Package org.sbml.jsbml.ext.spatial

Class AnalyticGeometry

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.AnalyticGeometry

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, SpatialNamedSBase, NamedSBase, SBase, TreeNodeWithChangeSupport

public class AnalyticGeometry
extends GeometryDefinition

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

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

Constructor	Description
AnalyticGeometry()
AnalyticGeometry(java.lang.String id, int level, int version)
AnalyticGeometry(AnalyticGeometry analyticGeometry)

Method Summary

Modifier and Type	Method	Description
boolean	addAnalyticVolume(AnalyticVolume analyticVolume)	Adds a new AnalyticVolume to the listOfAnalyticVolumes.
AnalyticGeometry	clone()	Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
AnalyticVolume	createAnalyticVolume()	Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list
AnalyticVolume	createAnalyticVolume(java.lang.String id)	Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list
boolean	equals(java.lang.Object object)	Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<AnalyticVolume>	getListOfAnalyticVolumes()	Returns the listOfAnalyticVolumes.
int	hashCode()	Returns a hash code value for this SBase instance.
boolean	isSetListOfAnalyticVolumes()	Returns true, if listOfAnalyticVolumes contains at least one element.
void	removeAnalyticVolume(int i)	Removes an element from the listOfAnalyticVolumes at the given index.
void	removeAnalyticVolume(java.lang.String id)
boolean	removeAnalyticVolume(AnalyticVolume analyticVolume)	Removes an element from the listOfAnalyticVolumes.
void	setListOfAnalyticVolumes(ListOf<AnalyticVolume> listOfAnalyticVolumes)	Sets the given ListOf<AnalyticVolume>.
boolean	unsetListOfAnalyticVolumes()	Returns true, if listOfAnalyticVolumes contain at least one element, otherwise false

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, 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, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, 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 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 org.sbml.jsbml.ext.spatial.GeometryDefinition

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

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isIdMandatory, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from class java.lang.Object

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

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

Constructor Detail

AnalyticGeometry

public AnalyticGeometry()

AnalyticGeometry

public AnalyticGeometry(AnalyticGeometry analyticGeometry)

Parameters:

analyticGeometry -

AnalyticGeometry

public AnalyticGeometry(java.lang.String id,
                        int level,
                        int version)

Parameters:

id -

level -

version -

Method Detail

clone

public AnalyticGeometry clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSpatialNamedSBase

Returns:

a copy of this object

isSetListOfAnalyticVolumes

public boolean isSetListOfAnalyticVolumes()

Returns true, if listOfAnalyticVolumes contains at least one element.

Returns:

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

getListOfAnalyticVolumes

public ListOf<AnalyticVolume> getListOfAnalyticVolumes()

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

Returns:

the listOfAnalyticVolumes

setListOfAnalyticVolumes

public void setListOfAnalyticVolumes(ListOf<AnalyticVolume> listOfAnalyticVolumes)

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

Parameters:

listOfAnalyticVolumes -

unsetListOfAnalyticVolumes

public boolean unsetListOfAnalyticVolumes()

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

Returns:

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

addAnalyticVolume

public boolean addAnalyticVolume(AnalyticVolume analyticVolume)

Adds a new AnalyticVolume to the listOfAnalyticVolumes.

The listOfAnalyticVolumes is initialized if necessary.

Parameters:

analyticVolume - the element to add to the list

Returns:

true (as specified by Collection#add)

removeAnalyticVolume

public boolean removeAnalyticVolume(AnalyticVolume analyticVolume)

Removes an element from the listOfAnalyticVolumes.

Parameters:

analyticVolume - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

removeAnalyticVolume

public void removeAnalyticVolume(int i)

Removes an element from the listOfAnalyticVolumes at the given index.

Parameters:

i - the index where to remove the AnalyticVolume

Throws:

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

removeAnalyticVolume

public void removeAnalyticVolume(java.lang.String id)

Parameters:

id -

createAnalyticVolume

public AnalyticVolume createAnalyticVolume()

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

Returns:

createAnalyticVolume

public AnalyticVolume createAnalyticVolume(java.lang.String id)

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

Parameters:

id -

Returns:

a new AnalyticVolume element

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

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class GeometryDefinition

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class GeometryDefinition

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()