Package org.sbml.jsbml.ext.spatial

Class CSGeometry

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.CSGeometry

All Implemented Interfaces:

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

public class CSGeometry
extends GeometryDefinition

Since:

1.0

Author:

Alex Thomas, Andreas Dräger

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
CSGeometry()
CSGeometry(int level, int version)
CSGeometry(java.lang.String id, int level, int version)
CSGeometry(CSGeometry csg)

Method Summary

Modifier and Type	Method	Description
boolean	addCSGObject(CSGObject csgo)	Adds a new CSGObject to the listOfCSGObjects.
CSGeometry	clone()
CSGObject	createCSGObject()	Creates a new CSGObject element and adds it to the ListOfCSGObjects list
CSGObject	createCSGObject(java.lang.String id)	Creates a new CSGObject element and adds it to the ListOfCSGObjects list
boolean	equals(java.lang.Object obj)
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
int	getCSGObjectCount()	Returns the number of CSGObjects in this CSGeometry.
java.lang.String	getElementName()
ListOf<CSGObject>	getListOfCSGObjects()	Returns the listOfCSGObjects.
int	getNumCSGObjects()	Returns the number of CSGObjects in this CSGeometry.
int	hashCode()
boolean	isSetListOfCSGObjects()	Returns true, if listOfCSGObjects contains at least one element.
void	removeCSGObject(int i)	Removes an element from the listOfCSGObjects at the given index.
boolean	removeCSGObject(CSGObject csgo)	Removes an element from the listOfCSGObjects.
void	setListOfCSGObjects(ListOf<CSGObject> listOfCSGObjects)	Sets the given ListOf<CSGObject>.
boolean	unsetListOfCSGObjects()	Returns true, if listOfCSGObjects contain at least one element, otherwise false

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, 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 class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, 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

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, 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

CSGeometry

public CSGeometry()

CSGeometry

public CSGeometry(CSGeometry csg)

Parameters:

csg -

CSGeometry

public CSGeometry(int level,
                  int version)

Parameters:

level -

version -

CSGeometry

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

Parameters:

id -

level -

version -

Method Detail

clone

public CSGeometry clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSpatialNamedSBase

equals

public boolean equals(java.lang.Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class GeometryDefinition

isSetListOfCSGObjects

public boolean isSetListOfCSGObjects()

Returns true, if listOfCSGObjects contains at least one element.

Returns:

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

getListOfCSGObjects

public ListOf<CSGObject> getListOfCSGObjects()

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

Returns:

the listOfCSGObjects

setListOfCSGObjects

public void setListOfCSGObjects(ListOf<CSGObject> listOfCSGObjects)

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

Parameters:

listOfCSGObjects -

unsetListOfCSGObjects

public boolean unsetListOfCSGObjects()

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

Returns:

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

addCSGObject

public boolean addCSGObject(CSGObject csgo)

Adds a new CSGObject to the listOfCSGObjects.

The listOfCSGObjects is initialized if necessary.

Parameters:

csgo - the element to add to the list

Returns:

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

removeCSGObject

public boolean removeCSGObject(CSGObject csgo)

Removes an element from the listOfCSGObjects.

Parameters:

csgo - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeCSGObject

public void removeCSGObject(int i)

Removes an element from the listOfCSGObjects at the given index.

Parameters:

i - the index where to remove the CSGObject

Throws:

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

createCSGObject

public CSGObject createCSGObject()

Creates a new CSGObject element and adds it to the ListOfCSGObjects list

Returns:

createCSGObject

public CSGObject createCSGObject(java.lang.String id)

Creates a new CSGObject element and adds it to the ListOfCSGObjects list

Parameters:

id -

Returns:

a new CSGObject element

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class GeometryDefinition

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

getCSGObjectCount

public int getCSGObjectCount()

Returns the number of CSGObjects in this CSGeometry.

Returns:

the number of CSGObjects in this CSGeometry.

getNumCSGObjects

public int getNumCSGObjects()

Returns the number of CSGObjects in this CSGeometry.

Returns:

the number of CSGObjects in this CSGeometry.

Note: this method is kept here as it exist in libSBML.

same as getCSGObjectCount()

getElementName

public java.lang.String getElementName()

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase