind coordinateSystem)
```
    Sets the value of coordinateSystem
    
    Parameters:
    
    coordinateSystem -
  - unsetCoordinateSystem
```
public boolean unsetCoordinateSystem()
```
    Unsets the variable coordinateSystem
    
    Returns:
    
    true, if coordinateSystem was set before, otherwise false
  - isSetListOfSampledFields
```
public boolean isSetListOfSampledFields()
```
    Returns true, if listOfSampledFields contains at least one element.
    
    Returns:
    
    true, if listOfSampledFields contains at least one element, otherwise false
  - getListOfSampledFields
```
public ListOf<SampledField> getListOfSampledFields()
```
    Returns the listOfSampledFields. Creates it if it is not already existing.
    
    Returns:
    
    the listOfSampledFields
  - setListOfSampledFields
```
public void setListOfSampledFields(ListOf<SampledField> listOfSampledFields)
```
    Sets the given ListOf<SampledField>. If listOfSampledFields was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfSampledFields -
  - unsetListOfSampledFields
```
public boolean unsetListOfSampledFields()
```
    Returns true, if listOfSampledFields contain at least one element, otherwise false
    
    Returns:
    
    true, if listOfSampledFields contain at least one element, otherwise false
  - addSampledField
```
public boolean addSampledField(SampledField sampledField)
```
    Adds a new SampledField to the listOfSampledFields.
    The listOfSampledFields is initialized if necessary.
    
    Parameters:
    
    sampledField - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - removeSampledField
```
public boolean removeSampledField(SampledField sampledField)
```
    Removes an element from the listOfSampledFields.
    
    Parameters:
    
    sampledField - the element to be removed from the list
    
    Returns:
    
    true if the list contained the specified element
    
    See Also:
    
    List.remove(Object)
  - removeSampledField
```
public void removeSampledField(int i)
```
    Removes an element from the listOfSampledFields at the given index.
    
    Parameters:
    
    i - the index where to remove the SampledField
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeSampledField
```
public void removeSampledField(java.lang.String id)
```
    Parameters:
    
    id -
  - createSampledField
```
public SampledField createSampledField()
```
    Creates a new SampledField element and adds it to the ListOfSampledFields list
    
    Returns:
  - createSampledField
```
public SampledField createSampledField(java.lang.String id)
```
    Creates a new SampledField element and adds it to the ListOfSampledFields list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new SampledField element
  - getSampledField
```
public SampledField getSampledField(int i)
```
    Gets an element from the listOfSampledFields at the given index.
    
    Parameters:
    
    i - the index of the SampledField element to get.
    
    Returns:
    
    an element from the listOfSampledFields at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getSampledField
```
public SampledField getSampledField(java.lang.String id)
```
    Gets an element from the listOfSampledFields, with the given id.
    
    Parameters:
    
    id - the id of the SampledField element to get.
    
    Returns:
    
    an element from the listOfSampledFields with the given id or null.
  - getSampledFieldCount
```
public int getSampledFieldCount()
```
    Returns the number of SampledFields in this Geometry.
    
    Returns:
    
    the number of SampledFields in this Geometry.
  - getNumSampledFields
```
public int getNumSampledFields()
```
    Returns the number of SampledFields in this Geometry.
    
    Returns:
    
    the number of SampledFields in this Geometry.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getSampledFieldCount()
  - isSetListOfGeometryDefinitions
```
public boolean isSetListOfGeometryDefinitions()
```
    Returns true, if listOfGeometryDefinitions contains at least one element.
    
    Returns:
    
    true, if listOfGeometryDefinitions contains at least one element, otherwise false
  - getListOfGeometryDefinitions
```
public ListOf<GeometryDefinition> getListOfGeometryDefinitions()
```
    Returns the listOfGeometryDefinitions. Creates it if it is not already existing.
    
    Returns:
    
    the listOfGeometryDefinitions
  - setListOfGeometryDefinitions
```
public void setListOfGeometryDefinitions(ListOf<GeometryDefinition> listOfGeometryDefinitions)
```
    Sets the given ListOf<GeometryDefinition>. If listOfGeometryDefinitions was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfGeometryDefinitions -
  - unsetListOfGeometryDefinitions
```
public boolean unsetListOfGeometryDefinitions()
```
    Returns true, if listOfGeometryDefinitions contain at least one element, otherwise false
    
    Returns:
    
    true, if listOfGeometryDefinitions contain at least one element, otherwise false
  - addGeometryDefinition
```
public boolean addGeometryDefinition(GeometryDefinition geometryDefinition)
```
    Adds a new GeometryDefinition to the listOfGeometryDefinitions.
    The listOfGeometryDefinitions is initialized if necessary.
    
    Parameters:
    
    geometryDefinition - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - removeGeometryDefinition
```
public boolean removeGeometryDefinition(GeometryDefinition geometryDefinition)
```
    Removes an element from the listOfGeometryDefinitions.
    
    Parameters:
    
    geometryDefinition - the element to be removed from the list
    
    Returns:
    
    true if the list contained the specified element
    
    See Also:
    
    List.remove(Object)
  - removeGeometryDefinition
```
public void removeGeometryDefinition(int i)
```
    Removes an element from the listOfGeometryDefinitions at the given index.
    
    Parameters:
    
    i - the index where to remove the GeometryDefinition
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeGeometryDefinition
```
public void removeGeometryDefinition(java.lang.String id)
```
    Parameters:
    
    id -
  - createSampledFieldGeometry
```
public SampledFieldGeometry createSampledFieldGeometry()
```
    Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
    
    Returns:
  - createAnalyticGeometry
```
public AnalyticGeometry createAnalyticGeometry()
```
    Returns:
  - createCSGeometry
```
public CSGeometry createCSGeometry()
```
    Returns:
  - createParametricGeometry
```
public ParametricGeometry createParametricGeometry()
```
    Returns:
  - createMixedGeometry
```
public MixedGeometry createMixedGeometry()
```
    Returns:
  - createMixedGeometry
```
public MixedGeometry createMixedGeometry(java.lang.String id)
```
    Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new GeometryDefinition element
  - createSampledFieldGeometry
```
public SampledFieldGeometry createSampledFieldGeometry(java.lang.String id)
```
    Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new GeometryDefinition element
  - createAnalyticGeometry
```
public AnalyticGeometry createAnalyticGeometry(java.lang.String id)
```
    Parameters:
    
    id -
    
    Returns:
  - createCSGeometry
```
public CSGeometry createCSGeometry(java.lang.String id)
```
    Parameters:
    
    id -
    
    Returns:
  - createParametricGeometry
```
public ParametricGeometry createParametricGeometry(java.lang.String id)
```
    Parameters:
    
    id -
    
    Returns:
  - getGeometryDefinition
```
public GeometryDefinition getGeometryDefinition(int i)
```
    Gets an element from the listOfGeometryDefinitions at the given index.
    
    Parameters:
    
    i - the index of the GeometryDefinition element to get.
    
    Returns:
    
    an element from the listOfGeometryDefinitions at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getGeometryDefinition
```
public GeometryDefinition getGeometryDefinition(java.lang.String id)
```
    Gets an element from the listOfGeometryDefinitions, with the given id.
    
    Parameters:
    
    id - the id of the GeometryDefinition element to get.
    
    Returns:
    
    an element from the listOfGeometryDefinitions with the given id or null.
  - getGeometryDefinitionCount
```
public int getGeometryDefinitionCount()
```
    Returns the number of GeometryDefinitions in this Geometry.
    
    Returns:
    
    the number of GeometryDefinitions in this Geometry.
  - getNumGeometryDefinitions
```
public int getNumGeometryDefinitions()
```
    Returns the number of GeometryDefinitions in this Geometry.
    
    Returns:
    
    the number of GeometryDefinitions in this Geometry.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getGeometryDefinitionCount()
  - isSetListOfAdjacentDomains
```
public boolean isSetListOfAdjacentDomains()
```
    Returns true, if listOfAdjacentDomains contains at least one element.
    
    Returns:
    
    true, if listOfAdjacentDomains contains at least one element, otherwise false
  - getListOfAdjacentDomains
```
public ListOf<AdjacentDomains> getListOfAdjacentDomains()
```
    Returns the listOfAdjacentDomains. Creates it if it is not already existing.
    
    Returns:
    
    the listOfAdjacentDomains
  - setListOfAdjacentDomains
```
public void setListOfAdjacentDomains(ListOf<AdjacentDomains> listOfAdjacentDomains)
```
    Sets the given ListOf<AdjacentDomain>. If listOfAdjacentDomains was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfAdjacentDomains -
  - unsetListOfAdjacentDomains
```
public boolean unsetListOfAdjacentDomains()
```
    Returns true, if listOfAdjacentDomains contain at least one element, otherwise false
    
    Returns:
    
    true, if listOfAdjacentDomains contain at least one element, otherwise false
  - addAdjacentDomain
```
public boolean addAdjacentDomain(AdjacentDomains adjacentDomains)
```
    Adds a new AdjacentDomains to the listOfAdjacentDomains.
    The listOfAdjacentDomains is initialized if necessary.
    
    Parameters:
    
    adjacentDomains - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - removeAdjacentDomain
```
public boolean removeAdjacentDomain(AdjacentDomains adjacentDomains)
```
    Removes an element from the listOfAdjacentDomains.
    
    Parameters:
    
    adjacentDomains - the element to be removed from the list
    
    Returns:
    
    true if the list contained the specified element
    
    See Also:
    
    List.remove(Object)
  - removeAdjacentDomain
```
public void removeAdjacentDomain(int i)
```
    Removes an element from the listOfAdjacentDomains at the given index.
    
    Parameters:
    
    i - the index where to remove the AdjacentDomains
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeAdjacentDomain
```
public void removeAdjacentDomain(java.lang.String id)
```
    Parameters:
    
    id -
  - createAdjacentDomain
```
public AdjacentDomains createAdjacentDomain()
```
    Creates a new AdjacentDomain element and adds it to the ListOfAdjacentDomains list
    
    Returns:
  - createAdjacentDomain
```
public AdjacentDomains createAdjacentDomain(java.lang.String id)
```
    Creates a new AdjacentDomains element and adds it to the listOfAdjacentDomains list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new AdjacentDomains element
  - getAdjacentDomains
```
public AdjacentDomains getAdjacentDomains(int i)
```
    Gets an element from the listOfAdjacentDomains at the given index.
    
    Parameters:
    
    i - the index of the AdjacentDomains element to get.
    
    Returns:
    
    an element from the listOfAdjacentDomains at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getAdjacentDomains
```
public AdjacentDomains getAdjacentDomains(java.lang.String id)
```
    Gets an element from the listOfAdjacentDomains, with the given id.
    
    Parameters:
    
    id - the id of the AdjacentDomains element to get.
    
    Returns:
    
    an element from the listOfAdjacentDomains with the given id or null.
  - getAdjacentDomainsCount
```
public int getAdjacentDomainsCount()
```
    Returns the number of AdjacentDomainss in this Geometry.
    
    Returns:
    
    the number of AdjacentDomainss in this Geometry.
  - getNumAdjacentDomains
```
public int getNumAdjacentDomains()
```
    Returns the number of AdjacentDomainss in this Geometry.
    
    Returns:
    
    the number of AdjacentDomainss in this Geometry.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getAdjacentDomainsCount()
  - isSetListOfDomainTypes
```
public boolean isSetListOfDomainTypes()
```
    Returns true, if listOfDomainTypes contains at least one element.
    
    Returns:
    
    true, if listOfDomainTypes contains at least one element, otherwise false
  - getListOfDomainTypes
```
public ListOf<DomainType> getListOfDomainTypes()
```
    Returns the listOfDomainTypes. Creates it if it is not already existing.
