org.sbml.jsbml.ext.spatial

Class MixedGeometry

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

org.sbml.jsbml.ext.spatial.GeometryDefinition

org.sbml.jsbml.ext.spatial.MixedGeometry

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SpatialNamedSBase, org.sbml.jsbml.SBase, org.sbml.jsbml.util.TreeNodeWithChangeSupport

public class MixedGeometry
extends GeometryDefinition

Since:

0.8

Version:

$Rev$

Author:

Alex Thomas

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
MixedGeometry()
MixedGeometry(int level, int version)
MixedGeometry(MixedGeometry mg)
MixedGeometry(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
boolean	addGeometryDefinition(GeometryDefinition listOfGeometryDefinitions) Adds a new GeometryDefinition to the listOfGeometryDefinitions.
boolean	addOrdinalMapping(OrdinalMapping ordinalMapping) Adds a new OrdinalMapping to the listOfOrdinalMappings.
MixedGeometry	clone()
AnalyticGeometry	createAnalyticGeometry()
AnalyticGeometry	createAnalyticGeometry(String id)
CSGeometry	createCSGeometry()
CSGeometry	createCSGeometry(String id)
MixedGeometry	createMixedGeometry()
MixedGeometry	createMixedGeometry(String id) Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
OrdinalMapping	createOrdinalMapping() Creates a new OrdinalMapping element and adds it to the ListOfOrdinalMappings list
ParametricGeometry	createParametricGeometry()
ParametricGeometry	createParametricGeometry(String id)
SampledFieldGeometry	createSampledFieldGeometry(String id) Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
SampledFieldGeometry	createSampledFieldGeometryn() Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
boolean	equals(Object object)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
org.sbml.jsbml.ListOf<GeometryDefinition>	getListOfGeometryDefinitions() Returns the listOfGeometryDefinitions.
org.sbml.jsbml.ListOf<OrdinalMapping>	getListOfOrdinalMappings() Returns the listOfOrdinalMappings.
int	hashCode()
boolean	isSetListOfGeometryDefinitions() Returns true, if listOfGeometryDefinitions contains at least one element.
boolean	isSetListOfOrdinalMappings() Returns true, if listOfOrdinalMappings contains at least one element.
boolean	removeGeometryDefinition(GeometryDefinition listOfGeometryDefinitions) Removes an element from the listOfGeometryDefinitions.
void	removeGeometryDefinition(int i) Removes an element from the listOfGeometryDefinitions at the given index.
void	removeOrdinalMapping(int i) Removes an element from the listOfOrdinalMappings at the given index.
boolean	removeOrdinalMapping(OrdinalMapping ordinalMapping) Removes an element from the listOfOrdinalMappings.
void	setListOfGeometryDefinitions(org.sbml.jsbml.ListOf<GeometryDefinition> listOfGeometryDefinitions) Sets the given ListOf<GeometryDefinition>.
void	setListOfOrdinalMappings(org.sbml.jsbml.ListOf<OrdinalMapping> listOfOrdinalMappings) Sets the given ListOf<OrdinalMapping>.
boolean	unsetListOfGeometryDefinitions() Returns true, if listOfGeometryDefinitions contain at least one element, otherwise false
boolean	unsetListOfOrdinalMappings() Returns true, if listOfOrdinalMappings contain at least one element, otherwise false

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

getIsActive, isActive, isSetIsActive, readAttribute, setIsActive, toString, unsetIsActive, writeXMLAttributes

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

getSpatialId, initDefaults, isSetSpatialId, setSpatialId, unsetSpatialId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

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, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, 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 org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Constructor Detail

MixedGeometry

public MixedGeometry()

MixedGeometry

public MixedGeometry(MixedGeometry mg)

Parameters:

mg -

MixedGeometry

public MixedGeometry(int level,
                     int version)

Parameters:

level -

version -

MixedGeometry

public MixedGeometry(String id,
                     int level,
                     int version)

Parameters:

id -

level -

version -

Method Detail

clone

public MixedGeometry clone()

Specified by:

clone in interface org.sbml.jsbml.SBase

Specified by:

clone in class AbstractSpatialNamedSBase

equals

public boolean equals(Object object)

Specified by:

equals in interface org.sbml.jsbml.SBase

Overrides:

equals in class GeometryDefinition

hashCode

public int hashCode()

Specified by:

hashCode in interface org.sbml.jsbml.SBase

Overrides:

hashCode in class GeometryDefinition

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 org.sbml.jsbml.ListOf<GeometryDefinition> getListOfGeometryDefinitions()

Returns the listOfGeometryDefinitions. Creates it if it is not already existing.

Returns:

the listOfGeometryDefinitions

setListOfGeometryDefinitions

public void setListOfGeometryDefinitions(org.sbml.jsbml.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 listOfGeometryDefinitions)

Adds a new GeometryDefinition to the listOfGeometryDefinitions.

The listOfGeometryDefinitions is initialized if necessary.

Parameters:

listOfGeometryDefinitions - the element to add to the list

Returns:

true (as specified by Collection.add(E))

removeGeometryDefinition

public boolean removeGeometryDefinition(GeometryDefinition listOfGeometryDefinitions)

Removes an element from the listOfGeometryDefinitions.

Parameters:

listOfGeometryDefinitions - 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:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

createSampledFieldGeometryn

public SampledFieldGeometry createSampledFieldGeometryn()

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(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(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(String id)

Parameters:

id -

Returns:

createCSGeometry

public CSGeometry createCSGeometry(String id)

Parameters:

id -

Returns:

createParametricGeometry

public ParametricGeometry createParametricGeometry(String id)

Parameters:

id -

Returns:

isSetListOfOrdinalMappings

public boolean isSetListOfOrdinalMappings()

Returns true, if listOfOrdinalMappings contains at least one element.

Returns:

true, if listOfOrdinalMappings contains at least one element, otherwise false

getListOfOrdinalMappings

public org.sbml.jsbml.ListOf<OrdinalMapping> getListOfOrdinalMappings()

Returns the listOfOrdinalMappings. Creates it if it is not already existing.

Returns:

the listOfOrdinalMappings

setListOfOrdinalMappings

public void setListOfOrdinalMappings(org.sbml.jsbml.ListOf<OrdinalMapping> listOfOrdinalMappings)

Sets the given ListOf<OrdinalMapping>. If listOfOrdinalMappings was defined before and contains some elements, they are all unset.

Parameters:

listOfOrdinalMappings -

unsetListOfOrdinalMappings

public boolean unsetListOfOrdinalMappings()

Returns true, if listOfOrdinalMappings contain at least one element, otherwise false

Returns:

true, if listOfOrdinalMappings contain at least one element, otherwise false

addOrdinalMapping

public boolean addOrdinalMapping(OrdinalMapping ordinalMapping)

Adds a new OrdinalMapping to the listOfOrdinalMappings.

The listOfOrdinalMappings is initialized if necessary.

Parameters:

ordinalMapping - the element to add to the list

Returns:

true (as specified by Collection.add(E))

removeOrdinalMapping

public boolean removeOrdinalMapping(OrdinalMapping ordinalMapping)

Removes an element from the listOfOrdinalMappings.

Parameters:

ordinalMapping - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeOrdinalMapping

public void removeOrdinalMapping(int i)

Removes an element from the listOfOrdinalMappings at the given index.

Parameters:

i - the index where to remove the OrdinalMapping

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

createOrdinalMapping

public OrdinalMapping createOrdinalMapping()

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

Returns:

a new OrdinalMapping element

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSpatialNamedSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSpatialNamedSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSpatialNamedSBase