org.sbml.jsbml.ext.fbc

Class LogicalOperator

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.fbc.LogicalOperator

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, Association, SBase, TreeNodeWithChangeSupport

Direct Known Subclasses:

And, Or

public abstract class LogicalOperator
extends AbstractSBase
implements Association

Represents a collection of genes in a logical expression.

Is is only ever instantiated as one of its subclasses: And and Or.

Since:

1.1

Author:

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 and Description
LogicalOperator() Creates a new LogicalOperator instance.
LogicalOperator(int level, int version) Creates a new LogicalOperator instance.
LogicalOperator(LogicalOperator association) Creates a new LogicalOperator instance.

Method Summary

Modifier and Type	Method and Description
void	addAllAssociations(List<Association> listOfAssociations) Sets the given ListOf<Association>.
boolean	addAssociation(Association association) Adds a new Association to the listOfAssociations.
void	addChild(Association child) Identical to calling addAssociation(Association).
abstract LogicalOperator	clone()
And	createAnd() Creates a new Association element and adds it to the listOfAssociations list.
GeneProductRef	createGeneProductRef() Creates a new Association element and adds it to the listOfAssociations list.
GeneProductRef	createGeneProductRef(String id) Creates a new Association element and adds it to the listOfAssociations list.
Or	createOr() Creates a new Association element and adds it to the listOfAssociations list.
boolean	getAllowsChildren()
Association	getAssociation(int i) Gets an element from the listOfAssociations at the given index.
int	getAssociationCount() Returns the number of Associations in this LogicalOperator.
TreeNode	getChildAt(int index)
int	getChildCount()
List<Association>	getListOfAssociations() Returns the listOfAssociations.
int	getNumAssociations() Returns the number of Associations in this LogicalOperator.
boolean	isSetListOfAssociations() Returns true if listOfAssociations contains at least one element.
boolean	removeAllAssociations() Returns true if listOfAssociations contains at least one element, otherwise false.
boolean	removeAssociation(Association association) Removes an element from the listOfAssociations.
Association	removeAssociation(int i) Removes an element from the listOfAssociations at the given index.

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, equals, 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, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, readAttribute, 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, writeXMLAttributes

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 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, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, readAttribute, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNotes, unsetPlugin, unsetSBOTerm, writeXMLAttributes

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

LogicalOperator

public LogicalOperator()

Creates a new LogicalOperator instance.

LogicalOperator

public LogicalOperator(int level,
                       int version)

Creates a new LogicalOperator instance.

Parameters:

level - the SBML level

version - the SBML version

LogicalOperator

public LogicalOperator(LogicalOperator association)

Creates a new LogicalOperator instance.

Parameters:

association - the instance to clone

Method Detail

addAllAssociations

public void addAllAssociations(List<Association> listOfAssociations)

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

Parameters:

listOfAssociations - the list of Associations to add

addAssociation

public boolean addAssociation(Association association)

Adds a new Association to the listOfAssociations.

The listOfAssociations is initialized if necessary.

Parameters:

association - the element to add to the list

Returns:

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

See Also:

Collection.add(Object)

addChild

public void addChild(Association child)

Identical to calling addAssociation(Association).

Parameters:

child - the association to add

See Also:

addAssociation(Association)

clone

public abstract LogicalOperator clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

createAnd

public And createAnd()

Creates a new Association element and adds it to the listOfAssociations list.

Returns:

the newly created Association element, which is the last element in the listOfAssociations.

createGeneProductRef

public GeneProductRef createGeneProductRef()

Creates a new Association element and adds it to the listOfAssociations list.

Returns:

the newly created element, i.e., the last item in the listOfAssociations

createGeneProductRef

public GeneProductRef createGeneProductRef(String id)

Creates a new Association element and adds it to the listOfAssociations list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created Association element, which is the last element in the listOfAssociations.

createOr

public Or createOr()

Creates a new Association element and adds it to the listOfAssociations list.

Returns:

the newly created Association element, which is the last element in the listOfAssociations.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getAssociation

public Association getAssociation(int i)

Gets an element from the listOfAssociations at the given index.

Parameters:

i - the index of the Association element to get.

Returns:

an element from the listOfAssociations at the given index.

Throws:

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

getAssociationCount

public int getAssociationCount()

Returns the number of Associations in this LogicalOperator.

Returns:

the number of Associations in this LogicalOperator.

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getListOfAssociations

public List<Association> getListOfAssociations()

Returns the listOfAssociations. Creates it if it does not already exist.

Returns:

the listOfAssociations.

getNumAssociations

public int getNumAssociations()

Returns the number of Associations in this LogicalOperator.

Returns:

the number of Associations in this LogicalOperator.

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

same as getAssociationCount()

isSetListOfAssociations

public boolean isSetListOfAssociations()

Returns true if listOfAssociations contains at least one element.

Returns:

true if listOfAssociations contains at least one element, otherwise false.

removeAllAssociations

public boolean removeAllAssociations()

Returns true if listOfAssociations contains at least one element, otherwise false.

Returns:

true if listOfAssociations contains at least one element, otherwise false.

removeAssociation

public boolean removeAssociation(Association association)

Removes an element from the listOfAssociations.

Parameters:

association - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removeAssociation

public Association removeAssociation(int i)

Removes an element from the listOfAssociations at the given index.

Parameters:

i - the index where to remove the Association.

Returns:

the specified element if it was successfully found and removed.

Throws:

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