    
    Returns:
    
    the listOfDomainTypes
  - setListOfDomainTypes
```
public void setListOfDomainTypes(ListOf<DomainType> listOfDomainTypes)
```
    Sets the given ListOf<DomainType>. If listOfDomainTypes was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfDomainTypes -
  - unsetListOfDomainTypes
```
public boolean unsetListOfDomainTypes()
```
    Returns true, if listOfDomainTypes contain at least one element, otherwise false
    
    Returns:
    
    true, if listOfDomainTypes contain at least one element, otherwise false
  - addDomainType
```
public boolean addDomainType(DomainType domainType)
```
    Adds a new DomainType to the listOfDomainTypes.
    The listOfDomainTypes is initialized if necessary.
    
    Parameters:
    
    domainType - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - removeDomainType
```
public boolean removeDomainType(DomainType domainType)
```
    Removes an element from the listOfDomainTypes.
    
    Parameters:
    
    domainType - the element to be removed from the list
    
    Returns:
    
    true if the list contained the specified element
    
    See Also:
    
    List.remove(Object)
  - removeDomainType
```
public void removeDomainType(int i)
```
    Removes an element from the listOfDomainTypes at the given index.
    
    Parameters:
    
    i - the index where to remove the DomainType
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeDomainType
```
public void removeDomainType(java.lang.String id)
```
    Parameters:
    
    id -
  - createDomainType
```
public DomainType createDomainType()
```
    Creates a new DomainType element and adds it to the ListOfDomainTypes list
    
    Returns:
  - createDomainType
```
public DomainType createDomainType(java.lang.String id)
```
    Creates a new DomainType element and adds it to the ListOfDomainTypes list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new DomainType element
  - getDomainType
```
public DomainType getDomainType(int i)
```
    Gets an element from the listOfDomainTypes at the given index.
    
    Parameters:
    
    i - the index of the DomainType element to get.
    
    Returns:
    
    an element from the listOfDomainTypes at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getDomainType
```
public DomainType getDomainType(java.lang.String id)
```
    Gets an element from the listOfDomainTypes, with the given id.
    
    Parameters:
    
    id - the id of the DomainType element to get.
    
    Returns:
    
    an element from the listOfDomainTypes with the given id or null.
  - getDomainTypeCount
```
public int getDomainTypeCount()
```
    Returns the number of DomainTypes in this Geometry.
    
    Returns:
    
    the number of DomainTypes in this Geometry.
  - getNumDomainTypes
```
public int getNumDomainTypes()
```
    Returns the number of DomainTypes in this Geometry.
    
    Returns:
    
    the number of DomainTypes in this Geometry.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getDomainTypeCount()
  - isSetListOfDomains
```
public boolean isSetListOfDomains()
```
    Returns true, if listOfDomains contains at least one element.
    
    Returns:
    
    true, if listOfDomains contains at least one element, otherwise false
  - getListOfDomains
```
public ListOf<Domain> getListOfDomains()
```
    Returns the listOfDomains. Creates it if it is not already existing.
    
    Returns:
    
    the listOfDomains
  - setListOfDomains
```
public void setListOfDomains(ListOf<Domain> listOfDomains)
```
    Sets the given ListOf<Domain>. If listOfDomains was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfDomains -
  - unsetListOfDomains
```
public boolean unsetListOfDomains()
```
    Returns true, if listOfDomains contain at least one element, otherwise false
    
    Returns:
    
    true, if listOfDomains contain at least one element, otherwise false
  - addDomain
```
public boolean addDomain(Domain domain)
```
    Adds a new Domain to the listOfDomains.
    The listOfDomains is initialized if necessary.
    
    Parameters:
    
    domain - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - removeDomain
```
public boolean removeDomain(Domain domain)
```
    Removes an element from the listOfDomains.
    
    Parameters:
    
    domain - the element to be removed from the list
    
    Returns:
    
    true if the list contained the specified element
    
    See Also:
    
    List.remove(Object)
  - removeDomain
```
public void removeDomain(int i)
```
    Removes an element from the listOfDomains at the given index.
    
    Parameters:
    
    i - the index where to remove the Domain
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeDomain
```
public void removeDomain(java.lang.String id)
```
    Parameters:
    
    id -
  - createDomain
```
public Domain createDomain()
```
    Creates a new Domain element and adds it to the ListOfDomains list
    
    Returns:
  - createDomain
```
public Domain createDomain(java.lang.String id)
```
    Creates a new Domain element and adds it to the ListOfDomains list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new Domain element
  - getDomain
```
public Domain getDomain(int i)
```
    Gets an element from the listOfDomains at the given index.
    
    Parameters:
    
    i - the index of the Domain element to get.
    
    Returns:
    
    an element from the listOfDomains at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getDomain
```
public Domain getDomain(java.lang.String id)
```
    Gets an element from the listOfDomains, with the given id.
    
    Parameters:
    
    id - the id of the Domain element to get.
    
    Returns:
    
    an element from the listOfDomains with the given id or null.
  - getDomainCount
```
public int getDomainCount()
```
    Returns the number of Domains in this Geometry.
    
    Returns:
    
    the number of Domains in this Geometry.
  - getNumDomains
```
public int getNumDomains()
```
    Returns the number of Domains in this Geometry.
    
    Returns:
    
    the number of Domains in this Geometry.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getDomainCount()
  - isSetListOfCoordinateComponents
```
public boolean isSetListOfCoordinateComponents()
```
    Returns true, if listOfCoordinateComponents contains at least one element.
    
    Returns:
    
    true, if listOfCoordinateComponents contains at least one element, otherwise false
  - getListOfCoordinateComponents
```
public ListOf<CoordinateComponent> getListOfCoordinateComponents()
```
    Returns the listOfCoordinateComponents. Creates it if it is not already existing.
    
    Returns:
    
    the listOfCoordinateComponents
  - setListOfCoordinateComponents
```
public void setListOfCoordinateComponents(ListOf<CoordinateComponent> listOfCoordinateComponents)
```
    Sets the given ListOf<CoordinateComponent>. If listOfCoordinateComponents was defined before and contains some elements, they are all unset.
    
    Parameters:
    
    listOfCoordinateComponents -
  - unsetListOfCoordinateComponents
```
public boolean unsetListOfCoordinateComponents()
```
    Returns true, if listOfCoordinateComponents contain at least one element, otherwise false
    
    Returns:
    
    true, if listOfCoordinateComponents contain at least one element, otherwise false
  - addCoordinateComponent
```
public boolean addCoordinateComponent(CoordinateComponent coordinateComponents)
```
    Adds a new CoordinateComponent to the listOfCoordinateComponents.
    The listOfCoordinateComponents is initialized if necessary.
    
    Parameters:
    
    coordinateComponents - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - removeCoordinateComponent
```
public boolean removeCoordinateComponent(CoordinateComponent coordinateComponents)
```
    Removes an element from the listOfCoordinateComponents.
    
    Parameters:
    
    coordinateComponents - the element to be removed from the list
    
    Returns:
    
    true if the list contained the specified element
    
    See Also:
    
    List.remove(Object)
  - removeCoordinateComponent
```
public void removeCoordinateComponent(int i)
```
    Removes an element from the listOfCoordinateComponents at the given index.
    
    Parameters:
    
    i - the index where to remove the CoordinateComponent
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeCoordinateComponent
```
public void removeCoordinateComponent(java.lang.String id)
```
    Parameters:
    
    id -
  - createCoordinateComponent
```
public CoordinateComponent createCoordinateComponent()
```
    Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list
    
    Returns:
  - createCoordinateComponent
```
public CoordinateComponent createCoordinateComponent(java.lang.String id)
```
    Creates a new CoordinateComponent element and adds it to the ListOfCoordinateComponents list
    
    Parameters:
    
    id -
    
    Returns:
    
    a new CoordinateComponent element
  - getCoordinateComponent
```
public CoordinateComponent getCoordinateComponent(int i)
```
    Gets an element from the listOfCoordinateComponents at the given index.
    
    Parameters:
    
    i - the index of the CoordinateComponent element to get.
    
    Returns:
    
    an element from the listOfCoordinateComponents at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getCoordinateComponent
```
public CoordinateComponent getCoordinateComponent(java.lang.String id)
```
    Gets an element from the listOfCoordinateComponents, with the given id.
    
    Parameters:
    
    id - the id of the CoordinateComponent element to get.
    
    Returns:
    
    an element from the listOfCoordinateComponents with the given id or null.
  - getCoordinateComponentCount
```
public int getCoordinateComponentCount()
```
    Returns the number of CoordinateComponents in this Geometry.
    
    Returns:
    
    the number of CoordinateComponents in this Geometry.
  - getNumCoordinateComponents
```
public int getNumCoordinateComponents()
```
    Returns the number of CoordinateComponents in this Geometry.
    
    Returns:
    
    the number of CoordinateComponents in this Geometry.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getCoordinateComponentCount()
  - readAttribute
```
public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)
```
    Specified by:
    
    readAttribute in interface SBase
    
    Overrides:
    
    readAttribute in class AbstractSBase
  - writeXMLAttributes
```
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
```
    Specified by:
    
    writeXMLAttributes in interface SBase
    
    Overrides:
    
    writeXMLAttributes in class AbstractSpatialNamedSBase
  - hashCode
```
public int hashCode()
```
    Specified by:
    
    hashCode in interface SBase
    
    Overrides:
    
    hashCode in class AbstractSpatialNamedSBase
  - getAllowsChildren
```
public boolean getAllowsChildren()
```
    Specified by:
    
    getAllowsChildren in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getAllowsChildren in class AbstractSpatialNamedSBase
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getChildCount in class AbstractSpatialNamedSBase
  - getChildAt
```
public javax.swing.tree.TreeNode getChildAt(int index)
```
    Specified by:
    
    getChildAt in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getChildAt in class AbstractSpatialNamedSBase

Class Geometry

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from interface org.sbml.jsbml.NamedSBase

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.SBase

Methods inherited from interface javax.swing.tree.TreeNode

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Constructor Detail

Geometry

Geometry

Geometry

Geometry

Method Detail

clone

equals

getCoordinateSystem

isSetCoordinateSystem

setCoordinateSystem

unsetCoordinateSystem

isSetListOfSampledFields

getListOfSampledFields

setListOfSampledFields

unsetListOfSampledFields

addSampledField

removeSampledField

removeSampledField

removeSampledField

createSampledField

createSampledField

getSampledField

getSampledField

getSampledFieldCount

getNumSampledFields

isSetListOfGeometryDefinitions

getListOfGeometryDefinitions

setListOfGeometryDefinitions

unsetListOfGeometryDefinitions

addGeometryDefinition

removeGeometryDefinition

removeGeometryDefinition

removeGeometryDefinition

createSampledFieldGeometry

createAnalyticGeometry

createCSGeometry

createParametricGeometry

createMixedGeometry

createMixedGeometry

createSampledFieldGeometry

createAnalyticGeometry

createCSGeometry

createParametricGeometry

getGeometryDefinition

getGeometryDefinition

getGeometryDefinitionCount

getNumGeometryDefinitions

isSetListOfAdjacentDomains

getListOfAdjacentDomains

setListOfAdjacentDomains

unsetListOfAdjacentDomains

addAdjacentDomain

removeAdjacentDomain

removeAdjacentDomain

removeAdjacentDomain

createAdjacentDomain

createAdjacentDomain

getAdjacentDomains

getAdjacentDomains

getAdjacentDomainsCount

getNumAdjacentDomains

isSetListOfDomainTypes

getListOfDomainTypes

setListOfDomainTypes

unsetListOfDomainTypes